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Generated by Doxygen 1.8.18
i
1 Main Page 1
1.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
2 Hierarchical Index 3
2.1 Class Hierarchy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
3 Class Index 11
3.1 Class List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
4 File Index 17
4.1 File List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
5 Class Documentation 21
5.1 RbtNM::AndCriteria< Criteria1, Criteria2 > Class Template Reference . . . . . . . . . . . . . . . . 21
5.2 CharmmType Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
5.3 Rbt::CyclicAtom Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
5.4 EvaluateVisitor Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
5.5 RbtPolarSF::f1prms Struct Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
5.6 FilterAddExp Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
5.7 FilterAndExp Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
5.8 FilterDivExp Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
5.9 FilterExpExp Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
5.10 FilterIfExp Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
5.11 FilterLogExp Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
5.12 FilterMulExp Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
5.13 FilterSubExp Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
5.14 FilterVbleExp Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
5.15 Rbt::GenomeCmp_Score Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
5.16 RbtCavityGridSF::HeavyAtomFactory Class Reference . . . . . . . . . . . . . . . . . . . . . . . . 28
5.17 HHS_Solvation Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
5.18 RbtTriposAtomType::info Struct Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
5.19 Rbt::InitHHS Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
5.20 Rbt::InteractionCenterCmp Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
5.21 Rbt::InvertSelectAtom Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
5.22 Rbt::isAtom_12Connected Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
5.23 Rbt::isAtom_13Connected Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
5.24 Rbt::isAtom_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
5.25 Rbt::isAtomAnionic Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
5.26 Rbt::isAtomBridgehead Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
5.27 Rbt::isAtomCationic Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
5.28 Rbt::isAtomCharged Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
5.29 Rbt::isAtomCyclic Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
5.30 Rbt::isAtomEnabled Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
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5.31 Rbt::isAtomExtended Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
5.32 Rbt::isAtomGuanidiniumCarbon Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
5.33 Rbt::isAtomHBondAcceptor Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
5.34 Rbt::isAtomHBondDonor Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
5.35 Rbt::isAtomicNo_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
5.36 Rbt::isAtomId_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
5.37 RbtDockingSite::isAtomInRange Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
5.38 Rbt::isAtomInsideCuboid Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
5.39 Rbt::isAtomInsideSphere Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
5.40 Rbt::isAtomIonic Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
5.41 Rbt::isAtomLipophilic Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
5.42 Rbt::isAtomMetal Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
5.43 Rbt::isAtomName_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
5.44 Rbt::isAtomNearCoordList Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
5.45 Rbt::isAtomNegCharged Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
5.46 Rbt::isAtomPlanar Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
5.47 Rbt::isAtomPosCharged Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
5.48 Rbt::isAtomPtr_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
5.49 Rbt::isAtomRNA Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
5.50 Rbt::isAtomSelected Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
5.51 Rbt::isBond_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
5.52 Rbt::isBondAmide Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
5.53 Rbt::isBondCyclic Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
5.54 Rbt::isBondPtr_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
5.55 Rbt::isBondRotatable Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
5.56 Rbt::isBondSelected Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
5.57 Rbt::isBondToNH3 Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
5.58 Rbt::isBondToOH Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
5.59 Rbt::isCavityNearCoord Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
5.60 Rbt::isCoordinationNumber_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
5.61 Rbt::isFFType_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
5.62 Rbt::isGenome_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
5.63 Rbt::isHHSSelected Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
5.64 Rbt::isHHSType_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
5.65 Rbt::isHybridState_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
5.66 Rbt::isInteractionCenterSelected Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . 48
5.67 Rbt::isInteractionD_lt Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
5.68 Rbt::isPiAtom Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
5.69 Rbt::isSegmentName_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
5.70 Rbt::isSubunitId_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
5.71 Rbt::isSubunitName_eq Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
5.72 RbtNM::IterationCriterion Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
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5.73 OccupancyTest Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
5.74 Rbt::OverlapHHS Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
5.75 Rbt::OverlapVariableHHS Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
5.76 Rbt::PartitionHHS Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
5.77 PrettyPrintVisitor Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
5.78 PrintVisitor Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
5.79 RbtDihedral::prms Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
5.80 RbtAlignTransform Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
5.81 Rbt::RbtAnn_Cmp_AtomId2 Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
5.82 RbtAnnotation Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
5.83 RbtAnnotationHandler Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
5.84 RbtAromIdxSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
5.85 RbtAssert Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
5.86 RbtAtom Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
5.87 Rbt::RbtAtomPtrCmp_AtomicNo Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
5.88 Rbt::RbtAtomPtrCmp_AtomId Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
5.89 Rbt::RbtAtomPtrCmp_AtomName Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . 59
5.90 Rbt::RbtAtomPtrCmp_Ptr Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
5.91 RbtBadArgument Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
5.92 RbtBadReceptorFile Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
5.93 RbtBaseBiMolTransform Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
5.94 RbtBaseFileSink Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
5.95 RbtBaseFileSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
5.96 RbtBaseGrid Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
5.97 RbtBaseIdxSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
5.98 RbtBaseInterSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
5.99 RbtBaseIntraSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
5.100 RbtBaseMolecularDataSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
5.101 RbtBaseMolecularFileSink Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
5.102 RbtBaseMolecularFileSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
5.103 RbtBaseObject Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
5.104 RbtBaseSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
5.105 RbtBaseTransform Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
5.106 RbtBaseUniMolTransform Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
5.107 RbtBiMolWorkSpace Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
5.108 RbtBond Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
5.109 Rbt::RbtBondPCmp_BondId Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
5.110 RbtCavity Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
5.111 RbtCavityFillSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
5.112 RbtCavityGridSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
5.113 Rbt::RbtCavityPtrCmp_Distance Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . 79
5.114 Rbt::RbtCavityPtrCmp_Volume Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
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5.115 RbtCellContext Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
5.116 RbtCellTokenIter Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
5.117 RbtCharmmDataSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
5.118 RbtCharmmTypesFileSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
5.119 RbtChrom Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
5.120 RbtChromDihedralElement Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
5.121 RbtChromDihedralRefData Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
5.122 RbtChromElement Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
5.123 RbtChromFactory Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
5.124 RbtChromOccupancyElement Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
5.125 RbtChromOccupancyRefData Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
5.126 RbtChromPositionElement Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
5.127 RbtChromPositionRefData Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
5.128 RbtChromTest Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
5.129 RbtCommands Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
5.130 RbtConstraint Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
5.131 RbtConstSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
5.132 RbtContext Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
5.133 RbtCoord Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
5.134 RbtCrdFileSink Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
5.135 RbtCrdFileSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
5.136 RbtCSVFileSink Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
5.137 RbtDihedral Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
5.138 RbtDihedralIntraSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
5.139 RbtDihedralSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
5.140 RbtDihedralTargetSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
5.141 RbtDirectorySource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
5.141.1 Detailed Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
5.142 RbtDirIsNotAccessible Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
5.143 RbtDockingError Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
5.144 RbtDockingSite Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
5.145 RbtElementData Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
5.146 RbtElementFileSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
5.147 RbtEnvNotDefined Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
5.148 RbtError Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
5.149 RbtEuler Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
5.150 RbtFFTGrid Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
5.151 RbtFFTPeak Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
5.152 RbtFileError Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
5.153 RbtFileMissingParameter Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
5.154 RbtFileParseError Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
5.155 RbtFileReadError Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
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5.156 RbtFileWriteError Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
5.157 RbtFilter Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
5.158 RbtFilterExpression Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
5.159 RbtFilterExpressionVisitor Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
5.160 RbtFlexAtomFactory Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
5.161 RbtFlexData Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
5.162 RbtFlexDataVisitor Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
5.163 RbtGATransform Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
5.164 RbtGenome Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
5.165 RbtHBAConstraint Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
5.166 RbtHBDConstraint Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
5.167 RbtHeavyConstraint Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
5.168 RbtHHSType Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
5.169 RbtHydroAliphaticConstraint Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
5.170 RbtHydroAromaticConstraint Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
5.171 RbtHydroConstraint Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
5.172 RbtInteractionCenter Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
5.173 RbtInteractionGrid Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
5.174 RbtInteractionGridTemplate< T > Class Template Reference . . . . . . . . . . . . . . . . . . . . 119
5.175 RbtInteractionGridTemplatePtr< T > Class Template Reference . . . . . . . . . . . . . . . . . . 120
5.176 RbtInteractionNode< T > Class Template Reference . . . . . . . . . . . . . . . . . . . . . . . . 120
5.177 RbtInteractionNodeList< T > Class Template Reference . . . . . . . . . . . . . . . . . . . . . . 120
5.178 RbtInteractionNodeListMap< T > Class Template Reference . . . . . . . . . . . . . . . . . . . . 121
5.179 RbtInteractionNodeListMapConstIter< T > Class Template Reference . . . . . . . . . . . . . . . 121
5.180 RbtInteractionNodeListMapIter< T > Class Template Reference . . . . . . . . . . . . . . . . . . 121
5.181 RbtInvalidRequest Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
5.182 RbtLigandError Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
5.183 RbtLigandFlexData Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
5.184 RbtLigandSiteMapper Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
5.185 RbtMCStats Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
5.186 RbtMdlFileSink Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
5.187 RbtMdlFileSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
5.188 RbtModel Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
5.189 RbtModelError Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
5.190 RbtModelMutator Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
5.191 RbtMOEGrid Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
5.192 RbtMOEGridPoint Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
5.193 RbtMOEGridShape Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
5.194 RbtMOL2FileSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
5.195 RbtMOL2Substructure Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
5.196 RbtNegChargeConstraint Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
5.197 RbtNmrRestraintFileSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
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5.198 RbtNmrSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
5.199 RbtNoeEndAtoms Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
5.200 RbtNoeEndNames Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
5.201 RbtNoeRestraintAtoms Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
5.202 RbtNoeRestraintNames Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
5.203 RbtNoFileInDir Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
5.204 RbtNonBondedGrid Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
5.205 RbtNonBondedHHSGrid Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
5.206 RbtNullTransform Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
5.207 RbtObserver Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
5.208 RbtParameterFileSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
5.209 RbtParamHandler Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
5.210 RbtParser Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
5.211 RbtPdbFileSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
5.212 RbtPharmaSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
5.213 RbtPlane Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
5.214 RbtPMFDirSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
5.215 RbtPMFGridSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
5.216 RbtPMFIdxSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
5.216.1 Detailed Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
5.216.2 Constructor & Destructor Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . 145
5.216.2.1 RbtPMFIdxSF() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
5.216.2.2 ∼RbtPMFIdxSF() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
5.216.3 Member Function Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
5.216.3.1 GetLinearCloseRangeValue() . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
5.216.3.2 RawScore() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
5.216.3.3 SetupLigand() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
5.216.3.4 SetupReceptor() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
5.216.3.5 SetupScore() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
5.216.3.6 Update() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
5.216.4 Member Data Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
5.216.4.1 _CT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
5.216.4.2 _PMFDIR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
5.217 RbtPMFValue Struct Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
5.217.1 Detailed Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
5.218 RbtPolarIdxSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
5.219 RbtPolarIntraSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
5.220 RbtPolarSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
5.221 RbtPopulation Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
5.222 RbtPosChargeConstraint Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
5.223 RbtPrincipalAxes Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
5.224 RbtPRMFactory Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
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5.225 RbtPseudoAtom Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
5.226 RbtPsfFileSink Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
5.227 RbtPsfFileSource Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
5.228 RbtQuat Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
5.229 RbtRand Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
5.230 RbtRandLigTransform Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
5.231 RbtRandPopTransform Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
5.232 RbtRealGrid Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
5.233 RbtReceptorFlexData Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
5.234 RbtRequest Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
5.235 RbtRequestHandler Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
5.236 RbtRingAromaticConstraint Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
5.237 RbtRotSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
5.238 RbtSAIdxSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
5.239 RbtSetupPMFSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
5.239.1 Member Function Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
5.239.1.1 GetPMFfor_lC() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
5.240 RbtSetupPolarSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
5.241 RbtSetupSASF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
5.242 RbtSFAgg Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
5.243 RbtSFDisableRequest Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
5.244 RbtSFEnableRequest Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
5.245 RbtSFFactory Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
5.246 RbtSFPartitionRequest Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
5.247 RbtSFSetParamRequest Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
5.248 RbtSimAnnTransform Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
5.249 RbtSimpleSolvationParameters Struct Reference . . . . . . . . . . . . . . . . . . . . . . . . . . 169
5.250 RbtSimplexCostFunction Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
5.251 RbtSimplexTransform Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
5.252 RbtSiteMapper Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
5.253 RbtSiteMapperFactory Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
5.254 RbtSolventFlexData Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
5.255 RbtSphereSiteMapper Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
5.256 RbtStdRestraintAtoms Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
5.257 RbtStdRestraintNames Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
5.258 RbtStringContext Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
5.259 RbtStringTokenIter Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
5.260 RbtStringTooLong Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
5.261 RbtSubject Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
5.262 RbtTetherSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
5.263 RbtToken Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
5.264 RbtTokenIter Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
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5.265 RbtTransformAgg Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
5.266 RbtTransformFactory Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
5.267 RbtTriposAtomType Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
5.268 RbtVariant Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
5.269 RbtVble Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
5.270 RbtVdwGridSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
5.271 RbtVdwIdxSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
5.272 RbtVdwIntraSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
5.273 RbtVdwSF Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
5.274 RbtWorkSpace Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
5.275 RbtNM::RelativeValueCriterion< DataType > Class Template Reference . . . . . . . . . . . . . . 186
5.276 Rbt::RestoreHHS Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
5.277 Rbt::RotateAtomUsingQuat Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
5.278 Rbt::RotateAtomUsingQuatIfSelected Class Reference . . . . . . . . . . . . . . . . . . . . . . . 187
5.279 Rbt::SaveHHS Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
5.280 SearchTest Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
5.281 Rbt::SelectAtom Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
5.282 Rbt::SelectFlexAtoms Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
5.283 Rbt::SelectInteractionCenter Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
5.284 RbtNM::Simplex< DataType, ParameterType, Function, Criterion > Class Template Reference . . 188
5.284.1 Detailed Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
5.284.2 Member Function Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
5.284.2.1 GetBestParameters() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
5.284.2.2 GetBestValue() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
5.285 Singleton< singleton_type > Class Template Reference . . . . . . . . . . . . . . . . . . . . . . 189
5.286 SmartPtr< T > Class Template Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
5.287 RbtNM::State< DataType, ParameterType > Struct Template Reference . . . . . . . . . . . . . . 190
5.287.1 Detailed Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
5.288 Rbt::TranslateAtom Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
5.289 Rbt::TranslateAtomIfSelected Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
6 File Documentation 193
6.1 RbtCSVFileSink.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
6.1.1 Detailed Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Index 195
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Chapter 1
Main Page
Figure 1.1 RxDock logo
1.1 Introduction
RxDock is a fast and versatile open-source docking program that can be used to dock small molecules againstproteins and nucleic acids. It is designed for high-throughput virtual screening (HTVS) campaigns and bindingmode prediction studies.
RxDock is mainly written in C++ and accessory scripts and programs are written in C++, Perl or Python languages.
1.2 Documentation
This documentation describes the code that makes up RxDock, a part of which is the application programminginterface (API).
This documentation does not describe the use of RxDock's command-line interface (CLI), the preparation of theinput files, or the post-processing options available for the output files. For usage instructions, please see theGetting started guide, the User guide, and the Reference manual.
While intended for developers, this documentation also does not describe how to format the code, customize thebuild system, use the version control software, write the documentation and tests for the code, or test the codechanges using existing tests. These topics are, among others, covered in the Developer guide.
2 Main Page
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Chapter 2
Hierarchical Index
2.1 Class Hierarchy
This inheritance list is sorted roughly, but not completely, alphabetically:
RbtNM::AndCriteria< Criteria1, Criteria2 > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21binary_function
Rbt::isAtom_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Rbt::isAtomId_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35Rbt::isAtomPtr_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40Rbt::isGenome_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
CharmmType . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21std::vector< T >::const_iterator
RbtInteractionNodeListMapConstIter< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121Rbt::CyclicAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22RbtPolarSF::f1prms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22Rbt::GenomeCmp_Score . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27HHS_Solvation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28RbtTriposAtomType::info . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29Rbt::InitHHS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29Rbt::InteractionCenterCmp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29Rbt::InvertSelectAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30RbtNM::IterationCriterion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50iterator
RbtInteractionNodeListMapIter< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121Rbt::OverlapHHS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51Rbt::OverlapVariableHHS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51Rbt::PartitionHHS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51RbtDihedral::prms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53Rbt::RbtAnn_Cmp_AtomId2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54RbtAnnotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54RbtAnnotationHandler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
RbtAromIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55RbtPMFIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144RbtPolarSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
RbtPolarIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147RbtPolarIntraSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
RbtSAIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161RbtVdwSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
RbtVdwIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
4 Hierarchical Index
RbtVdwIntraSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
RbtAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
RbtPseudoAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Rbt::RbtAtomPtrCmp_AtomicNo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59Rbt::RbtAtomPtrCmp_AtomId . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59Rbt::RbtAtomPtrCmp_AtomName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59Rbt::RbtAtomPtrCmp_Ptr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59RbtBaseFileSink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
RbtBaseMolecularFileSink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68RbtCrdFileSink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94RbtCSVFileSink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95RbtMdlFileSink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125RbtPsfFileSink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
RbtBaseFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
RbtBaseMolecularFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69RbtCrdFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95RbtMdlFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126RbtMOL2FileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130RbtPdbFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140RbtPsfFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
RbtCharmmTypesFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81RbtElementFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101RbtNmrRestraintFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132RbtParameterFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
RbtBaseGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
RbtInteractionGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118RbtInteractionGridTemplate< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119RbtNonBondedGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135RbtNonBondedHHSGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136RbtRealGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
RbtFFTGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
RbtBaseMolecularDataSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
RbtBaseMolecularFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
RbtBond . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76Rbt::RbtBondPCmp_BondId . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76RbtBondUnaryPredicate
Rbt::isBond_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41Rbt::isBondAmide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42Rbt::isBondCyclic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42Rbt::isBondPtr_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Rbt::isBondRotatable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Rbt::isBondSelected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Rbt::isBondToNH3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44Rbt::isBondToOH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
RbtCavity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77Rbt::RbtCavityPtrCmp_Distance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79Rbt::RbtCavityPtrCmp_Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79RbtCharmmDataSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81RbtChromDihedralRefData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83RbtChromElement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
RbtChrom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81RbtChromDihedralElement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82RbtChromOccupancyElement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86RbtChromPositionElement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
RbtChromOccupancyRefData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87RbtChromPositionRefData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
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RbtCommands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90RbtConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
RbtHBAConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113RbtHBDConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114RbtHeavyConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114RbtHydroAliphaticConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116RbtHydroAromaticConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116RbtHydroConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117RbtNegChargeConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131RbtPosChargeConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151RbtRingAromaticConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
RbtContext . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
RbtCellContext . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79RbtStringContext . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
RbtCoord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93RbtDihedral . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96RbtDirectorySource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
RbtPMFDirSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
RbtDockingSite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100RbtElementData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101RbtError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
RbtAssert . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56RbtBadArgument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60RbtBadReceptorFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60RbtDockingError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100RbtFileError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
RbtDirIsNotAccessible . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99RbtEnvNotDefined . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102RbtFileMissingParameter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106RbtFileParseError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106RbtFileReadError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107RbtFileWriteError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107RbtNoFileInDir . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135RbtStringTooLong . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
RbtInvalidRequest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122RbtLigandError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122RbtModelError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
RbtEuler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103RbtFFTPeak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105RbtFilterExpression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
FilterAddExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23FilterAndExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23FilterDivExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24FilterExpExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24FilterIfExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25FilterLogExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25FilterMulExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26FilterSubExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26FilterVbleExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
RbtFilterExpressionVisitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
EvaluateVisitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22PrettyPrintVisitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52PrintVisitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
RbtFlexDataVisitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
RbtCavityGridSF::HeavyAtomFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28RbtChromFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
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6 Hierarchical Index
RbtFlexAtomFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
RbtGenome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113RbtHHSType . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115RbtInteractionCenter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117RbtInteractionNode< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120RbtMCStats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124RbtModel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126RbtModelMutator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129RbtMOEGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129RbtMOEGridPoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130RbtMOEGridShape . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130RbtMOL2Substructure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131RbtNoeEndAtoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133RbtNoeEndNames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134RbtNoeRestraintAtoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134RbtNoeRestraintNames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135RbtObserver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
RbtBaseObject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71RbtBaseSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
RbtBaseIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65RbtAromIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55RbtNmrSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133RbtPMFIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144RbtPolarIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147RbtSAIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161RbtVdwIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
RbtBaseInterSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66RbtAromIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55RbtCavityFillSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77RbtCavityGridSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78RbtConstSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92RbtDihedralTargetSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98RbtNmrSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133RbtPharmaSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141RbtPMFGridSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143RbtPMFIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144RbtPolarIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147RbtRotSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160RbtSAIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161RbtSetupPMFSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162RbtSetupPolarSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163RbtSetupSASF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164RbtTetherSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176RbtVdwGridSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181RbtVdwIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
RbtBaseIntraSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67RbtDihedralIntraSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96RbtPolarIntraSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148RbtVdwIntraSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
RbtDihedralSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97RbtDihedralIntraSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96RbtDihedralTargetSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
RbtPolarSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149RbtSFAgg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165RbtVdwSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
RbtBaseTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73RbtBaseBiMolTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Generated by Doxygen
2.1 Class Hierarchy 7
RbtAlignTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53RbtGATransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112RbtRandPopTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156RbtSimAnnTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168RbtSimplexTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
RbtBaseUniMolTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74RbtRandLigTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
RbtNullTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137RbtTransformAgg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
RbtFilter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108RbtSiteMapper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
RbtLigandSiteMapper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124RbtSphereSiteMapper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
RbtParamHandler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
RbtBaseObject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71RbtFlexData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
RbtLigandFlexData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123RbtSolventFlexData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
RbtReceptorFlexData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158RbtWorkSpace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
RbtBiMolWorkSpace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
RbtParser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140RbtPlane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142RbtPMFValue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147RbtPopulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150RbtPrincipalAxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151RbtPRMFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152RbtQuat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154RbtRand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155RbtRequest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
RbtSFDisableRequest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166RbtSFEnableRequest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166RbtSFPartitionRequest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167RbtSFSetParamRequest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
RbtRequestHandler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
RbtBaseObject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
RbtSFFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167RbtSimpleSolvationParameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169RbtSimplexCostFunction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169RbtSiteMapperFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171RbtStdRestraintAtoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173RbtStdRestraintNames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173RbtSubject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
RbtWorkSpace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
RbtToken . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177RbtTokenIter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
RbtCellTokenIter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80RbtStringTokenIter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
RbtTransformFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179RbtTriposAtomType . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179RbtVariant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180RbtVble . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180RbtNM::RelativeValueCriterion< DataType > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186Rbt::RestoreHHS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186Rbt::RotateAtomUsingQuat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186Rbt::RotateAtomUsingQuatIfSelected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Generated by Doxygen
8 Hierarchical Index
Rbt::SaveHHS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187Rbt::SelectAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188Rbt::SelectFlexAtoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188Rbt::SelectInteractionCenter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188RbtNM::Simplex< DataType, ParameterType, Function, Criterion > . . . . . . . . . . . . . . . . . . . . 188Singleton< singleton_type > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189SmartPtr< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtAtom > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtBaseMolecularFileSink > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtBiMolWorkSpace > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtCharmmDataSource > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtChromDihedralRefData > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtChromElement > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtChromOccupancyRefData > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtChromPositionRefData > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtContext > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtDockingSite > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtElementFileSource > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtFFTGrid > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtFilter > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtFilterExpression > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtInteractionGrid > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtInteractionGridTemplate< T > > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
RbtInteractionGridTemplatePtr< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
SmartPtr< RbtMCStats > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtModel > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtModelMutator > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtNonBondedGrid > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtNonBondedHHSGrid > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtParameterFileSource > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtPopulation > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtRealGrid > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtRequest > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtSFAgg > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< RbtToken > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190SmartPtr< std::istream > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190RbtNM::State< DataType, ParameterType > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190Test
OccupancyTest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50RbtChromTest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89SearchTest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Rbt::TranslateAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191Rbt::TranslateAtomIfSelected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191unary_function
Rbt::isAtom_12Connected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Rbt::isAtom_13Connected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Rbt::isAtomAnionic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Rbt::isAtomBridgehead . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Rbt::isAtomCationic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32Rbt::isAtomCharged . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32Rbt::isAtomCyclic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33Rbt::isAtomEnabled . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33Rbt::isAtomExtended . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33Rbt::isAtomGuanidiniumCarbon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34Rbt::isAtomHBondAcceptor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34Rbt::isAtomHBondDonor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35Rbt::isAtomicNo_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35Rbt::isAtomInsideCuboid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
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2.1 Class Hierarchy 9
Rbt::isAtomInsideSphere . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37Rbt::isAtomIonic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37Rbt::isAtomLipophilic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37Rbt::isAtomMetal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Rbt::isAtomName_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Rbt::isAtomNearCoordList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Rbt::isAtomNegCharged . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Rbt::isAtomPlanar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Rbt::isAtomPosCharged . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40Rbt::isAtomRNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41Rbt::isAtomSelected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41Rbt::isCavityNearCoord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45Rbt::isCoordinationNumber_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45Rbt::isFFType_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46Rbt::isHHSSelected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46Rbt::isHHSType_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47Rbt::isHybridState_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47Rbt::isInteractionCenterSelected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Rbt::isInteractionD_lt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Rbt::isPiAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Rbt::isSegmentName_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49Rbt::isSubunitId_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49Rbt::isSubunitName_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50RbtDockingSite::isAtomInRange . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
std::vector< T >RbtInteractionNodeList< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120RbtInteractionNodeListMap< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
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10 Hierarchical Index
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Chapter 3
Class Index
3.1 Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
RbtNM::AndCriteria< Criteria1, Criteria2 > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21CharmmType . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21Rbt::CyclicAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22EvaluateVisitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22RbtPolarSF::f1prms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22FilterAddExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23FilterAndExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23FilterDivExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24FilterExpExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24FilterIfExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25FilterLogExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25FilterMulExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26FilterSubExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26FilterVbleExp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27Rbt::GenomeCmp_Score . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27RbtCavityGridSF::HeavyAtomFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28HHS_Solvation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28RbtTriposAtomType::info . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29Rbt::InitHHS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29Rbt::InteractionCenterCmp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29Rbt::InvertSelectAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Rbt::isAtom_12Connected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Rbt::isAtom_13Connected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Rbt::isAtom_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Rbt::isAtomAnionic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Rbt::isAtomBridgehead . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Rbt::isAtomCationic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32Rbt::isAtomCharged . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32Rbt::isAtomCyclic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33Rbt::isAtomEnabled . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33Rbt::isAtomExtended . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33Rbt::isAtomGuanidiniumCarbon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34Rbt::isAtomHBondAcceptor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34Rbt::isAtomHBondDonor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35Rbt::isAtomicNo_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
12 Class Index
Rbt::isAtomId_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35RbtDockingSite::isAtomInRange . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Rbt::isAtomInsideCuboid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Rbt::isAtomInsideSphere . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37Rbt::isAtomIonic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37Rbt::isAtomLipophilic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37Rbt::isAtomMetal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Rbt::isAtomName_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Rbt::isAtomNearCoordList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Rbt::isAtomNegCharged . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Rbt::isAtomPlanar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Rbt::isAtomPosCharged . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40Rbt::isAtomPtr_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40Rbt::isAtomRNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41Rbt::isAtomSelected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41Rbt::isBond_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41Rbt::isBondAmide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42Rbt::isBondCyclic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42Rbt::isBondPtr_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Rbt::isBondRotatable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Rbt::isBondSelected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Rbt::isBondToNH3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44Rbt::isBondToOH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44Rbt::isCavityNearCoord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45Rbt::isCoordinationNumber_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45Rbt::isFFType_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46Rbt::isGenome_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46Rbt::isHHSSelected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46Rbt::isHHSType_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47Rbt::isHybridState_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47Rbt::isInteractionCenterSelected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Rbt::isInteractionD_lt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Rbt::isPiAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Rbt::isSegmentName_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49Rbt::isSubunitId_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49Rbt::isSubunitName_eq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50RbtNM::IterationCriterion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50OccupancyTest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50Rbt::OverlapHHS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51Rbt::OverlapVariableHHS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51Rbt::PartitionHHS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51PrettyPrintVisitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52PrintVisitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52RbtDihedral::prms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53RbtAlignTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53Rbt::RbtAnn_Cmp_AtomId2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54RbtAnnotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54RbtAnnotationHandler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55RbtAromIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55RbtAssert . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56RbtAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57Rbt::RbtAtomPtrCmp_AtomicNo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59Rbt::RbtAtomPtrCmp_AtomId . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59Rbt::RbtAtomPtrCmp_AtomName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59Rbt::RbtAtomPtrCmp_Ptr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59RbtBadArgument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60RbtBadReceptorFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60RbtBaseBiMolTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
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3.1 Class List 13
RbtBaseFileSink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61RbtBaseFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62RbtBaseGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63RbtBaseIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65RbtBaseInterSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66RbtBaseIntraSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67RbtBaseMolecularDataSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68RbtBaseMolecularFileSink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68RbtBaseMolecularFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69RbtBaseObject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71RbtBaseSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72RbtBaseTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73RbtBaseUniMolTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74RbtBiMolWorkSpace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75RbtBond . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76Rbt::RbtBondPCmp_BondId . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76RbtCavity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77RbtCavityFillSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77RbtCavityGridSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78Rbt::RbtCavityPtrCmp_Distance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79Rbt::RbtCavityPtrCmp_Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79RbtCellContext . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79RbtCellTokenIter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80RbtCharmmDataSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81RbtCharmmTypesFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81RbtChrom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81RbtChromDihedralElement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82RbtChromDihedralRefData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83RbtChromElement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84RbtChromFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85RbtChromOccupancyElement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86RbtChromOccupancyRefData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87RbtChromPositionElement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87RbtChromPositionRefData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88RbtChromTest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89RbtCommands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90RbtConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90RbtConstSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92RbtContext . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92RbtCoord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93RbtCrdFileSink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94RbtCrdFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95RbtCSVFileSink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95RbtDihedral . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96RbtDihedralIntraSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96RbtDihedralSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97RbtDihedralTargetSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98RbtDirectorySource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98RbtDirIsNotAccessible . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99RbtDockingError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100RbtDockingSite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100RbtElementData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101RbtElementFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101RbtEnvNotDefined . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102RbtError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102RbtEuler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103RbtFFTGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104RbtFFTPeak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Generated by Doxygen
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RbtFileError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105RbtFileMissingParameter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106RbtFileParseError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106RbtFileReadError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107RbtFileWriteError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107RbtFilter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108RbtFilterExpression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109RbtFilterExpressionVisitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110RbtFlexAtomFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110RbtFlexData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111RbtFlexDataVisitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111RbtGATransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112RbtGenome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113RbtHBAConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113RbtHBDConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114RbtHeavyConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114RbtHHSType . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115RbtHydroAliphaticConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116RbtHydroAromaticConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116RbtHydroConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117RbtInteractionCenter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117RbtInteractionGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118RbtInteractionGridTemplate< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119RbtInteractionGridTemplatePtr< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120RbtInteractionNode< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120RbtInteractionNodeList< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120RbtInteractionNodeListMap< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121RbtInteractionNodeListMapConstIter< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121RbtInteractionNodeListMapIter< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121RbtInvalidRequest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122RbtLigandError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122RbtLigandFlexData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123RbtLigandSiteMapper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124RbtMCStats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124RbtMdlFileSink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125RbtMdlFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126RbtModel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126RbtModelError . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128RbtModelMutator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129RbtMOEGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129RbtMOEGridPoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130RbtMOEGridShape . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130RbtMOL2FileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130RbtMOL2Substructure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131RbtNegChargeConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131RbtNmrRestraintFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132RbtNmrSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133RbtNoeEndAtoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133RbtNoeEndNames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134RbtNoeRestraintAtoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134RbtNoeRestraintNames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135RbtNoFileInDir . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135RbtNonBondedGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135RbtNonBondedHHSGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136RbtNullTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137RbtObserver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138RbtParameterFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139RbtParamHandler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
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RbtParser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140RbtPdbFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140RbtPharmaSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141RbtPlane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142RbtPMFDirSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142RbtPMFGridSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143RbtPMFIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144RbtPMFValue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147RbtPolarIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147RbtPolarIntraSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148RbtPolarSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149RbtPopulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150RbtPosChargeConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151RbtPrincipalAxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151RbtPRMFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152RbtPseudoAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152RbtPsfFileSink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153RbtPsfFileSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153RbtQuat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154RbtRand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155RbtRandLigTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155RbtRandPopTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156RbtRealGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157RbtReceptorFlexData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158RbtRequest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159RbtRequestHandler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159RbtRingAromaticConstraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160RbtRotSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160RbtSAIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161RbtSetupPMFSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162RbtSetupPolarSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163RbtSetupSASF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164RbtSFAgg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165RbtSFDisableRequest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166RbtSFEnableRequest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166RbtSFFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167RbtSFPartitionRequest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167RbtSFSetParamRequest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167RbtSimAnnTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168RbtSimpleSolvationParameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169RbtSimplexCostFunction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169RbtSimplexTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170RbtSiteMapper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171RbtSiteMapperFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171RbtSolventFlexData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172RbtSphereSiteMapper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172RbtStdRestraintAtoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173RbtStdRestraintNames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173RbtStringContext . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174RbtStringTokenIter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174RbtStringTooLong . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175RbtSubject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175RbtTetherSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176RbtToken . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177RbtTokenIter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177RbtTransformAgg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178RbtTransformFactory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179RbtTriposAtomType . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
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16 Class Index
RbtVariant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180RbtVble . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180RbtVdwGridSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181RbtVdwIdxSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182RbtVdwIntraSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183RbtVdwSF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184RbtWorkSpace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185RbtNM::RelativeValueCriterion< DataType > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186Rbt::RestoreHHS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186Rbt::RotateAtomUsingQuat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186Rbt::RotateAtomUsingQuatIfSelected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187Rbt::SaveHHS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187SearchTest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187Rbt::SelectAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188Rbt::SelectFlexAtoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188Rbt::SelectInteractionCenter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188RbtNM::Simplex< DataType, ParameterType, Function, Criterion > . . . . . . . . . . . . . . . . . . . . 188Singleton< singleton_type > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189SmartPtr< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190RbtNM::State< DataType, ParameterType > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190Rbt::TranslateAtom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191Rbt::TranslateAtomIfSelected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Generated by Doxygen
Chapter 4
File Index
4.1 File List
Here is a list of all documented files with brief descriptions:
OccupancyTest.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??Rbt.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtAlignTransform.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtAnnotation.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtAnnotationHandler.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtAromIdxSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtAtom.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtAtomFuncs.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseBiMolTransform.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseFileSink.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseFileSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseGrid.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseIdxSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseInterSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseIntraSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseMolecularDataSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseMolecularFileSink.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseMolecularFileSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseObject.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseTransform.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBaseUniMolTransform.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBiMolWorkSpace.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtBond.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtCavity.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtCavityFillSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtCavityGridSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtCellTokenIter.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtCharmmDataSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtCharmmTypesFileSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtChrom.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtChromDihedralElement.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtChromDihedralRefData.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtChromElement.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtChromFactory.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??
18 File Index
RbtChromOccupancyElement.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtChromOccupancyRefData.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtChromPositionElement.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtChromPositionRefData.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtChromTest.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtCommands.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtConfig.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtConstraint.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtConstSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtContext.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtCoord.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtCrdFileSink.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtCrdFileSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtCSVFileSink.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193RbtDebug.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtDihedralIntraSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtDihedralSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtDihedralTargetSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtDirectorySource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtDockingError.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtDockingSite.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtElementFileSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtError.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtEuler.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtFFTGrid.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtFileError.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtFilter.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtFilterExpression.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtFilterExpressionVisitor.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtFlexAtomFactory.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtFlexData.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtFlexDataVisitor.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtGATransform.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtGenome.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtInteractionGrid.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtInteractionTemplate.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtLigandError.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtLigandFlexData.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtLigandSiteMapper.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtMdlFileSink.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtMdlFileSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtModel.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtModelError.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtModelMutator.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtMOEGrid.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtMOL2FileSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtNMCriteria.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtNmrRestraintFileSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtNmrSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtNMSimplex.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtNMState.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtNoeRestraint.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtNonBondedGrid.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtNonBondedHHSGrid.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtNullTransform.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtObserver.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtParameterFileSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtParamHandler.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??
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4.1 File List 19
RbtParser.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPdbFileSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPharmaSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPlane.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPMF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPMFDirSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPMFGridSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPMFIdxSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPolarIdxSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPolarIntraSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPolarSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPopulation.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPrincipalAxes.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPRMFactory.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPseudoAtom.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPsfFileSink.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtPsfFileSource.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtQuat.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtRand.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtRandLigTransform.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtRandPopTransform.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtRealGrid.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtReceptorFlexData.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtRequest.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtRequestHandler.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtResources.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtRotSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSAIdxSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSATypes.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSetupPMFSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSetupPolarSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSetupSASF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSFAgg.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSFFactory.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSFRequest.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSimAnnTransform.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSimplexCostFunction.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSimplexTransform.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSiteMapper.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSiteMapperFactory.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSmartPointer.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSmarts.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSolventFlexData.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSphereSiteMapper.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtStringTokenIter.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtSubject.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtTetherSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtToken.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtTokenIter.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtTransformAgg.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtTransformFactory.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtTriposAtomType.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtVariant.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtVble.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtVdwGridSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtVdwIdxSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtVdwIntraSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??RbtVdwSF.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??
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20 File Index
RbtWorkSpace.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??SearchTest.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??Singleton.h . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??
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Chapter 5
Class Documentation
5.1 RbtNM::AndCriteria< Criteria1, Criteria2 > Class TemplateReference
Public Member Functions
• AndCriteria (const Criteria1 &criteria1, const Criteria2 &criteria2)
• template<class State >
bool operator() (const State &state)
The documentation for this class was generated from the following file:
• RbtNMCriteria.h
5.2 CharmmType Class Reference
Public Attributes
• int nAtomType• std::string strAtomType• double mass• std::string element• std::string comment
The documentation for this class was generated from the following file:
• RbtCharmmTypesFileSource.h
22 Class Documentation
5.3 Rbt::CyclicAtom Class Reference
Public Member Functions
• CyclicAtom (bool bb)• void operator() (RbtAtom ∗pAtom)
The documentation for this class was generated from the following file:
• RbtAtom.h
5.4 EvaluateVisitor Class Reference
Inheritance diagram for EvaluateVisitor:
EvaluateVisitor
RbtFilterExpressionVisitor
Public Member Functions
• EvaluateVisitor (RbtContextPtr)• virtual void VisitVbleExp (FilterVbleExp ∗)• virtual void VisitAddExp (FilterAddExp ∗)• virtual void VisitSubExp (FilterSubExp ∗)• virtual void VisitMulExp (FilterMulExp ∗)• virtual void VisitDivExp (FilterDivExp ∗)• virtual void VisitAndExp (FilterAndExp ∗)• virtual void VisitLogExp (FilterLogExp ∗)• virtual void VisitExpExp (FilterExpExp ∗)• virtual void VisitIfExp (FilterIfExp ∗)
The documentation for this class was generated from the following file:
• RbtFilterExpressionVisitor.h
5.5 RbtPolarSF::f1prms Struct Reference
Public Member Functions
• f1prms (double R, double DMin, double DMax)
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5.6 FilterAddExp Class Reference 23
Public Attributes
• double R0• double DRMin• double DRMax• double slope
The documentation for this struct was generated from the following file:
• RbtPolarSF.h
5.6 FilterAddExp Class Reference
Inheritance diagram for FilterAddExp:
FilterAddExp
RbtFilterExpression
Public Member Functions
• FilterAddExp (RbtFilterExpressionPtr, RbtFilterExpressionPtr)• void Accept (RbtFilterExpressionVisitor &visitor)• void Print ()• virtual int GetNOps ()• RbtFilterExpressionPtr GetOp (int i)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFilterExpression.h
5.7 FilterAndExp Class Reference
Inheritance diagram for FilterAndExp:
FilterAndExp
RbtFilterExpression
Generated by Doxygen
24 Class Documentation
Public Member Functions
• FilterAndExp (RbtFilterExpressionPtr, RbtFilterExpressionPtr)• void Accept (RbtFilterExpressionVisitor &visitor)• void Print ()• virtual int GetNOps ()• RbtFilterExpressionPtr GetOp (int i)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFilterExpression.h
5.8 FilterDivExp Class Reference
Inheritance diagram for FilterDivExp:
FilterDivExp
RbtFilterExpression
Public Member Functions
• FilterDivExp (RbtFilterExpressionPtr, RbtFilterExpressionPtr)• void Accept (RbtFilterExpressionVisitor &visitor)• void Print ()• virtual int GetNOps ()• RbtFilterExpressionPtr GetOp (int i)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFilterExpression.h
5.9 FilterExpExp Class Reference
Inheritance diagram for FilterExpExp:
FilterExpExp
RbtFilterExpression
Generated by Doxygen
5.10 FilterIfExp Class Reference 25
Public Member Functions
• FilterExpExp (RbtFilterExpressionPtr)• void Accept (RbtFilterExpressionVisitor &visitor)• void Print ()• virtual int GetNOps ()• RbtFilterExpressionPtr GetOp (int i)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFilterExpression.h
5.10 FilterIfExp Class Reference
Inheritance diagram for FilterIfExp:
FilterIfExp
RbtFilterExpression
Public Member Functions
• FilterIfExp (RbtFilterExpressionPtr, RbtFilterExpressionPtr, RbtFilterExpressionPtr)• void Accept (RbtFilterExpressionVisitor &visitor)• void Print ()• virtual int GetNOps ()• RbtFilterExpressionPtr GetOp (int i)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFilterExpression.h
5.11 FilterLogExp Class Reference
Inheritance diagram for FilterLogExp:
FilterLogExp
RbtFilterExpression
Generated by Doxygen
26 Class Documentation
Public Member Functions
• FilterLogExp (RbtFilterExpressionPtr)• void Accept (RbtFilterExpressionVisitor &visitor)• void Print ()• virtual int GetNOps ()• RbtFilterExpressionPtr GetOp (int i)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFilterExpression.h
5.12 FilterMulExp Class Reference
Inheritance diagram for FilterMulExp:
FilterMulExp
RbtFilterExpression
Public Member Functions
• FilterMulExp (RbtFilterExpressionPtr, RbtFilterExpressionPtr)• void Accept (RbtFilterExpressionVisitor &visitor)• void Print ()• virtual int GetNOps ()• RbtFilterExpressionPtr GetOp (int i)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFilterExpression.h
5.13 FilterSubExp Class Reference
Inheritance diagram for FilterSubExp:
FilterSubExp
RbtFilterExpression
Generated by Doxygen
5.14 FilterVbleExp Class Reference 27
Public Member Functions
• FilterSubExp (RbtFilterExpressionPtr, RbtFilterExpressionPtr)• void Accept (RbtFilterExpressionVisitor &visitor)• void Print ()• virtual int GetNOps ()• RbtFilterExpressionPtr GetOp (int i)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFilterExpression.h
5.14 FilterVbleExp Class Reference
Inheritance diagram for FilterVbleExp:
FilterVbleExp
RbtFilterExpression
Public Member Functions
• FilterVbleExp (const RbtVble &)• void Accept (RbtFilterExpressionVisitor &visitor)• void Print ()• int GetNOps ()• const RbtVble & GetVble () const• RbtFilterExpressionPtr GetOp (int i)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFilterExpression.h
5.15 Rbt::GenomeCmp_Score Class Reference
Public Member Functions
• bool operator() (const RbtGenome ∗pG1, const RbtGenome ∗pG2) const
The documentation for this class was generated from the following file:
• RbtGenome.h
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28 Class Documentation
5.16 RbtCavityGridSF::HeavyAtomFactory Class Reference
Inheritance diagram for RbtCavityGridSF::HeavyAtomFactory:
RbtCavityGridSF::HeavyAtomFactory
RbtFlexDataVisitor
Public Member Functions
• HeavyAtomFactory (RbtModelList modelList)• virtual void VisitReceptorFlexData (RbtReceptorFlexData ∗)• virtual void VisitLigandFlexData (RbtLigandFlexData ∗)• virtual void VisitSolventFlexData (RbtSolventFlexData ∗)• RbtAtomRList GetAtomList () const
The documentation for this class was generated from the following file:
• RbtCavityGridSF.h
5.17 HHS_Solvation Class Reference
Public Member Functions
• HHS_Solvation (RbtHHSType::eType t, RbtAtom ∗a, double p=1.0, double r=1.0, double s=0.0)• double GetA_i (void) const• double GetS_i (void) const• double GetP_i (void) const• double GetR_i (void) const• double GetSigma (void) const• RbtHHSType::eType GetHHSType () const• RbtAtom ∗ GetAtom () const• double GetArea () const• double GetEnergy () const• void Init ()• void Save ()• void Restore ()• void Overlap (HHS_Solvation ∗h, double p_ij)• const std::vector< HHS_Solvation ∗ > & GetVariable () const• int GetNumVariable () const• void AddVariable (HHS_Solvation ∗anAtom)• void OverlapVariable ()• void OverlapVariableEnabledOnly ()• void Partition (double d=0.0)
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5.18 RbtTriposAtomType::info Struct Reference 29
Static Public Attributes
• static const double r_s• static const double d_s• static const double Pij_12• static const double Pij_13• static const double Pij_14
The documentation for this class was generated from the following file:
• RbtSATypes.h
5.18 RbtTriposAtomType::info Struct Reference
Public Member Functions
• info (const std::string &n, int a, int h)
Public Attributes
• std::string name• int atomicNo• int hybrid
The documentation for this struct was generated from the following file:
• RbtTriposAtomType.h
5.19 Rbt::InitHHS Class Reference
Public Member Functions
• void operator() (HHS_Solvation ∗pHHS)
The documentation for this class was generated from the following file:
• RbtSATypes.h
5.20 Rbt::InteractionCenterCmp Class Reference
Public Member Functions
• bool operator() (const RbtInteractionCenter ∗pIC1, const RbtInteractionCenter ∗pIC2) const
The documentation for this class was generated from the following file:
• RbtInteractionGrid.h
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30 Class Documentation
5.21 Rbt::InvertSelectAtom Class Reference
Public Member Functions
• void operator() (RbtAtom ∗pAtom)
The documentation for this class was generated from the following file:
• RbtAtom.h
5.22 Rbt::isAtom_12Connected Class Reference
Inheritance diagram for Rbt::isAtom_12Connected:
Rbt::isAtom_12Connected
std::unary_function< RbtAtom *, bool >
Public Member Functions
• isAtom_12Connected (RbtAtom ∗spAtom)• bool operator() (RbtAtom ∗spAtom2) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.23 Rbt::isAtom_13Connected Class Reference
Inheritance diagram for Rbt::isAtom_13Connected:
Rbt::isAtom_13Connected
std::unary_function< RbtAtom *, bool >
Public Member Functions
• isAtom_13Connected (RbtAtom ∗pAtom)• bool operator() (RbtAtom ∗pAtom2) const
The documentation for this class was generated from the following file:
• RbtAtom.h
Generated by Doxygen
5.24 Rbt::isAtom_eq Class Reference 31
5.24 Rbt::isAtom_eq Class Reference
Inheritance diagram for Rbt::isAtom_eq:
Rbt::isAtom_eq
std::binary_function< RbtAtom *, RbtAtom *, bool >
Public Member Functions
• bool operator() (const RbtAtom ∗pAtom1, const RbtAtom ∗pAtom2) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.25 Rbt::isAtomAnionic Class Reference
Inheritance diagram for Rbt::isAtomAnionic:
Rbt::isAtomAnionic
std::unary_function< RbtAtom *, bool >
Public Member Functions
• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.26 Rbt::isAtomBridgehead Class Reference
Inheritance diagram for Rbt::isAtomBridgehead:
Rbt::isAtomBridgehead
std::unary_function< RbtAtom *, bool >
Generated by Doxygen
32 Class Documentation
Public Member Functions
• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.27 Rbt::isAtomCationic Class Reference
Inheritance diagram for Rbt::isAtomCationic:
Rbt::isAtomCationic
std::unary_function< RbtAtom *, bool >
Public Member Functions
• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.28 Rbt::isAtomCharged Class Reference
Inheritance diagram for Rbt::isAtomCharged:
Rbt::isAtomCharged
std::unary_function< RbtAtom *, bool >
Public Member Functions
• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
Generated by Doxygen
5.29 Rbt::isAtomCyclic Class Reference 33
5.29 Rbt::isAtomCyclic Class Reference
Inheritance diagram for Rbt::isAtomCyclic:
Rbt::isAtomCyclic
std::unary_function< RbtAtom *, bool >
Public Member Functions
• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.30 Rbt::isAtomEnabled Class Reference
Inheritance diagram for Rbt::isAtomEnabled:
Rbt::isAtomEnabled
std::unary_function< RbtAtom *, bool >
Public Member Functions
• bool operator() (RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.31 Rbt::isAtomExtended Class Reference
Inheritance diagram for Rbt::isAtomExtended:
Rbt::isAtomExtended
std::unary_function< RbtAtom *, bool >
Generated by Doxygen
34 Class Documentation
Public Member Functions
• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.32 Rbt::isAtomGuanidiniumCarbon Class Reference
Inheritance diagram for Rbt::isAtomGuanidiniumCarbon:
Rbt::isAtomGuanidiniumCarbon
std::unary_function< RbtAtom *, bool >
Public Member Functions
• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.33 Rbt::isAtomHBondAcceptor Class Reference
Inheritance diagram for Rbt::isAtomHBondAcceptor:
Rbt::isAtomHBondAcceptor
std::unary_function< RbtAtom *, bool >
Public Member Functions
• RBTDLL_EXPORT bool operator() (const RbtAtom ∗) const
The documentation for this class was generated from the following file:
• RbtAtom.h
Generated by Doxygen
5.34 Rbt::isAtomHBondDonor Class Reference 35
5.34 Rbt::isAtomHBondDonor Class Reference
Inheritance diagram for Rbt::isAtomHBondDonor:
Rbt::isAtomHBondDonor
std::unary_function< RbtAtom *, bool >
Public Member Functions
• RBTDLL_EXPORT bool operator() (const RbtAtom ∗) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.35 Rbt::isAtomicNo_eq Class Reference
Inheritance diagram for Rbt::isAtomicNo_eq:
Rbt::isAtomicNo_eq
std::unary_function< RbtAtom *, bool >
Public Member Functions
• isAtomicNo_eq (int nn)• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.36 Rbt::isAtomId_eq Class Reference
Inheritance diagram for Rbt::isAtomId_eq:
Rbt::isAtomId_eq
std::binary_function< RbtAtom *, RbtAtom *, bool >
Generated by Doxygen
36 Class Documentation
Public Member Functions
• bool operator() (const RbtAtom ∗pAtom1, const RbtAtom ∗pAtom2) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.37 RbtDockingSite::isAtomInRange Class Reference
Inheritance diagram for RbtDockingSite::isAtomInRange:
RbtDockingSite::isAtomInRange
std::unary_function< RbtAtomPtr, bool >
Public Member Functions
• isAtomInRange (RbtRealGrid ∗pGrid, double minDist, double maxDist)• bool operator() (RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtDockingSite.h
5.38 Rbt::isAtomInsideCuboid Class Reference
Inheritance diagram for Rbt::isAtomInsideCuboid:
Rbt::isAtomInsideCuboid
std::unary_function< RbtAtom *, bool >
Public Member Functions
• isAtomInsideCuboid (const RbtCoord &ccmin, const RbtCoord &ccmax)• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
Generated by Doxygen
5.39 Rbt::isAtomInsideSphere Class Reference 37
5.39 Rbt::isAtomInsideSphere Class Reference
Inheritance diagram for Rbt::isAtomInsideSphere:
Rbt::isAtomInsideSphere
std::unary_function< RbtAtom *, bool >
Public Member Functions
• isAtomInsideSphere (const RbtCoord &cc, double rr)• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.40 Rbt::isAtomIonic Class Reference
Inheritance diagram for Rbt::isAtomIonic:
Rbt::isAtomIonic
std::unary_function< RbtAtom *, bool >
Public Member Functions
• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.41 Rbt::isAtomLipophilic Class Reference
Inheritance diagram for Rbt::isAtomLipophilic:
Rbt::isAtomLipophilic
std::unary_function< RbtAtom *, bool >
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38 Class Documentation
Public Member Functions
• RBTDLL_EXPORT bool operator() (RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.42 Rbt::isAtomMetal Class Reference
Inheritance diagram for Rbt::isAtomMetal:
Rbt::isAtomMetal
std::unary_function< RbtAtom *, bool >
Public Member Functions
• RBTDLL_EXPORT bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.43 Rbt::isAtomName_eq Class Reference
Inheritance diagram for Rbt::isAtomName_eq:
Rbt::isAtomName_eq
std::unary_function< RbtAtom *, bool >
Public Member Functions
• isAtomName_eq (std::string ss)• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
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5.44 Rbt::isAtomNearCoordList Class Reference 39
5.44 Rbt::isAtomNearCoordList Class Reference
Inheritance diagram for Rbt::isAtomNearCoordList:
Rbt::isAtomNearCoordList
std::unary_function< RbtAtom *, bool >
Public Member Functions
• isAtomNearCoordList (const RbtCoordList &ccl, double rr)• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.45 Rbt::isAtomNegCharged Class Reference
Inheritance diagram for Rbt::isAtomNegCharged:
Rbt::isAtomNegCharged
std::unary_function< RbtAtom *, bool >
Public Member Functions
• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.46 Rbt::isAtomPlanar Class Reference
Inheritance diagram for Rbt::isAtomPlanar:
Rbt::isAtomPlanar
std::unary_function< RbtAtom *, bool >
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40 Class Documentation
Public Member Functions
• bool operator() (const RbtAtom ∗) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.47 Rbt::isAtomPosCharged Class Reference
Inheritance diagram for Rbt::isAtomPosCharged:
Rbt::isAtomPosCharged
std::unary_function< RbtAtom *, bool >
Public Member Functions
• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.48 Rbt::isAtomPtr_eq Class Reference
Inheritance diagram for Rbt::isAtomPtr_eq:
Rbt::isAtomPtr_eq
std::binary_function< const RbtAtom *, const RbtAtom *, bool >
Public Member Functions
• bool operator() (const RbtAtom ∗pAtom1, const RbtAtom ∗pAtom2) const
The documentation for this class was generated from the following file:
• RbtAtom.h
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5.49 Rbt::isAtomRNA Class Reference 41
5.49 Rbt::isAtomRNA Class Reference
Inheritance diagram for Rbt::isAtomRNA:
Rbt::isAtomRNA
std::unary_function< RbtAtom *, bool >
Public Member Functions
• bool operator() (const RbtAtom ∗) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.50 Rbt::isAtomSelected Class Reference
Inheritance diagram for Rbt::isAtomSelected:
Rbt::isAtomSelected
std::unary_function< RbtAtom *, bool >
Public Member Functions
• bool operator() (RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.51 Rbt::isBond_eq Class Reference
Inheritance diagram for Rbt::isBond_eq:
Rbt::isBond_eq
RbtBondUnaryPredicate
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42 Class Documentation
Public Member Functions
• isBond_eq (RbtBond ∗pp)• bool operator() (RbtBond ∗pBond) const
The documentation for this class was generated from the following file:
• RbtBond.h
5.52 Rbt::isBondAmide Class Reference
Inheritance diagram for Rbt::isBondAmide:
Rbt::isBondAmide
RbtBondUnaryPredicate
Public Member Functions
• RBTDLL_EXPORT bool operator() (RbtBond ∗) const
The documentation for this class was generated from the following file:
• RbtBond.h
5.53 Rbt::isBondCyclic Class Reference
Inheritance diagram for Rbt::isBondCyclic:
Rbt::isBondCyclic
RbtBondUnaryPredicate
Public Member Functions
• bool operator() (RbtBond ∗pBond) const
The documentation for this class was generated from the following file:
• RbtBond.h
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5.54 Rbt::isBondPtr_eq Class Reference 43
5.54 Rbt::isBondPtr_eq Class Reference
Inheritance diagram for Rbt::isBondPtr_eq:
Rbt::isBondPtr_eq
RbtBondUnaryPredicate
Public Member Functions
• isBondPtr_eq (RbtBond ∗pp)• bool operator() (RbtBond ∗pBond) const
The documentation for this class was generated from the following file:
• RbtBond.h
5.55 Rbt::isBondRotatable Class Reference
Inheritance diagram for Rbt::isBondRotatable:
Rbt::isBondRotatable
RbtBondUnaryPredicate
Public Member Functions
• RBTDLL_EXPORT bool operator() (RbtBond ∗) const
The documentation for this class was generated from the following file:
• RbtBond.h
5.56 Rbt::isBondSelected Class Reference
Inheritance diagram for Rbt::isBondSelected:
Rbt::isBondSelected
RbtBondUnaryPredicate
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44 Class Documentation
Public Member Functions
• bool operator() (RbtBond ∗pBond) const
The documentation for this class was generated from the following file:
• RbtBond.h
5.57 Rbt::isBondToNH3 Class Reference
Inheritance diagram for Rbt::isBondToNH3:
Rbt::isBondToNH3
RbtBondUnaryPredicate
Public Member Functions
• RBTDLL_EXPORT bool operator() (RbtBond ∗) const
The documentation for this class was generated from the following file:
• RbtBond.h
5.58 Rbt::isBondToOH Class Reference
Inheritance diagram for Rbt::isBondToOH:
Rbt::isBondToOH
RbtBondUnaryPredicate
Public Member Functions
• RBTDLL_EXPORT bool operator() (RbtBond ∗pBond) const
The documentation for this class was generated from the following file:
• RbtBond.h
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5.59 Rbt::isCavityNearCoord Class Reference 45
5.59 Rbt::isCavityNearCoord Class Reference
Inheritance diagram for Rbt::isCavityNearCoord:
Rbt::isCavityNearCoord
std::unary_function< RbtCavityPtr, bool >
Public Member Functions
• isCavityNearCoord (const RbtCoord &cc, double rr)
• bool operator() (RbtCavityPtr spCavity) const
The documentation for this class was generated from the following file:
• RbtCavity.h
5.60 Rbt::isCoordinationNumber_eq Class Reference
Inheritance diagram for Rbt::isCoordinationNumber_eq:
Rbt::isCoordinationNumber_eq
std::unary_function< RbtAtom *, bool >
Public Member Functions
• isCoordinationNumber_eq (unsigned int nn)
• isCoordinationNumber_eq (unsigned int nn, int nAt)
• isCoordinationNumber_eq (unsigned int nn, std::string strType)
• isCoordinationNumber_eq (unsigned int nn, RbtAtom::eHybridState eState)
• bool operator() (RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
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46 Class Documentation
5.61 Rbt::isFFType_eq Class Reference
Inheritance diagram for Rbt::isFFType_eq:
Rbt::isFFType_eq
std::unary_function< RbtAtom *, bool >
Public Member Functions
• isFFType_eq (std::string ss)• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.62 Rbt::isGenome_eq Class Reference
Inheritance diagram for Rbt::isGenome_eq:
Rbt::isGenome_eq
std::binary_function< RbtGenome *, RbtGenome *, bool >
Public Member Functions
• isGenome_eq (double threshold)• bool operator() (const RbtGenome ∗pG1, const RbtGenome ∗pG2) const
The documentation for this class was generated from the following file:
• RbtGenome.h
5.63 Rbt::isHHSSelected Class Reference
Inheritance diagram for Rbt::isHHSSelected:
Rbt::isHHSSelected
std::unary_function< HHS_Solvation *, bool >
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5.64 Rbt::isHHSType_eq Class Reference 47
Public Member Functions
• bool operator() (const HHS_Solvation ∗pHHS) const
The documentation for this class was generated from the following file:
• RbtSATypes.h
5.64 Rbt::isHHSType_eq Class Reference
Inheritance diagram for Rbt::isHHSType_eq:
Rbt::isHHSType_eq
std::unary_function< HHS_Solvation *, bool >
Public Member Functions
• isHHSType_eq (RbtHHSType::eType tt)• bool operator() (const HHS_Solvation ∗pHHS) const
The documentation for this class was generated from the following file:
• RbtSATypes.h
5.65 Rbt::isHybridState_eq Class Reference
Inheritance diagram for Rbt::isHybridState_eq:
Rbt::isHybridState_eq
std::unary_function< RbtAtom *, bool >
Public Member Functions
• isHybridState_eq (RbtAtom::eHybridState ee)• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
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48 Class Documentation
5.66 Rbt::isInteractionCenterSelected Class Reference
Inheritance diagram for Rbt::isInteractionCenterSelected:
Rbt::isInteractionCenterSelected
std::unary_function< RbtInteractionCenter *, bool >
Public Member Functions
• bool operator() (const RbtInteractionCenter ∗pIC) const
The documentation for this class was generated from the following file:
• RbtInteractionGrid.h
5.67 Rbt::isInteractionD_lt Class Reference
Inheritance diagram for Rbt::isInteractionD_lt:
Rbt::isInteractionD_lt
std::unary_function< RbtInteractionCenter *, bool >
Public Member Functions
• isInteractionD_lt (const RbtInteractionCenter ∗pIC1, double dd)• bool operator() (const RbtInteractionCenter ∗pIC2) const
The documentation for this class was generated from the following file:
• RbtInteractionGrid.h
5.68 Rbt::isPiAtom Class Reference
Inheritance diagram for Rbt::isPiAtom:
Rbt::isPiAtom
std::unary_function< RbtAtom *, bool >
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5.69 Rbt::isSegmentName_eq Class Reference 49
Public Member Functions
• RBTDLL_EXPORT bool operator() (const RbtAtom ∗) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.69 Rbt::isSegmentName_eq Class Reference
Inheritance diagram for Rbt::isSegmentName_eq:
Rbt::isSegmentName_eq
std::unary_function< RbtAtom *, bool >
Public Member Functions
• isSegmentName_eq (std::string ss)• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.70 Rbt::isSubunitId_eq Class Reference
Inheritance diagram for Rbt::isSubunitId_eq:
Rbt::isSubunitId_eq
std::unary_function< RbtAtom *, bool >
Public Member Functions
• isSubunitId_eq (std::string ss)• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
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50 Class Documentation
5.71 Rbt::isSubunitName_eq Class Reference
Inheritance diagram for Rbt::isSubunitName_eq:
Rbt::isSubunitName_eq
std::unary_function< RbtAtom *, bool >
Public Member Functions
• isSubunitName_eq (std::string ss)• bool operator() (const RbtAtom ∗pAtom) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.72 RbtNM::IterationCriterion Class Reference
Public Member Functions
• IterationCriterion (long max_iterations)• template<class State >
bool operator() (const State &state)
The documentation for this class was generated from the following file:
• RbtNMCriteria.h
5.73 OccupancyTest Class Reference
Inheritance diagram for OccupancyTest:
OccupancyTest
Test
Protected Member Functions
• void SetUp () override• void TearDown () override• double CompareScoresForDisabledAndNoSolvent ()• double CompareScoresForSolventModes ()• bool testFlexAtomFactory (RbtModel ∗pModel, int expected[9][3])
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5.74 Rbt::OverlapHHS Class Reference 51
Protected Attributes
• RbtBiMolWorkSpacePtr m_workSpace• RbtModelList m_solventList
Static Protected Attributes
• static double TINY = 1E-4
The documentation for this class was generated from the following files:
• OccupancyTest.h• OccupancyTest.cxx
5.74 Rbt::OverlapHHS Class Reference
Public Member Functions
• OverlapHHS (HHS_Solvation ∗pHHS, double p)• void operator() (HHS_Solvation ∗pHHSj)
The documentation for this class was generated from the following file:
• RbtSATypes.h
5.75 Rbt::OverlapVariableHHS Class Reference
Public Member Functions
• void operator() (HHS_Solvation ∗pHHS)
The documentation for this class was generated from the following file:
• RbtSATypes.h
5.76 Rbt::PartitionHHS Class Reference
Public Member Functions
• PartitionHHS (double dd)• void operator() (HHS_Solvation ∗pHHS)
The documentation for this class was generated from the following file:
• RbtSATypes.h
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52 Class Documentation
5.77 PrettyPrintVisitor Class Reference
Inheritance diagram for PrettyPrintVisitor:
PrettyPrintVisitor
RbtFilterExpressionVisitor
Public Member Functions
• PrettyPrintVisitor (RbtContextPtr)• virtual void VisitVbleExp (FilterVbleExp ∗)• virtual void VisitAddExp (FilterAddExp ∗)• virtual void VisitSubExp (FilterSubExp ∗)• virtual void VisitMulExp (FilterMulExp ∗)• virtual void VisitDivExp (FilterDivExp ∗)• virtual void VisitAndExp (FilterAndExp ∗)• virtual void VisitLogExp (FilterLogExp ∗)• virtual void VisitExpExp (FilterExpExp ∗)• virtual void VisitIfExp (FilterIfExp ∗)
The documentation for this class was generated from the following file:
• RbtFilterExpressionVisitor.h
5.78 PrintVisitor Class Reference
Inheritance diagram for PrintVisitor:
PrintVisitor
RbtFilterExpressionVisitor
Public Member Functions
• PrintVisitor (RbtContextPtr)• virtual void VisitVbleExp (FilterVbleExp ∗)• virtual void VisitAddExp (FilterAddExp ∗)• virtual void VisitSubExp (FilterSubExp ∗)• virtual void VisitMulExp (FilterMulExp ∗)• virtual void VisitDivExp (FilterDivExp ∗)• virtual void VisitAndExp (FilterAndExp ∗)• virtual void VisitLogExp (FilterLogExp ∗)• virtual void VisitExpExp (FilterExpExp ∗)• virtual void VisitIfExp (FilterIfExp ∗)
The documentation for this class was generated from the following file:
• RbtFilterExpressionVisitor.h
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5.79 RbtDihedral::prms Class Reference 53
5.79 RbtDihedral::prms Class Reference
Public Member Functions
• prms (double ss=3.0, double kk=0.2, double o=0.0)
Public Attributes
• double s• double k• double sign• double offset
The documentation for this class was generated from the following file:
• RbtDihedralSF.h
5.80 RbtAlignTransform Class Reference
Inheritance diagram for RbtAlignTransform:
RbtAlignTransform
RbtBaseBiMolTransform
RbtBaseTransform
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtAlignTransform (const std::string &strName="ALIGN")
Static Public Attributes
• static std::string _CT• static std::string _COM• static std::string _AXES
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54 Class Documentation
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupTransform ()• virtual void Execute ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtAlignTransform.h
5.81 Rbt::RbtAnn_Cmp_AtomId2 Class Reference
Public Member Functions
• bool operator() (RbtAnnotation ∗pAnn1, RbtAnnotation ∗pAnn2) const
The documentation for this class was generated from the following file:
• RbtAnnotation.h
5.82 RbtAnnotation Class Reference
Public Member Functions
• RbtAnnotation (const RbtAtom ∗pAtom1, const RbtAtom ∗pAtom2, double dist, double score)• const RbtAtom ∗ GetAtom1Ptr () const• const RbtAtom ∗ GetAtom2Ptr () const• double GetDistance () const• double GetScore () const• std::string GetFQResName () const• void SetAtom1Ptr (const RbtAtom ∗pAt1)• void SetAtom2Ptr (const RbtAtom ∗pAt2)• void SetDistance (double d)• void SetScore (double s)• std::string Render () const• void operator+= (const RbtAnnotation &ann)
The documentation for this class was generated from the following file:
• RbtAnnotation.h
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5.83 RbtAnnotationHandler Class Reference 55
5.83 RbtAnnotationHandler Class Reference
Inheritance diagram for RbtAnnotationHandler:
RbtAnnotationHandler
RbtAromIdxSF RbtPMFIdxSF RbtPolarSF RbtSAIdxSF RbtVdwSF
RbtPolarIdxSF RbtPolarIntraSF RbtVdwIdxSF RbtVdwIntraSF
Public Member Functions
• bool isAnnotationEnabled () const• const RbtAnnotationList & GetAnnotationList () const• int GetNumAnnotations () const• void RenderAnnotationList (const std::string &strName, std::vector< std::string > &retVal) const
Static Public Attributes
• static std::string _ANNOTATION_FIELD
Protected Member Functions
• void AddAnnotation (RbtAnnotationPtr spAnnotation) const• void ClearAnnotationList () const• void EnableAnnotations (bool bEnabled) const
The documentation for this class was generated from the following file:
• RbtAnnotationHandler.h
5.84 RbtAromIdxSF Class Reference
Inheritance diagram for RbtAromIdxSF:
RbtAromIdxSF
RbtBaseInterSF RbtBaseIdxSF RbtAnnotationHandler
RbtBaseSF RbtBaseSF
RbtBaseObject RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtAromIdxSF (const std::string &strName="AROM")
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56 Class Documentation
Static Public Attributes
• static std::string _CT• static std::string _INCR• static std::string _R12• static std::string _DR12MIN• static std::string _DR12MAX• static std::string _DAMIN• static std::string _DAMAX• static std::string _THRESHOLD
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupScore ()• virtual double RawScore () const• void ClearReceptor ()• void ClearLigand ()• void ParameterUpdated (const std::string &strName)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtAromIdxSF.h
5.85 RbtAssert Class Reference
Inheritance diagram for RbtAssert:
RbtAssert
RbtError
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtError.h
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5.86 RbtAtom Class Reference 57
5.86 RbtAtom Class Reference
Inheritance diagram for RbtAtom:
RbtAtom
RbtPseudoAtom
Public Types
• enum eHybridState {UNDEFINED = 0, SP = 1, SP2 = 2, SP3 = 3,AROM = 4, TRI = 5 }
Public Member Functions
• RBTDLL_EXPORT RbtAtom (int nAtomId, int nAtomicNo=6, std::string strAtomName="C", std::string str←↩
SubunitId="1", std::string strSubunitName="RES", std::string strSegmentName="SEG1", eHybridState e←↩
State=UNDEFINED, unsigned int nHydrogens=0, int nFormalCharge=0)• RbtAtom (const RbtAtom &atom)• RbtAtom & operator= (const RbtAtom &atom)• virtual std::ostream & Print (std::ostream &s) const• RBTDLL_EXPORT bool GetEnabled () const• int GetAtomId () const• void SetAtomId (const int nAtomId)• int GetAtomicNo () const• void SetAtomicNo (const int nAtomicNo)• std::string GetName () const• void SetAtomName (const std::string &strAtomName)• RBTDLL_EXPORT std::string GetFullAtomName () const• std::string GetSubunitId () const• void SetSubunitId (const std::string &strSubunitId)• std::string GetSubunitName () const• void SetSubunitName (const std::string &strSubunitName)• std::string GetSegmentName () const• void SetSegmentName (const std::string &strSegmentName)• eHybridState GetHybridState () const• void SetHybridState (const eHybridState eState)• unsigned int GetNumImplicitHydrogens () const• void SetNumImplicitHydrogens (const unsigned int nHydrogens)• int GetFormalCharge () const• void SetFormalCharge (const int nFormalCharge)• bool GetCyclicFlag () const• void SetCyclicFlag (bool bCyclic=true)• bool GetSelectionFlag () const• void SetSelectionFlag (bool bSelected=true)• void InvertSelectionFlag ()• bool GetUser1Flag () const• void SetUser1Flag (bool bUser1=true)• double GetUser1Value () const
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58 Class Documentation
• void SetUser1Value (double dUser1=0.0)• double GetUser2Value () const• void SetUser2Value (double dUser2=0.0)• RbtModel ∗ GetModelPtr () const• void SetModelPtr (RbtModel ∗pModel=nullptr)• unsigned int GetNumBonds () const• const RbtBondMap & GetBondMap () const• bool AddBond (RbtBond ∗pBond)• bool RemoveBond (RbtBond ∗pBond)• unsigned int GetNumCyclicBonds () const• RbtBondMap GetCyclicBondMap () const• int GetTotalFormalBondOrder () const• int GetMaxFormalBondOrder () const• const RbtCoord & GetCoords () const• double GetX () const• double GetY () const• double GetZ () const• void SetCoords (const RbtCoord &coord)• void SetCoords (const double x, const double y, const double z)• void SetX (const double x)• void SetY (const double y)• void SetZ (const double z)• double GetPartialCharge () const• void SetPartialCharge (const double dPartialCharge)• double GetGroupCharge () const• void SetGroupCharge (const double dGroupCharge)• double GetAtomicMass () const• void SetAtomicMass (const double dAtomicMass)• double GetVdwRadius () const• void SetVdwRadius (const double dVdwRadius)• std::string GetFFType () const• void SetFFType (const std::string &strFFType)• RbtPMFType GetPMFType () const• void SetPMFType (RbtPMFType aType)• RbtTriposAtomType::eType GetTriposType () const• void SetTriposType (RbtTriposAtomType::eType aType)• void SaveCoords (unsigned int coordNum=0)• void RevertCoords (unsigned int coordNum=0)• void Translate (const RbtVector &vector)• void Translate (const double vx, const double vy, const double vz)• void RotateUsingQuat (const RbtQuat &q)• unsigned int GetCoordinationNumber () const• unsigned int GetCoordinationNumber (int nAtomicNo) const• unsigned int GetCoordinationNumber (const std::string &strFFType) const• unsigned int GetCoordinationNumber (eHybridState e) const
Friends
• RBTDLL_EXPORT friend std::ostream & operator<< (std::ostream &s, const RbtAtom &atom)
The documentation for this class was generated from the following file:
• RbtAtom.h
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5.87 Rbt::RbtAtomPtrCmp_AtomicNo Class Reference 59
5.87 Rbt::RbtAtomPtrCmp_AtomicNo Class Reference
Public Member Functions
• bool operator() (RbtAtom ∗pAtom1, RbtAtom ∗pAtom2) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.88 Rbt::RbtAtomPtrCmp_AtomId Class Reference
Public Member Functions
• bool operator() (RbtAtom ∗pAtom1, RbtAtom ∗pAtom2) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.89 Rbt::RbtAtomPtrCmp_AtomName Class Reference
Public Member Functions
• bool operator() (RbtAtom ∗pAtom1, RbtAtom ∗pAtom2) const
The documentation for this class was generated from the following file:
• RbtAtom.h
5.90 Rbt::RbtAtomPtrCmp_Ptr Class Reference
Public Member Functions
• bool operator() (RbtAtom ∗pAtom1, RbtAtom ∗pAtom2) const
The documentation for this class was generated from the following file:
• RbtAtom.h
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60 Class Documentation
5.91 RbtBadArgument Class Reference
Inheritance diagram for RbtBadArgument:
RbtBadArgument
RbtError
Public Member Functions
• RbtBadArgument (const std::string &strFile, int nLine, const std::string &strMessage="")
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtError.h
5.92 RbtBadReceptorFile Class Reference
Inheritance diagram for RbtBadReceptorFile:
RbtBadReceptorFile
RbtError
Public Member Functions
• RbtBadReceptorFile (const std::string &strFile, int nLine, const std::string &strMessage="")
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtError.h
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5.93 RbtBaseBiMolTransform Class Reference 61
5.93 RbtBaseBiMolTransform Class Reference
Inheritance diagram for RbtBaseBiMolTransform:
RbtBaseBiMolTransform
RbtBaseTransform
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
RbtAlignTransform RbtGATransform RbtRandPopTransform RbtSimAnnTransform RbtSimplexTransform
Public Member Functions
• RbtModelPtr GetReceptor () const• RbtModelPtr GetLigand () const• RbtModelList GetSolvent () const• virtual void Update (RbtSubject ∗theChangedSubject)
Static Public Attributes
• static std::string _CT
Protected Member Functions
• RbtBaseBiMolTransform (const std::string &strClass, const std::string &strName)• virtual void SetupReceptor ()=0• virtual void SetupLigand ()=0• virtual void SetupSolvent ()• virtual void SetupTransform ()=0
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtBaseBiMolTransform.h
5.94 RbtBaseFileSink Class Reference
Inheritance diagram for RbtBaseFileSink:
RbtBaseFileSink
RbtBaseMolecularFileSink
RbtCrdFileSink RbtCSVFileSink RbtMdlFileSink RbtPsfFileSink
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62 Class Documentation
Public Member Functions
• RbtBaseFileSink (const std::string &fileName)• std::string GetFileName () const• void SetFileName (const std::string &fileName)• bool StatusOK ()• RbtError Status ()• virtual void Render ()=0
Protected Member Functions
• void Write (bool bClearCache=true)• void AddLine (const std::string &fileRec)• void ReplaceLine (const std::string &fileRec, unsigned int nRec)• bool isCacheEmpty () const• bool GetAppend () const• void SetAppend (bool bAppend)
The documentation for this class was generated from the following file:
• RbtBaseFileSink.h
5.95 RbtBaseFileSource Class Reference
Inheritance diagram for RbtBaseFileSource:
RbtBaseFileSource
RbtBaseMolecularFileSource RbtCharmmTypesFileSource RbtElementFileSource RbtNmrRestraintFileSource RbtParameterFileSource
RbtCrdFileSource RbtMdlFileSource RbtMOL2FileSource RbtPdbFileSource RbtPsfFileSource
Public Member Functions
• RbtBaseFileSource (const std::string &fileName)• RbtBaseFileSource (const std::string &fileName, const std::string &strRecDelim)• RBTDLL_EXPORT std::string GetFileName ()• void SetFileName (const std::string &fileName)• bool StatusOK ()• RBTDLL_EXPORT RbtError Status ()• RBTDLL_EXPORT bool FileStatusOK ()• RbtError FileStatus ()• bool isMultiRecordSupported ()• RBTDLL_EXPORT void NextRecord ()• void Rewind ()• RBTDLL_EXPORT std::size_t GetEstimatedNumRecords ()
Protected Member Functions
• virtual void Parse ()=0• void Read (bool aDelimiterAtEnd=true)
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5.96 RbtBaseGrid Class Reference 63
Protected Attributes
• bool m_bParsedOK• RbtFileRecList m_lineRecs
The documentation for this class was generated from the following file:
• RbtBaseFileSource.h
5.96 RbtBaseGrid Class Reference
Inheritance diagram for RbtBaseGrid:
RbtBaseGrid
RbtInteractionGrid RbtInteractionGridTemplate< T > RbtNonBondedGrid RbtNonBondedHHSGrid RbtRealGrid
RbtFFTGrid
Public Member Functions
• RbtBaseGrid (const RbtCoord &gridMin, const RbtVector &gridStep, unsigned int NX, unsigned int NY,unsigned int NZ, unsigned int NPad=0)
• RbtBaseGrid (std::istream &istr)• RbtBaseGrid (const RbtBaseGrid &)• RbtBaseGrid & operator= (const RbtBaseGrid &)• virtual void Print (std::ostream &ostr) const• virtual void Write (std::ostream &ostr) const• virtual void Read (std::istream &istr)• unsigned int GetNX () const• unsigned int GetNY () const• unsigned int GetNZ () const• unsigned int GetN () const• unsigned int GetStrideX () const• unsigned int GetStrideY () const• unsigned int GetStrideZ () const• int GetnXMin () const• int GetnYMin () const• int GetnZMin () const• int GetnXMax () const• int GetnYMax () const• int GetnZMax () const• const RbtCoord & GetGridMin () const• const RbtCoord & GetGridMax () const• const RbtVector & GetGridStep () const• RbtCoord GetGridCenter () const• RbtCoord GetGridSize () const• unsigned int GetPad () const• const RbtCoord & GetPadMin () const• const RbtCoord & GetPadMax () const• void SetGridMin (const RbtCoord &gridMin)
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64 Class Documentation
• void TranslateGrid (const RbtVector &vec)
• void SetGridCenter (const RbtCoord &gridCenter)
• void SetGridStep (const RbtVector &gridStep)
• void SetPad (unsigned int NPad=0)
• bool isValid (const RbtCoord &c) const
• bool isValid (unsigned int iX, unsigned int iY, unsigned int iZ) const
• bool isValid (unsigned int iXYZ) const
• unsigned int GetIX (const RbtCoord &c) const
• unsigned int GetIY (const RbtCoord &c) const
• unsigned int GetIZ (const RbtCoord &c) const
• unsigned int GetIX (double x) const
• unsigned int GetIY (double y) const
• unsigned int GetIZ (double z) const
• unsigned int GetIX (unsigned int iXYZ) const
• unsigned int GetIY (unsigned int iXYZ) const
• unsigned int GetIZ (unsigned int iXYZ) const
• unsigned int GetIXYZ (unsigned int iX, unsigned int iY, unsigned int iZ) const
• unsigned int GetIXYZ (const RbtCoord &c) const
• RbtCoord GetCoord (unsigned int iX, unsigned int iY, unsigned int iZ) const
• double GetXCoord (unsigned int iX) const
• double GetYCoord (unsigned int iY) const
• double GetZCoord (unsigned int iZ) const
• RbtCoord GetCoord (unsigned int iXYZ) const
• RbtCoordList GetCoordList (const std::set< unsigned int > &iXYZSet) const
• void GetSphereIndices (const RbtCoord &c, double radius, std::vector< unsigned int > &sIndices) const
Static Public Attributes
• static std::string _CT
Protected Member Functions
• void OwnPrint (std::ostream &ostr) const
• void OwnWrite (std::ostream &ostr) const
• void OwnRead (std::istream &istr)
Friends
• std::ostream & operator<< (std::ostream &s, const RbtBaseGrid &grid)
The documentation for this class was generated from the following file:
• RbtBaseGrid.h
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5.97 RbtBaseIdxSF Class Reference 65
5.97 RbtBaseIdxSF Class Reference
Inheritance diagram for RbtBaseIdxSF:
RbtBaseIdxSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
RbtAromIdxSF RbtNmrSF RbtPMFIdxSF RbtPolarIdxSF RbtSAIdxSF RbtVdwIdxSF
Public Member Functions
• double GetGridStep () const
• void SetGridStep (double step)
• double GetBorder () const
• void SetBorder (double border)
Static Public Attributes
• static std::string _CT
• static std::string _GRIDSTEP
• static std::string _BORDER
Protected Member Functions
• RbtInteractionGridPtr CreateInteractionGrid () const
• RbtNonBondedGridPtr CreateNonBondedGrid () const
• RbtNonBondedHHSGridPtr CreateNonBondedHHSGrid () const
• double GetMaxError () const
• double GetCorrectedRange () const
• void OwnParameterUpdated (const std::string &strName)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtBaseIdxSF.h
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66 Class Documentation
5.98 RbtBaseInterSF Class Reference
Inheritance diagram for RbtBaseInterSF:
RbtBaseInterSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
RbtAromIdxSF
RbtCavityFillSF
RbtCavityGridSF
RbtConstSF
RbtDihedralTargetSF
RbtNmrSF
RbtPharmaSF
RbtPMFGridSF
RbtPMFIdxSF
RbtPolarIdxSF
RbtRotSF
RbtSAIdxSF
RbtSetupPMFSF
RbtSetupPolarSF
RbtSetupSASF
RbtTetherSF
RbtVdwGridSF
RbtVdwIdxSF
Public Member Functions
• RbtModelPtr GetReceptor () const• RbtModelPtr GetLigand () const• RbtModelList GetSolvent () const• virtual void Update (RbtSubject ∗theChangedSubject)
Static Public Attributes
• static std::string _CT
Protected Member Functions
• virtual void SetupReceptor ()=0• virtual void SetupLigand ()=0• virtual void SetupSolvent ()• virtual void SetupScore ()=0
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5.99 RbtBaseIntraSF Class Reference 67
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtBaseInterSF.h
5.99 RbtBaseIntraSF Class Reference
Inheritance diagram for RbtBaseIntraSF:
RbtBaseIntraSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
RbtDihedralIntraSF RbtPolarIntraSF RbtVdwIntraSF
Public Member Functions
• RbtModelPtr GetLigand () const• virtual void Update (RbtSubject ∗theChangedSubject)• virtual void ScoreMap (RbtStringVariantMap &scoreMap) const
Static Public Attributes
• static std::string _CT
Protected Member Functions
• virtual void SetupScore ()=0
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtBaseIntraSF.h
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68 Class Documentation
5.100 RbtBaseMolecularDataSource Class Reference
Inheritance diagram for RbtBaseMolecularDataSource:
RbtBaseMolecularDataSource
RbtBaseMolecularFileSource
RbtCrdFileSource RbtMdlFileSource RbtMOL2FileSource RbtPdbFileSource RbtPsfFileSource
Public Member Functions
• RbtBaseMolecularDataSource (std::string strName)• std::string GetName ()• virtual bool isTitleListSupported ()• virtual bool isAtomListSupported ()• virtual bool isCoordinatesSupported ()• virtual bool isBondListSupported ()• virtual void Reset ()=0• virtual int GetNumTitles ()=0• virtual int GetNumAtoms ()=0• virtual int GetNumBonds ()=0• virtual int GetNumSegments ()=0• virtual std::vector< std::string > GetTitleList ()=0• virtual RbtAtomList GetAtomList ()=0• virtual RbtBondList GetBondList ()=0• virtual RbtSegmentMap GetSegmentMap ()=0• virtual bool isDataSupported ()• virtual int GetNumData ()=0• virtual std::vector< std::string > GetDataFieldList ()=0• virtual RbtStringVariantMap GetDataMap ()=0• virtual bool isDataFieldPresent (const std::string &strDataField)=0• virtual RbtVariant GetDataValue (const std::string &strDataField)=0
The documentation for this class was generated from the following file:
• RbtBaseMolecularDataSource.h
5.101 RbtBaseMolecularFileSink Class Reference
Inheritance diagram for RbtBaseMolecularFileSink:
RbtBaseMolecularFileSink
RbtBaseFileSink
RbtCrdFileSink RbtCSVFileSink RbtMdlFileSink RbtPsfFileSink
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5.102 RbtBaseMolecularFileSource Class Reference 69
Public Member Functions
• RbtBaseMolecularFileSink (const std::string &fileName, RbtModelPtr spModel, bool bUseModelSegment←↩
Names=true)
• virtual bool isMultiConfSupported ()
• RbtModelPtr GetModel () const
• RBTDLL_EXPORT void SetModel (RbtModelPtr spModel, bool bUseModelSegmentNames=false)
• void SetNextSegmentId (int nSegmentId)
• bool GetMultiConf () const
• void SetMultiConf (bool bMultiConf)
• void WriteMultiConf ()
• RbtModelList GetSolvent () const
• void SetSolvent (RbtModelList solventList)
Protected Member Functions
• void Reset ()
Protected Attributes
• int m_nAtomId
• int m_nSubunitId
• int m_nSegmentId
• bool m_bUseModelSegmentNames
The documentation for this class was generated from the following file:
• RbtBaseMolecularFileSink.h
5.102 RbtBaseMolecularFileSource Class Reference
Inheritance diagram for RbtBaseMolecularFileSource:
RbtBaseMolecularFileSource
RbtBaseFileSource RbtBaseMolecularDataSource
RbtCrdFileSource RbtMdlFileSource RbtMOL2FileSource RbtPdbFileSource RbtPsfFileSource
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70 Class Documentation
Public Member Functions
• RBTDLL_EXPORT RbtBaseMolecularFileSource (const std::string &fileName, const std::string &source←↩
Name)
• RbtBaseMolecularFileSource (const std::string &fileName, const std::string &strRecDelim, const std::string&sourceName)
• void Reset ()
• int GetNumTitles ()
• int GetNumAtoms ()
• int GetNumBonds ()
• int GetNumSegments ()
• std::vector< std::string > GetTitleList ()
• RbtAtomList GetAtomList ()
• RbtBondList GetBondList ()
• RbtSegmentMap GetSegmentMap ()
• virtual int GetNumData ()
• virtual std::vector< std::string > GetDataFieldList ()
• virtual RbtStringVariantMap GetDataMap ()
• virtual bool isDataFieldPresent (const std::string &strDataField)
• virtual RbtVariant GetDataValue (const std::string &strDataField)
• RbtSegmentMap GetSegmentFilterMap ()
• RBTDLL_EXPORT void SetSegmentFilterMap (const RbtSegmentMap &segmentFilterMap)
• void ClearSegmentFilterMap ()
• bool isSegmentFilterMapDefined ()
Protected Member Functions
• void ClearMolCache ()
• void RemoveAtom (RbtAtomPtr spAtom)
• void RenumberAtomsAndBonds ()
• void SetupPartialIonicGroups (RbtAtomList &atoms, RbtParameterFileSourcePtr spParamSource)
Protected Attributes
• std::vector< std::string > m_titleList
• RbtAtomList m_atomList
• RbtBondList m_bondList
• RbtSegmentMap m_segmentMap
• RbtStringVariantMap m_dataMap
The documentation for this class was generated from the following file:
• RbtBaseMolecularFileSource.h
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5.103 RbtBaseObject Class Reference 71
5.103 RbtBaseObject Class Reference
Inheritance diagram for RbtBaseObject:
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
RbtBaseSF RbtBaseTransform RbtFilter RbtSiteMapper
RbtBaseIdxSF
RbtBaseInterSF
RbtBaseIntraSF
RbtDihedralSF
RbtPolarSF
RbtSFAgg
RbtVdwSF
RbtBaseBiMolTransform
RbtBaseUniMolTransform
RbtNullTransform
RbtTransformAgg
RbtLigandSiteMapper
RbtSphereSiteMapper
Public Member Functions
• std::string GetClass () const• std::string GetName () const• void SetName (const std::string &)• virtual std::string GetFullName () const• void Enable ()• void Disable ()• bool isEnabled () const• int GetTrace () const• RBTDLL_EXPORT void SetTrace (int)• virtual void Register (RbtWorkSpace ∗)• virtual void Unregister ()• RbtWorkSpace ∗ GetWorkSpace () const• virtual void Deleted (RbtSubject ∗theDeletedSubject)• virtual void HandleRequest (RbtRequestPtr spRequest)• virtual void Print (std::ostream &s) const
Static Public Member Functions
• static RBTDLL_EXPORT std::string & GetTraceStr ()
Static Public Attributes
• static std::string _CT• static std::string _CLASS• static std::string _NAME• static std::string _ENABLED• static std::string _TRACE
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72 Class Documentation
Protected Member Functions
• RbtBaseObject (const std::string &strClass, const std::string &strName)• void ParameterUpdated (const std::string &strName)
The documentation for this class was generated from the following file:
• RbtBaseObject.h
5.104 RbtBaseSF Class Reference
Inheritance diagram for RbtBaseSF:
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
RbtBaseIdxSF RbtBaseInterSF RbtBaseIntraSF RbtDihedralSF RbtPolarSF RbtSFAgg RbtVdwSF
RbtAromIdxSF
RbtNmrSF
RbtPMFIdxSF
RbtPolarIdxSF
RbtSAIdxSF
RbtVdwIdxSF
RbtAromIdxSF
RbtCavityFillSF
RbtCavityGridSF
RbtConstSF
RbtDihedralTargetSF
RbtNmrSF
RbtPharmaSF
RbtPMFGridSF
RbtPMFIdxSF
RbtPolarIdxSF
RbtRotSF
RbtSAIdxSF
RbtSetupPMFSF
RbtSetupPolarSF
RbtSetupSASF
RbtTetherSF
RbtVdwGridSF
RbtVdwIdxSF
RbtDihedralIntraSF
RbtPolarIntraSF
RbtVdwIntraSF
RbtDihedralIntraSF
RbtDihedralTargetSF
RbtPolarIdxSF
RbtPolarIntraSF
RbtVdwIdxSF
RbtVdwIntraSF
Public Member Functions
• std::string GetFullName () const• double GetWeight () const• void SetWeight (double)• double GetRange () const• RBTDLL_EXPORT void SetRange (double)• RBTDLL_EXPORT double Score () const• virtual void ScoreMap (RbtStringVariantMap &scoreMap) const• virtual void Add (RbtBaseSF ∗)• virtual void Remove (RbtBaseSF ∗)• virtual bool isAgg () const• virtual unsigned int GetNumSF () const• virtual RbtBaseSF ∗ GetSF (unsigned int iSF) const• void Orphan ()• RbtBaseSF ∗ GetParentSF () const
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5.105 RbtBaseTransform Class Reference 73
Static Public Attributes
• static std::string _CT• static std::string _WEIGHT• static std::string _RANGE• static std::string _SYSTEM_SF• static std::string _INTRA_SF
Protected Member Functions
• RbtBaseSF (const std::string &strClass, const std::string &strName)• virtual double RawScore () const =0• void ParameterUpdated (const std::string &strName)• void AddToParentMapEntry (RbtStringVariantMap &scoreMap, double rs) const
Friends
• class RbtSFAgg
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtBaseSF.h
5.105 RbtBaseTransform Class Reference
Inheritance diagram for RbtBaseTransform:
RbtBaseTransform
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
RbtBaseBiMolTransform RbtBaseUniMolTransform RbtNullTransform RbtTransformAgg
RbtAlignTransform RbtGATransform RbtRandPopTransform RbtSimAnnTransform RbtSimplexTransform RbtRandLigTransform
Public Member Functions
• std::string GetFullName () const• void Go ()• virtual void Add (RbtBaseTransform ∗)• virtual void Remove (RbtBaseTransform ∗)• virtual bool isAgg () const• virtual unsigned int GetNumTransforms () const• virtual RbtBaseTransform ∗ GetTransform (unsigned int) const• void Orphan ()• RbtBaseTransform ∗ GetParentTransform () const• void AddSFRequest (RbtRequestPtr)• void ClearSFRequests ()• void SendSFRequests ()
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74 Class Documentation
Static Public Attributes
• static std::string _CT
Protected Member Functions
• RbtBaseTransform (const std::string &strClass, const std::string &strName)
Friends
• class RbtTransformAgg
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtBaseTransform.h
5.106 RbtBaseUniMolTransform Class Reference
Inheritance diagram for RbtBaseUniMolTransform:
RbtBaseUniMolTransform
RbtBaseTransform
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
RbtRandLigTransform
Public Member Functions
• RbtModelPtr GetLigand () const• virtual void Update (RbtSubject ∗theChangedSubject)
Static Public Attributes
• static std::string _CT
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5.107 RbtBiMolWorkSpace Class Reference 75
Protected Member Functions
• RbtBaseUniMolTransform (const std::string &strClass, const std::string &strName)• virtual void SetupTransform ()=0
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtBaseUniMolTransform.h
5.107 RbtBiMolWorkSpace Class Reference
Inheritance diagram for RbtBiMolWorkSpace:
RbtBiMolWorkSpace
RbtWorkSpace
RbtSubject RbtParamHandler
Public Member Functions
• RBTDLL_EXPORT RbtModelPtr GetReceptor () const• RBTDLL_EXPORT RbtModelPtr GetLigand () const• RBTDLL_EXPORT RbtModelList GetSolvent () const• RBTDLL_EXPORT bool hasSolvent () const• RBTDLL_EXPORT void SetReceptor (RbtModelPtr spReceptor)• RBTDLL_EXPORT void SetLigand (RbtModelPtr spLigand)• RBTDLL_EXPORT void SetSolvent (RbtModelList solventList)• RBTDLL_EXPORT void RemoveSolvent ()• RBTDLL_EXPORT void UpdateModelCoordsFromChromRecords (RbtBaseMolecularFileSource ∗p←↩
Source, int iTrace)• virtual void Save (bool bSaveScores=true)• virtual void SaveHistory (bool bSaveScores=true)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtBiMolWorkSpace.h
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76 Class Documentation
5.108 RbtBond Class Reference
Public Member Functions
• RbtBond (int nBondId, RbtAtomPtr &spAtom1, RbtAtomPtr &spAtom2, int nFormalBondOrder=1)
• RbtBond (const RbtBond &bond)
• RbtBond & operator= (const RbtBond &bond)
• int GetBondId () const
• void SetBondId (const int nBondId)
• RbtAtomPtr GetAtom1Ptr () const
• RbtAtomPtr GetAtom2Ptr () const
• void SetAtom1Ptr (RbtAtomPtr &spAtom1)
• void SetAtom2Ptr (RbtAtomPtr &spAtom2)
• int GetFormalBondOrder () const
• void SetFormalBondOrder (const int nFormalBondOrder)
• double GetPartialBondOrder () const
• void SetPartialBondOrder (const double dPartialBondOrder)
• bool GetCyclicFlag () const
• void SetCyclicFlag (bool bCyclic=true)
• bool GetSelectionFlag () const
• void SetSelectionFlag (bool bSelected=true)
• double Length () const
Friends
• RBTDLL_EXPORT friend std::ostream & operator<< (std::ostream &s, const RbtBond &bond)
The documentation for this class was generated from the following file:
• RbtBond.h
5.109 Rbt::RbtBondPCmp_BondId Class Reference
Public Member Functions
• bool operator() (RbtBond ∗pBond1, RbtBond ∗pBond2) const
The documentation for this class was generated from the following file:
• RbtAtom.h
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5.110 RbtCavity Class Reference 77
5.110 RbtCavity Class Reference
Public Member Functions
• RbtCavity (const RbtCoordList &coordList, const RbtVector gridStep)• RbtCavity (std::istream &istr)• virtual void Print (std::ostream &s) const• virtual void Write (std::ostream &ostr) const• virtual void Read (std::istream &istr)• RbtRealGridPtr GetGrid () const• const RbtCoord & GetCenterOfMass () const• const RbtPrincipalAxes & GetPrincipalAxes () const• int GetNumCoords () const• const RbtCoordList & GetCoordList () const• const RbtCoord & GetMinCoord () const• const RbtCoord & GetMaxCoord () const• const RbtVector & GetGridStep () const• double GetVolume () const
Friends
• std::ostream & operator<< (std::ostream &s, const RbtCavity &cavity)
The documentation for this class was generated from the following file:
• RbtCavity.h
5.111 RbtCavityFillSF Class Reference
Inheritance diagram for RbtCavityFillSF:
RbtCavityFillSF
RbtBaseInterSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtCavityFillSF (const std::string &strName="CAVFILL")
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78 Class Documentation
Static Public Attributes
• static std::string _CT
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupScore ()• virtual double RawScore () const• void ParameterUpdated (const std::string &strName)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtCavityFillSF.h
5.112 RbtCavityGridSF Class Reference
Inheritance diagram for RbtCavityGridSF:
RbtCavityGridSF
RbtBaseInterSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Classes
• class HeavyAtomFactory
Public Member Functions
• RbtCavityGridSF (const std::string &strName="CAVITY")
Static Public Attributes
• static std::string _CT• static std::string _RMAX• static std::string _QUADRATIC
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5.113 Rbt::RbtCavityPtrCmp_Distance Class Reference 79
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupSolvent ()• virtual void SetupScore ()• virtual double RawScore () const• void ParameterUpdated (const std::string &strName)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtCavityGridSF.h
5.113 Rbt::RbtCavityPtrCmp_Distance Class Reference
Public Member Functions
• RbtCavityPtrCmp_Distance (const RbtCoord &cc)• bool operator() (RbtCavityPtr spCav1, RbtCavityPtr spCav2) const
The documentation for this class was generated from the following file:
• RbtCavity.h
5.114 Rbt::RbtCavityPtrCmp_Volume Class Reference
Public Member Functions
• bool operator() (RbtCavityPtr spCav1, RbtCavityPtr spCav2) const
The documentation for this class was generated from the following file:
• RbtCavity.h
5.115 RbtCellContext Class Reference
Inheritance diagram for RbtCellContext:
RbtCellContext
RbtContext
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80 Class Documentation
Public Member Functions
• RbtCellContext (std::ifstream &ifile)• RbtCellContext (const RbtCellContext &c)• void Assign (int key, RbtReturnType val)• void Assign (std::string s, RbtReturnType val)• const RbtVble & GetVble (int key)• void SetVble (int key, const RbtVble &v)• const RbtVble & GetVble (std::string key)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtContext.h
5.116 RbtCellTokenIter Class Reference
Inheritance diagram for RbtCellTokenIter:
RbtCellTokenIter
RbtTokenIter
Public Member Functions
• RbtCellTokenIter (const RbtCellTokenIter &)• RbtCellTokenIter (const RbtGPChromosomePtr, RbtContextPtr)• virtual void copy (const RbtCellTokenIter &)• void Next (RbtContextPtr)• RbtTokenPtr Current ()
Static Public Attributes
• static std::string _CT
The documentation for this class was generated from the following file:
• RbtCellTokenIter.h
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5.117 RbtCharmmDataSource Class Reference 81
5.117 RbtCharmmDataSource Class Reference
Public Member Functions
• RbtCharmmDataSource (const std::string &strMassesFile=Rbt::GetRbtFileName("data", "masses.rtf"))• std::string AtomTypeString (int nAtomType)• int ImplicitHydrogens (const std::string &strFFType)• int AtomicNumber (const std::string &strFFType)• int FormalCharge (const std::string &strFFType)• RbtAtom::eHybridState HybridState (const std::string &strFFType)
The documentation for this class was generated from the following file:
• RbtCharmmDataSource.h
5.118 RbtCharmmTypesFileSource Class Reference
Inheritance diagram for RbtCharmmTypesFileSource:
RbtCharmmTypesFileSource
RbtBaseFileSource
Public Member Functions
• RbtCharmmTypesFileSource (const char ∗fileName)• RbtCharmmTypesFileSource (const std::string fileName)• int GetNumTypes ()• RbtCharmmTypeList GetTypeList ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtCharmmTypesFileSource.h
5.119 RbtChrom Class Reference
Inheritance diagram for RbtChrom:
RbtChrom
RbtChromElement
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82 Class Documentation
Public Member Functions
• RbtChrom (const RbtModelList &modelList)
• virtual void Reset ()
• virtual void Randomise ()
• virtual void Mutate (double relStepSize)
• virtual void SyncFromModel ()
• virtual void SyncToModel ()
• virtual RbtChromElement ∗ clone () const
• virtual int GetLength () const
• virtual int GetXOverLength () const
• virtual void GetVector (std::vector< double > &v) const
• virtual void GetVector (RbtXOverList &v) const
• virtual void SetVector (const std::vector< double > &v, int &i)
• virtual void SetVector (const RbtXOverList &v, int &i)
• virtual void GetStepVector (std::vector< double > &v) const
• virtual double CompareVector (const std::vector< double > &v, int &i) const
• virtual void Print (std::ostream &s) const
• virtual void Add (RbtChromElement ∗pChromElement)
Static Public Attributes
• static std::string _CT
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtChrom.h
5.120 RbtChromDihedralElement Class Reference
Inheritance diagram for RbtChromDihedralElement:
RbtChromDihedralElement
RbtChromElement
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5.121 RbtChromDihedralRefData Class Reference 83
Public Member Functions
• RBTDLL_EXPORT RbtChromDihedralElement (RbtBondPtr spBond, RbtAtomList tetheredAtoms, doublestepSize, RbtChromElement::eMode mode=RbtChromElement::FREE, double maxDihedral=0.0)
• virtual void Reset ()• virtual void Randomise ()• virtual void Mutate (double relStepSize)• virtual void SyncFromModel ()• virtual void SyncToModel ()• virtual RbtChromElement ∗ clone () const• virtual int GetLength () const• virtual int GetXOverLength () const• virtual void GetVector (std::vector< double > &v) const• virtual void GetVector (RbtXOverList &v) const• virtual void SetVector (const std::vector< double > &v, int &i)• virtual void SetVector (const RbtXOverList &v, int &i)• virtual void GetStepVector (std::vector< double > &v) const• virtual double CompareVector (const std::vector< double > &v, int &i) const• virtual void Print (std::ostream &s) const
Static Public Member Functions
• static double StandardisedValue (double dihedralAngle)
Static Public Attributes
• static std::string _CT
Protected Member Functions
• RbtChromDihedralElement (RbtChromDihedralRefDataPtr spRefData, double value)• void CorrectTetheredDihedral ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtChromDihedralElement.h
5.121 RbtChromDihedralRefData Class Reference
Public Member Functions
• RbtChromDihedralRefData (RbtBondPtr spBond, RbtAtomList tetheredAtoms, double stepSize, Rbt←↩
ChromElement::eMode mode=RbtChromElement::FREE, double maxDihedral=0.0)• double GetStepSize () const• RbtChromElement::eMode GetMode () const• double GetMaxDihedral () const• double GetModelValue () const• void SetModelValue (double dihedralAngle)• double GetInitialValue () const
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84 Class Documentation
Static Public Attributes
• static std::string _CT
The documentation for this class was generated from the following file:
• RbtChromDihedralRefData.h
5.122 RbtChromElement Class Reference
Inheritance diagram for RbtChromElement:
RbtChromElement
RbtChrom RbtChromDihedralElement RbtChromOccupancyElement RbtChromPositionElement
Public Types
• enum eMode { FIXED = 0, TETHERED = 1, FREE = 2 }
Public Member Functions
• virtual void Reset ()=0• virtual void Randomise ()=0• virtual void Mutate (double relStepSize)=0• virtual void SyncFromModel ()=0• virtual void SyncToModel ()=0• virtual RbtChromElement ∗ clone () const =0• virtual int GetLength () const =0• virtual int GetXOverLength () const =0• virtual void GetVector (std::vector< double > &v) const =0• virtual void GetVector (RbtXOverList &v) const =0• virtual void SetVector (const std::vector< double > &v, int &i)=0• virtual void SetVector (const RbtXOverList &v, int &i)=0• virtual void GetStepVector (std::vector< double > &v) const =0• virtual double CompareVector (const std::vector< double > &v, int &i) const =0• virtual void Add (RbtChromElement ∗pChromElement)• virtual void Print (std::ostream &s) const• RbtRand & GetRand () const• void CauchyMutate (double mean, double variance)• RBTDLL_EXPORT double Compare (const RbtChromElement &c) const• bool Equals (const RbtChromElement &c, double threshold) const• void SetVector (const std::vector< double > &v)• void SetVector (const RbtXOverList &v)
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5.123 RbtChromFactory Class Reference 85
Static Public Member Functions
• static RBTDLL_EXPORT double & GetThreshold ()• static eMode StrToMode (const std::string &modeStr)• static std::string RBTDLL_EXPORT ModeToStr (eMode mode)
Static Public Attributes
• static std::string _CT• static double _THRESHOLD
Protected Member Functions
• RBTDLL_EXPORT RbtChromElement (const RbtChromElement &c)• RBTDLL_EXPORT RbtChromElement & operator= (const RbtChromElement &c)• bool VectorOK (const std::vector< double > &v, unsigned int i) const• bool VectorOK (const RbtXOverList &v, unsigned int i) const
Friends
• RBTDLL_EXPORT friend bool operator== (const RbtChromElement &c1, const RbtChromElement &c2)• RBTDLL_EXPORT friend bool operator!= (const RbtChromElement &c1, const RbtChromElement &c2)• RBTDLL_EXPORT friend std::ostream & operator<< (std::ostream &s, const RbtChromElement &c)
The documentation for this class was generated from the following file:
• RbtChromElement.h
5.123 RbtChromFactory Class Reference
Inheritance diagram for RbtChromFactory:
RbtChromFactory
RbtFlexDataVisitor
Public Member Functions
• virtual void VisitReceptorFlexData (RbtReceptorFlexData ∗)• virtual void VisitLigandFlexData (RbtLigandFlexData ∗)• virtual void VisitSolventFlexData (RbtSolventFlexData ∗)• RbtChromElement ∗ GetChrom () const• RbtModelMutatorPtr GetModelMutator () const
The documentation for this class was generated from the following file:
• RbtChromFactory.h
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86 Class Documentation
5.124 RbtChromOccupancyElement Class Reference
Inheritance diagram for RbtChromOccupancyElement:
RbtChromOccupancyElement
RbtChromElement
Public Member Functions
• RBTDLL_EXPORT RbtChromOccupancyElement (RbtModel ∗pModel, double stepSize, double threshold)• virtual void Reset ()• virtual void Randomise ()• virtual void Mutate (double relStepSize)• virtual void SyncFromModel ()• virtual void SyncToModel ()• virtual RbtChromElement ∗ clone () const• virtual int GetLength () const• virtual int GetXOverLength () const• virtual void GetVector (std::vector< double > &v) const• virtual void GetVector (RbtXOverList &v) const• virtual void SetVector (const std::vector< double > &v, int &i)• virtual void SetVector (const RbtXOverList &v, int &i)• virtual void GetStepVector (std::vector< double > &v) const• virtual double CompareVector (const std::vector< double > &v, int &i) const• virtual void Print (std::ostream &s) const
Static Public Member Functions
• static double StandardisedValue (double occupancy)
Static Public Attributes
• static std::string _CT
Protected Member Functions
• RbtChromOccupancyElement (RbtChromOccupancyRefDataPtr spRefData, double value)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtChromOccupancyElement.h
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5.125 RbtChromOccupancyRefData Class Reference 87
5.125 RbtChromOccupancyRefData Class Reference
Public Member Functions
• RbtChromOccupancyRefData (RbtModel ∗pModel, double stepSize, double threshold)• double GetStepSize () const• double GetModelValue () const• void SetModelValue (double occupancy)• double GetInitialValue () const
Static Public Attributes
• static std::string _CT
The documentation for this class was generated from the following file:
• RbtChromOccupancyRefData.h
5.126 RbtChromPositionElement Class Reference
Inheritance diagram for RbtChromPositionElement:
RbtChromPositionElement
RbtChromElement
Public Member Functions
• RBTDLL_EXPORT RbtChromPositionElement (const RbtModel ∗pModel, const RbtDockingSite ∗p←↩
DockSite, double transStepSize, double rotStepSize, RbtChromElement::eMode transMode=RbtChrom←↩
Element::FREE, RbtChromElement::eMode rotMode=RbtChromElement::FREE, double maxTrans=0.0, dou-ble maxRot=0.0)
• virtual void Reset ()• virtual void Randomise ()• virtual void Mutate (double relStepSize)• virtual void SyncFromModel ()• virtual void SyncToModel ()• virtual RbtChromElement ∗ clone () const• virtual int GetLength () const• virtual int GetXOverLength () const• virtual void GetVector (std::vector< double > &v) const• virtual void GetVector (RbtXOverList &v) const• virtual void SetVector (const std::vector< double > &v, int &i)• virtual void SetVector (const RbtXOverList &v, int &i)• virtual void GetStepVector (std::vector< double > &v) const• virtual double CompareVector (const std::vector< double > &v, int &i) const• virtual void Print (std::ostream &s) const
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88 Class Documentation
Static Public Member Functions
• static double StandardisedValue (double rotationAngle)
Static Public Attributes
• static std::string _CT
Protected Member Functions
• RbtChromPositionElement (RbtChromPositionRefDataPtr spRefData, const RbtCoord &com, constRbtEuler &orientation)
• void RandomiseCOM ()• void RandomiseOrientation ()• void MutateCOM (double relStepSize)• void MutateOrientation (double relStepSize)• void CorrectTetheredCOM ()• void CorrectTetheredOrientation ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtChromPositionElement.h
5.127 RbtChromPositionRefData Class Reference
Public Member Functions
• RbtChromPositionRefData (const RbtModel ∗pModel, const RbtDockingSite ∗pDockSite, double trans←↩
StepSize, double rotStepSize, RbtChromElement::eMode transMode=RbtChromElement::FREE, Rbt←↩
ChromElement::eMode rotMode=RbtChromElement::FREE, double maxTrans=0.0, double maxRot=0.0)• int GetNumStartCoords () const• const RbtCoord & GetStartCoord (int iCoord) const• double GetTransStepSize () const• double GetRotStepSize () const• RbtChromElement::eMode GetTransMode () const• RbtChromElement::eMode GetRotMode () const• int GetLength () const• int GetXOverLength () const• bool IsTransFixed () const• bool IsRotFixed () const• double GetMaxTrans () const• double GetMaxRot () const• const RbtCoord & GetInitialCOM () const• const RbtEuler & GetInitialOrientation () const• const RbtQuat & GetInitialQuat () const• void GetModelValue (RbtCoord &com, RbtEuler &orientation) const• void SetModelValue (const RbtCoord &com, const RbtEuler &orientation)
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5.128 RbtChromTest Class Reference 89
Static Public Attributes
• static std::string _CT• static const RbtPrincipalAxes CARTESIAN_AXES
The documentation for this class was generated from the following file:
• RbtChromPositionRefData.h
5.128 RbtChromTest Class Reference
Inheritance diagram for RbtChromTest:
RbtChromTest
Test
Protected Member Functions
• void SetUp () override• void TearDown () override• void setupWorkSpace ()• double rmsd (const RbtCoordList &rc, const RbtCoordList &c)• void measureRandOrMutateDiff (RbtChromElement ∗chrom, int nTrials, bool bMutate, double &meanDiff,
double &minDiff, double &maxDiff)• void measureCrossoverDiff (RbtChromElement ∗chrom, int nTrials, double &meanDiff, double &minDiff,
double &maxDiff)
Protected Attributes
• RbtModelPtr m_recep_1koc• RbtModelPtr m_lig_1koc• RbtDockingSitePtr m_site_1koc• RbtChromElementPtr m_chrom_1koc• RbtAtomList m_atomList• RbtBiMolWorkSpacePtr m_workSpace• RbtSFAggPtr m_SF
Static Protected Attributes
• static double TINY = 1E-4
The documentation for this class was generated from the following files:
• RbtChromTest.h• RbtChromTest.cxx
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90 Class Documentation
5.129 RbtCommands Class Reference
Public Types
• enum RbtCommName {ADD = 0, SUB = 1, MUL = 2, DIV = 3,IF = 4, LOG = 5, EXP = 6, RCTE = 7,AND = 8, NULLC = -1 }
Public Member Functions
• RbtCommands (const RbtCommands &c)
• RbtCommands (int ncomm)
• RbtCommName GetName () const
• int GetNArgs () const
• bool IsAdd () const
• bool IsSub () const
• bool IsMul () const
• bool IsDiv () const
• bool IsIf () const
• bool IsLog () const
• bool IsExp () const
• bool IsRCte () const
• bool IsAnd () const
• virtual void copy (const RbtCommands &c)
The documentation for this class was generated from the following file:
• RbtCommands.h
5.130 RbtConstraint Class Reference
Inheritance diagram for RbtConstraint:
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5.130 RbtConstraint Class Reference 91
RbtConstraint
RbtHBAConstraint
RbtHBDConstraint
RbtHeavyConstraint
RbtHydroAliphaticConstraint
RbtHydroAromaticConstraint
RbtHydroConstraint
RbtNegChargeConstraint
RbtPosChargeConstraint
RbtRingAromaticConstraint
Public Member Functions
• RbtConstraint (RbtCoord, double)• RbtConstraint (const RbtConstraint &)• void copy (const RbtConstraint &)• std::ostream & Print (std::ostream &) const• RbtCoord GetCoords () const• double GetTolerance () const• virtual void AddAtomList (RbtModelPtr, bool bCheck=true)=0• double Score () const
Static Public Attributes
• static std::string _CT
Protected Attributes
• RbtCoord coord• double tolerance• RbtAtomList m_atomList
Friends
• std::ostream & operator<< (std::ostream &, const RbtConstraint &)
The documentation for this class was generated from the following file:
• RbtConstraint.h
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92 Class Documentation
5.131 RbtConstSF Class Reference
Inheritance diagram for RbtConstSF:
RbtConstSF
RbtBaseInterSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtConstSF (const std::string &strName="CONST")• virtual void ScoreMap (RbtStringVariantMap &scoreMap) const
Static Public Attributes
• static std::string _CT• static std::string _SOLVENT_PENALTY
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupScore ()• virtual double RawScore () const• void ParameterUpdated (const std::string &strName)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtConstSF.h
5.132 RbtContext Class Reference
Inheritance diagram for RbtContext:
RbtContext
RbtCellContext RbtStringContext
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5.133 RbtCoord Class Reference 93
Public Member Functions
• RbtContext (const RbtContext &c)
• virtual void Assign (std::string, RbtReturnType)=0
• virtual void Assign (int, RbtReturnType)=0
• virtual const RbtVble & GetVble (int)=0
• virtual const RbtVble & GetVble (std::string)=0
• virtual void SetVble (int key, const RbtVble &v)=0
Static Public Attributes
• static std::string _CT
The documentation for this class was generated from the following file:
• RbtContext.h
5.133 RbtCoord Class Reference
Public Member Functions
• RbtCoord (double x1, double y1, double z1)
• RbtCoord (Eigen::Vector3d xyz1)
• RbtCoord (const RbtCoord &coord)
• std::ostream & Write (std::ostream &ostr) const
• std::istream & Read (std::istream &istr)
• RbtCoord & operator= (const RbtCoord &coord)
• RbtCoord & operator= (const double &d)
• void operator+= (const RbtCoord &coord)
• void operator+= (const double &d)
• void operator-= (const RbtCoord &coord)
• void operator-= (const double &d)
• void operator∗= (const double &d)
• void operator/= (const double &d)
• double Length2 () const
• double Length () const
• RbtCoord Unit () const
• RbtCoord Cross (const RbtCoord &v2) const
• double Dot (const RbtCoord &v2) const
Public Attributes
• Eigen::Vector3d xyz
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94 Class Documentation
Friends
• std::ostream & operator<< (std::ostream &s, const RbtCoord &coord)• std::istream & operator>> (std::istream &s, RbtCoord &coord)• bool operator== (const RbtCoord &coord1, const RbtCoord &coord2)• bool operator!= (const RbtCoord &coord1, const RbtCoord &coord2)• bool operator> (const RbtCoord &coord1, const RbtCoord &coord2)• bool operator>= (const RbtCoord &coord1, const RbtCoord &coord2)• bool operator< (const RbtCoord &coord1, const RbtCoord &coord2)• bool operator<= (const RbtCoord &coord1, const RbtCoord &coord2)• RbtCoord operator+ (const RbtCoord &coord1, const RbtCoord &coord2)• RbtCoord operator+ (const RbtCoord &coord1, double d)• RbtCoord operator+ (double d, const RbtCoord &coord1)• RbtCoord operator- (const RbtCoord &coord1, const RbtCoord &coord2)• RbtCoord operator- (const RbtCoord &coord1, double d)• RbtCoord operator- (double d, const RbtCoord &coord1)• RbtCoord operator- (const RbtCoord &coord)• RbtCoord operator∗ (const RbtCoord &coord, const double &d)• RbtCoord operator∗ (const double &d, const RbtCoord &coord)• RbtCoord operator∗ (const RbtCoord &coord1, const RbtCoord &coord2)• RbtCoord operator/ (const RbtCoord &coord, const double &d)
The documentation for this class was generated from the following file:
• RbtCoord.h
5.134 RbtCrdFileSink Class Reference
Inheritance diagram for RbtCrdFileSink:
RbtCrdFileSink
RbtBaseMolecularFileSink
RbtBaseFileSink
Public Member Functions
• RBTDLL_EXPORT RbtCrdFileSink (const std::string &fileName, RbtModelPtr spModel)• virtual bool isMultiConfSupported ()• virtual void Render ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtCrdFileSink.h
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5.135 RbtCrdFileSource Class Reference 95
5.135 RbtCrdFileSource Class Reference
Inheritance diagram for RbtCrdFileSource:
RbtCrdFileSource
RbtBaseMolecularFileSource
RbtBaseFileSource RbtBaseMolecularDataSource
Public Member Functions
• RbtCrdFileSource (const char ∗fileName)• RbtCrdFileSource (const std::string fileName)• virtual bool isTitleListSupported ()• virtual bool isAtomListSupported ()• virtual bool isCoordinatesSupported ()• virtual bool isBondListSupported ()
Protected Member Functions
• virtual void Parse ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtCrdFileSource.h
5.136 RbtCSVFileSink Class Reference
Inheritance diagram for RbtCSVFileSink:
RbtCSVFileSink
RbtBaseMolecularFileSink
RbtBaseFileSink
Public Member Functions
• RBTDLL_EXPORT RbtCSVFileSink (const std::string &fileName, RbtModelPtr spModel, std::size_t nAtoms,std::size_t nDataFields)
• virtual void Render ()
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96 Class Documentation
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtCSVFileSink.h
5.137 RbtDihedral Class Reference
Classes
• class prms
Public Member Functions
• RbtDihedral (RbtAtom ∗pAtom1, RbtAtom ∗pAtom2, RbtAtom ∗pAtom3, RbtAtom ∗pAtom4, const prms&dihprms)
• double operator() () const• RbtAtom ∗ GetAtom1Ptr () const• RbtAtom ∗ GetAtom2Ptr () const• RbtAtom ∗ GetAtom3Ptr () const• RbtAtom ∗ GetAtom4Ptr () const• void AddTerm (const prms &dihprms)
The documentation for this class was generated from the following file:
• RbtDihedralSF.h
5.138 RbtDihedralIntraSF Class Reference
Inheritance diagram for RbtDihedralIntraSF:
RbtDihedralIntraSF
RbtBaseIntraSF RbtDihedralSF
RbtBaseSF RbtBaseSF
RbtBaseObject RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtDihedralIntraSF (const std::string &strName="DIHEDRAL")
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5.139 RbtDihedralSF Class Reference 97
Static Public Attributes
• static std::string _CT
Protected Member Functions
• virtual void SetupScore ()• virtual double RawScore () const• void ClearModel ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtDihedralIntraSF.h
5.139 RbtDihedralSF Class Reference
Inheritance diagram for RbtDihedralSF:
RbtDihedralSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
RbtDihedralIntraSF RbtDihedralTargetSF
Static Public Attributes
• static std::string _CT• static std::string _IMPL_H_CORR
Protected Member Functions
• RbtDihedralList CreateDihedralList (const RbtBondList &bondList)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtDihedralSF.h
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98 Class Documentation
5.140 RbtDihedralTargetSF Class Reference
Inheritance diagram for RbtDihedralTargetSF:
RbtDihedralTargetSF
RbtBaseInterSF RbtDihedralSF
RbtBaseSF RbtBaseSF
RbtBaseObject RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtDihedralTargetSF (const std::string &strName="DIHEDRAL")
Static Public Attributes
• static std::string _CT
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupScore ()• virtual double RawScore () const• void ClearReceptor ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtDihedralTargetSF.h
5.141 RbtDirectorySource Class Reference
#include <RbtDirectorySource.h>
Inheritance diagram for RbtDirectorySource:
RbtDirectorySource
RbtPMFDirSource
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5.142 RbtDirIsNotAccessible Class Reference 99
Public Member Functions
• RbtDirectorySource (const std::string &)
Static Public Attributes
• static std::string _CT
Protected Member Functions
• void CheckDirectory (std::string &)
Protected Attributes
• struct stat fStat• int fNum• struct dirent ∗∗ fNameList• std::ifstream inFile• std::string thePath
5.141.1 Detailed Description
RbtDirectorySource Reads all (or the given number) of files into a <vector> that are in a directory. To extend withother file formasts include other ReadFiles () methods
The documentation for this class was generated from the following file:
• RbtDirectorySource.h
5.142 RbtDirIsNotAccessible Class Reference
Inheritance diagram for RbtDirIsNotAccessible:
RbtDirIsNotAccessible
RbtFileError
RbtError
Public Member Functions
• RbtDirIsNotAccessible (const std::string &strFile, int nLine, const std::string &strMessage="")
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100 Class Documentation
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFileError.h
5.143 RbtDockingError Class Reference
Inheritance diagram for RbtDockingError:
RbtDockingError
RbtError
Public Member Functions
• RbtDockingError (const std::string &strFile, int nLine, const std::string &strMessage="")
Protected Member Functions
• RbtDockingError (const std::string &strName, const std::string &strFile, int nLine, const std::string &str←↩
Message="")
The documentation for this class was generated from the following file:
• RbtDockingError.h
5.144 RbtDockingSite Class Reference
Classes
• class isAtomInRange
Public Member Functions
• RBTDLL_EXPORT RbtDockingSite (const RbtCavityList &cavList, double border)• RBTDLL_EXPORT RbtDockingSite (std::istream &istr)• virtual void Print (std::ostream &s) const• void Read (std::istream &istr)• RBTDLL_EXPORT void Write (std::ostream &ostr)• RBTDLL_EXPORT RbtRealGridPtr GetGrid ()• double GetBorder () const• RbtCoord GetMinCoord () const• RbtCoord GetMaxCoord () const• RbtCavityList GetCavityList () const• int GetNumCavities () const• RBTDLL_EXPORT double GetVolume () const• void GetCoordList (RbtCoordList &retVal) const• RBTDLL_EXPORT RbtAtomList GetAtomList (const RbtAtomList &atomList, double minDist, double max←↩
Dist)• RBTDLL_EXPORT RbtAtomList GetAtomList (const RbtAtomList &atomList, double maxDist)• unsigned int GetNumAtoms (const RbtAtomList &atomList, double minDist, double maxDist)
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5.145 RbtElementData Class Reference 101
Static Public Attributes
• static std::string _CT
Friends
• RBTDLL_EXPORT friend std::ostream & operator<< (std::ostream &s, const RbtDockingSite &site)
The documentation for this class was generated from the following file:
• RbtDockingSite.h
5.145 RbtElementData Class Reference
Public Attributes
• int atomicNo• std::string element• int minVal• int maxVal• int commonVal• double mass• double vdwRadius
The documentation for this class was generated from the following file:
• RbtElementFileSource.h
5.146 RbtElementFileSource Class Reference
Inheritance diagram for RbtElementFileSource:
RbtElementFileSource
RbtBaseFileSource
Public Member Functions
• RbtElementFileSource (const std::string &fileName)• RBTDLL_EXPORT std::string GetTitle ()• std::string GetVersion ()• unsigned int GetNumElements ()• std::vector< std::string > GetElementNameList ()• std::vector< int > GetAtomicNumberList ()• RbtElementData GetElementData (const std::string &strElementName)• RbtElementData GetElementData (int nAtomicNumber)• bool isElementNamePresent (const std::string &strElementName)• bool isAtomicNumberPresent (int nAtomicNumber)• double GetHBondRadiusIncr ()• double GetImplicitRadiusIncr ()
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102 Class Documentation
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtElementFileSource.h
5.147 RbtEnvNotDefined Class Reference
Inheritance diagram for RbtEnvNotDefined:
RbtEnvNotDefined
RbtFileError
RbtError
Public Member Functions• RbtEnvNotDefined (const std::string &strFile, int nLine, const std::string &strMessage="")
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFileError.h
5.148 RbtError Class Reference
Inheritance diagram for RbtError:
RbtError
RbtAssert
RbtBadArgument
RbtBadReceptorFile
RbtDockingError
RbtFileError
RbtInvalidRequest
RbtLigandError
RbtModelError
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5.149 RbtEuler Class Reference 103
Public Member Functions
• RbtError (const std::string &strFile, int nLine, const std::string &strMessage="")• std::string File () const• int Line () const• std::string Message () const• std::string Name () const• bool isOK () const• void AddMessage (const std::string &strMessage)
Protected Member Functions
• RbtError (const std::string &strName, const std::string &strFile, int nLine, const std::string &strMessage="")
Friends
• std::ostream & operator<< (std::ostream &s, const RbtError &error)
The documentation for this class was generated from the following file:
• RbtError.h
5.149 RbtEuler Class Reference
Public Member Functions
• RbtEuler (double heading=0.0, double attitude=0.0, double bank=0.0)• RbtEuler (const RbtQuat &q)• bool isStandardised () const• void Standardise ()• double GetHeading () const• double GetAttitude () const• double GetBank () const• RBTDLL_EXPORT RbtQuat ToQuat () const• RBTDLL_EXPORT void FromQuat (const RbtQuat &q)• void Rotate (const RbtQuat &q)• void Rotate (const RbtVector &axis, double theta)
Friends
• std::ostream & operator<< (std::ostream &s, const RbtEuler &euler)
The documentation for this class was generated from the following file:
• RbtEuler.h
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104 Class Documentation
5.150 RbtFFTGrid Class Reference
Inheritance diagram for RbtFFTGrid:
RbtFFTGrid
RbtRealGrid
RbtBaseGrid
Public Member Functions
• RbtFFTGrid (const RbtCoord &gridMin, const RbtCoord &gridStep, unsigned int NX, unsigned int NY, un-signed int NZ, unsigned int NPad=0)
• RbtFFTGrid (std::istream &istr)
• RbtFFTGrid (const RbtFFTGrid &)
• RbtFFTGrid (const RbtRealGrid &)
• RbtFFTGrid (const RbtBaseGrid &)
• RbtFFTGrid & operator= (const RbtFFTGrid &)
• RbtFFTGrid & operator= (const RbtRealGrid &)
• RbtFFTGrid & operator= (const RbtBaseGrid &)
• virtual void Print (std::ostream &ostr) const
• virtual void Write (std::ostream &ostr) const
• virtual void Read (std::istream &istr)
• RbtFFTPeakMap FindPeaks (double threshold, unsigned int minVol=1)
• RbtFFTPeak FindMaxPeak () const
Static Public Attributes
• static std::string _CT
Protected Member Functions
• void OwnPrint (std::ostream &ostr) const
• void OwnWrite (std::ostream &ostr) const
• void OwnRead (std::istream &istr)
The documentation for this class was generated from the following file:
• RbtFFTGrid.h
Generated by Doxygen
5.151 RbtFFTPeak Class Reference 105
5.151 RbtFFTPeak Class Reference
Public Attributes
• unsigned int index• RbtCoord coord• double height• unsigned int volume• std::set< unsigned int > points
The documentation for this class was generated from the following file:
• RbtFFTGrid.h
5.152 RbtFileError Class Reference
Inheritance diagram for RbtFileError:
RbtFileError
RbtError
RbtDirIsNotAccessible
RbtEnvNotDefined
RbtFileMissingParameter
RbtFileParseError
RbtFileReadError
RbtFileWriteError
RbtNoFileInDir
RbtStringTooLong
Public Member Functions
• RbtFileError (const std::string &strFile, int nLine, const std::string &strMessage="")
Generated by Doxygen
106 Class Documentation
Protected Member Functions
• RbtFileError (const std::string &strName, const std::string &strFile, int nLine, const std::string &str←↩
Message="")
The documentation for this class was generated from the following file:
• RbtFileError.h
5.153 RbtFileMissingParameter Class Reference
Inheritance diagram for RbtFileMissingParameter:
RbtFileMissingParameter
RbtFileError
RbtError
Public Member Functions
• RbtFileMissingParameter (const std::string &strFile, int nLine, const std::string &strMessage="")
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFileError.h
5.154 RbtFileParseError Class Reference
Inheritance diagram for RbtFileParseError:
RbtFileParseError
RbtFileError
RbtError
Generated by Doxygen
5.155 RbtFileReadError Class Reference 107
Public Member Functions
• RbtFileParseError (const std::string &strFile, int nLine, const std::string &strMessage="")
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFileError.h
5.155 RbtFileReadError Class Reference
Inheritance diagram for RbtFileReadError:
RbtFileReadError
RbtFileError
RbtError
Public Member Functions
• RbtFileReadError (const std::string &strFile, int nLine, const std::string &strMessage="")
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFileError.h
5.156 RbtFileWriteError Class Reference
Inheritance diagram for RbtFileWriteError:
RbtFileWriteError
RbtFileError
RbtError
Generated by Doxygen
108 Class Documentation
Public Member Functions
• RbtFileWriteError (const std::string &strFile, int nLine, const std::string &strMessage="")
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFileError.h
5.157 RbtFilter Class Reference
Inheritance diagram for RbtFilter:
RbtFilter
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RBTDLL_EXPORT RbtFilter (std::string strfilter, bool filter=false)• virtual void Update (RbtSubject ∗theChangedSubject)• void SetupReceptor ()• void SetupLigand ()• void SetupScore ()• RBTDLL_EXPORT bool Write ()• RBTDLL_EXPORT bool Terminate ()• RbtModelPtr GetReceptor () const• RbtModelPtr GetLigand () const• void SetMaxNRuns (int n)
Static Public Attributes
• static std::string _CT
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFilter.h
Generated by Doxygen
5.158 RbtFilterExpression Class Reference 109
5.158 RbtFilterExpression Class Reference
Inheritance diagram for RbtFilterExpression:
RbtFilterExpression
FilterAddExp
FilterAndExp
FilterDivExp
FilterExpExp
FilterIfExp
FilterLogExp
FilterMulExp
FilterSubExp
FilterVbleExp
Public Member Functions
• virtual void Print ()=0• virtual void Accept (RbtFilterExpressionVisitor &)=0• virtual int GetNOps ()=0• virtual SmartPtr< RbtFilterExpression > GetOp (int)=0• RbtReturnType GetValue ()• void SetValue (RbtReturnType v)
Static Public Attributes
• static std::string _CT
Protected Attributes
• RbtReturnType value
The documentation for this class was generated from the following file:
• RbtFilterExpression.h
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110 Class Documentation
5.159 RbtFilterExpressionVisitor Class Reference
Inheritance diagram for RbtFilterExpressionVisitor:
RbtFilterExpressionVisitor
EvaluateVisitor PrettyPrintVisitor PrintVisitor
Public Member Functions
• virtual void VisitVbleExp (FilterVbleExp ∗)=0• virtual void VisitAddExp (FilterAddExp ∗)=0• virtual void VisitSubExp (FilterSubExp ∗)=0• virtual void VisitMulExp (FilterMulExp ∗)=0• virtual void VisitDivExp (FilterDivExp ∗)=0• virtual void VisitAndExp (FilterAndExp ∗)=0• virtual void VisitLogExp (FilterLogExp ∗)=0• virtual void VisitExpExp (FilterExpExp ∗)=0• virtual void VisitIfExp (FilterIfExp ∗)=0
The documentation for this class was generated from the following file:
• RbtFilterExpressionVisitor.h
5.160 RbtFlexAtomFactory Class Reference
Inheritance diagram for RbtFlexAtomFactory:
RbtFlexAtomFactory
RbtFlexDataVisitor
Public Member Functions
• RbtFlexAtomFactory (RbtModel ∗)• RbtFlexAtomFactory (RbtModelList)• void Visit (RbtModel ∗)• void Clear ()• virtual void VisitReceptorFlexData (RbtReceptorFlexData ∗)• virtual void VisitLigandFlexData (RbtLigandFlexData ∗)• virtual void VisitSolventFlexData (RbtSolventFlexData ∗)• RbtAtomRList GetFixedAtomList () const• RbtAtomRList GetTetheredAtomList () const• RbtAtomRList GetFreeAtomList () const
The documentation for this class was generated from the following file:
• RbtFlexAtomFactory.h
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5.161 RbtFlexData Class Reference 111
5.161 RbtFlexData Class Reference
Inheritance diagram for RbtFlexData:
RbtFlexData
RbtParamHandler
RbtLigandFlexData RbtReceptorFlexData
RbtSolventFlexData
Public Member Functions
• RbtModel ∗ GetModel () const• void SetModel (RbtModel ∗pModel)• RbtDockingSite ∗ GetDockingSite () const• virtual void Accept (RbtFlexDataVisitor &)=0
Protected Member Functions
• RbtFlexData (RbtDockingSite ∗pDockSite)
The documentation for this class was generated from the following file:
• RbtFlexData.h
5.162 RbtFlexDataVisitor Class Reference
Inheritance diagram for RbtFlexDataVisitor:
RbtFlexDataVisitor
RbtCavityGridSF::HeavyAtomFactory RbtChromFactory RbtFlexAtomFactory
Public Member Functions
• virtual void VisitReceptorFlexData (RbtReceptorFlexData ∗)=0• virtual void VisitLigandFlexData (RbtLigandFlexData ∗)=0• virtual void VisitSolventFlexData (RbtSolventFlexData ∗)=0
The documentation for this class was generated from the following file:
• RbtFlexDataVisitor.h
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112 Class Documentation
5.163 RbtGATransform Class Reference
Inheritance diagram for RbtGATransform:
RbtGATransform
RbtBaseBiMolTransform
RbtBaseTransform
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RBTDLL_EXPORT RbtGATransform (const std::string &strName="GAGENRW")
Static Public Attributes
• static std::string _CT• static std::string _NEW_FRACTION• static std::string _PCROSSOVER• static std::string _XOVERMUT• static std::string _CMUTATE• static std::string _STEP_SIZE• static std::string _EQUALITY_THRESHOLD• static std::string _NCYCLES• static std::string _NCONVERGENCE• static std::string _HISTORY_FREQ
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupTransform ()• virtual void Execute ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtGATransform.h
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5.164 RbtGenome Class Reference 113
5.164 RbtGenome Class Reference
Public Member Functions
• RbtGenome (RbtChromElement ∗pChr)• RbtGenome (const RbtGenome &)• RbtGenome & operator= (const RbtGenome &)• RbtGenome ∗ clone () const• RbtChromElement ∗ GetChrom () const• void SetScore (RbtBaseSF ∗pSF)• double GetScore () const• double SetRWFitness (double sigmaOffset, double partialSum)• void NormaliseRWFitness (double total)• double GetRWFitness () const• bool Equals (const RbtGenome &g, double threshold) const• void Print (std::ostream &) const
Static Public Attributes
• static std::string _CT
Friends
• bool operator== (const RbtGenome &g1, const RbtGenome &g2)• std::ostream & operator<< (std::ostream &s, const RbtGenome &g)
The documentation for this class was generated from the following file:
• RbtGenome.h
5.165 RbtHBAConstraint Class Reference
Inheritance diagram for RbtHBAConstraint:
RbtHBAConstraint
RbtConstraint
Public Member Functions
• RbtHBAConstraint (RbtCoord c, double t)• void AddAtomList (RbtModelPtr, bool bCheck=true)
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114 Class Documentation
Static Public Attributes
• static unsigned int counter
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtConstraint.h
5.166 RbtHBDConstraint Class Reference
Inheritance diagram for RbtHBDConstraint:
RbtHBDConstraint
RbtConstraint
Public Member Functions
• RbtHBDConstraint (RbtCoord c, double t)• void AddAtomList (RbtModelPtr, bool bCheck=true)
Static Public Attributes
• static unsigned int counter
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtConstraint.h
5.167 RbtHeavyConstraint Class Reference
Inheritance diagram for RbtHeavyConstraint:
RbtHeavyConstraint
RbtConstraint
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5.168 RbtHHSType Class Reference 115
Public Member Functions
• RbtHeavyConstraint (RbtCoord c, double t)• void AddAtomList (RbtModelPtr, bool bCheck=true)
Static Public Attributes
• static unsigned int counter
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtConstraint.h
5.168 RbtHHSType Class Reference
Public Types
• enum eType {UNDEFINED = 0, C_sp3, CH_sp3, CH2_sp3,CH3_sp3, C_sp2, CH_sp2, CH2_sp2,C_sp2p, C_ar, CH_ar, C_sp,C_sp3_P, CH_sp3_P, CH2_sp3_P, CH3_sp3_P,C_sp2_P, CH_sp2_P, CH2_sp2_P, C_ar_P,CH_ar_P, H, HO, HN,HNp, HS, O_sp3, OH_sp3,OW, O_tri, OH_tri, O_sp2,ON, Om, N_sp3, NH_sp3,NH2_sp3, N_sp3p, N_tri, NH_tri,NH2_tri, N_sp2, N_sp2p, N_ar,N_sp, S_sp3, S_sp2, P,F, Cl, Br, I,Metal, MAXTYPES }
Public Member Functions
• eType operator() (RbtAtom ∗anAtom) const• std::string Type2Str (eType) const• eType Str2Type (const std::string &) const
The documentation for this class was generated from the following file:
• RbtSATypes.h
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116 Class Documentation
5.169 RbtHydroAliphaticConstraint Class Reference
Inheritance diagram for RbtHydroAliphaticConstraint:
RbtHydroAliphaticConstraint
RbtConstraint
Public Member Functions
• RbtHydroAliphaticConstraint (RbtCoord c, double t)• void AddAtomList (RbtModelPtr, bool bCheck=true)
Static Public Attributes
• static unsigned int counter
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtConstraint.h
5.170 RbtHydroAromaticConstraint Class Reference
Inheritance diagram for RbtHydroAromaticConstraint:
RbtHydroAromaticConstraint
RbtConstraint
Public Member Functions
• RbtHydroAromaticConstraint (RbtCoord c, double t)• void AddAtomList (RbtModelPtr, bool bCheck=true)
Static Public Attributes
• static unsigned int counter
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5.171 RbtHydroConstraint Class Reference 117
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtConstraint.h
5.171 RbtHydroConstraint Class Reference
Inheritance diagram for RbtHydroConstraint:
RbtHydroConstraint
RbtConstraint
Public Member Functions
• RbtHydroConstraint (RbtCoord c, double t)
• void AddAtomList (RbtModelPtr, bool bCheck=true)
Static Public Attributes
• static unsigned int counter
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtConstraint.h
5.172 RbtInteractionCenter Class Reference
Public Types
• enum eLP { NONE, PLANE, LONEPAIR }
Generated by Doxygen
118 Class Documentation
Public Member Functions
• RbtInteractionCenter (RbtAtom ∗pAtom1=nullptr, RbtAtom ∗pAtom2=nullptr, RbtAtom ∗pAtom3=nullptr,eLP LP=NONE)
• RbtAtom ∗ GetAtom1Ptr () const• RbtAtom ∗ GetAtom2Ptr () const• RbtAtom ∗ GetAtom3Ptr () const• eLP LP () const• RbtAtomRList GetAtomList () const• bool isSelected () const
The documentation for this class was generated from the following file:
• RbtInteractionGrid.h
5.173 RbtInteractionGrid Class Reference
Inheritance diagram for RbtInteractionGrid:
RbtInteractionGrid
RbtBaseGrid
Public Member Functions
• RbtInteractionGrid (const RbtCoord &gridMin, const RbtCoord &gridStep, unsigned int NX, unsigned intNY, unsigned int NZ, unsigned int NPad=0)
• RbtInteractionGrid (std::istream &istr)• RbtInteractionGrid (const RbtInteractionGrid &)• RbtInteractionGrid (const RbtBaseGrid &)• RbtInteractionGrid & operator= (const RbtInteractionGrid &)• RbtInteractionGrid & operator= (const RbtBaseGrid &)• virtual void Print (std::ostream &ostr) const• virtual void Write (std::ostream &ostr) const• virtual void Read (std::istream &istr)• const RbtInteractionCenterList & GetInteractionList (unsigned int iXYZ) const• const RbtInteractionCenterList & GetInteractionList (const RbtCoord &c) const• void SetInteractionLists (RbtInteractionCenter ∗pIntn, double radius)• void ClearInteractionLists ()• void UniqueInteractionLists ()
Static Public Attributes
• static std::string _CT
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5.174 RbtInteractionGridTemplate< T > Class Template Reference 119
Protected Member Functions
• void OwnPrint (std::ostream &ostr) const• void OwnWrite (std::ostream &ostr) const• void OwnRead (std::istream &istr)
The documentation for this class was generated from the following file:
• RbtInteractionGrid.h
5.174 RbtInteractionGridTemplate< T > Class Template Reference
Inheritance diagram for RbtInteractionGridTemplate< T >:
RbtInteractionGridTemplate< T >
RbtBaseGrid
Public Member Functions
• RbtInteractionGridTemplate (const RbtCoord &gridMin, const RbtCoord &gridStep, unsigned int NX, un-signed int NY, unsigned int NZ, unsigned int NPad=0)
• RbtInteractionGridTemplate (std::istream &istr)• RbtInteractionGridTemplate (const RbtInteractionGridTemplate &aGrid)• RbtInteractionGridTemplate (const RbtBaseGrid &)• RbtInteractionGridTemplate & operator= (const RbtInteractionGridTemplate &aGrid)• RbtInteractionGridTemplate & operator= (const RbtBaseGrid &aGrid)• virtual void Print (std::ostream &ostr) const• virtual void Write (std::ostream &ostr) const• virtual void Read (std::istream &istr)• const RbtInteractionNodeList< T > & GetInteractionList (unsigned int iXYZ) const• const RbtInteractionNodeList< T > & GetInteractionList (const RbtCoord &c) const• void SetInteractionLists (T ∗pIntn, double radius)• void ClearInteractionLists ()
Static Public Attributes
• static std::string _CT
Protected Member Functions
• void OwnPrint (std::ostream &ostr) const• void OwnWrite (std::ostream &ostr) const• void OwnRead (std::istream &istr)
The documentation for this class was generated from the following file:
• RbtInteractionTemplate.h
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120 Class Documentation
5.175 RbtInteractionGridTemplatePtr< T > Class Template Reference
Inheritance diagram for RbtInteractionGridTemplatePtr< T >:
RbtInteractionGridTemplatePtr< T >
SmartPtr< RbtInteractionGridTemplate< T > >
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtInteractionTemplate.h
5.176 RbtInteractionNode< T > Class Template Reference
Public Member Functions
• RbtInteractionNode (T aProperty)• T GetProperty () const• void SetProperty (T aProperty)
The documentation for this class was generated from the following file:
• RbtInteractionTemplate.h
5.177 RbtInteractionNodeList< T > Class Template Reference
Inheritance diagram for RbtInteractionNodeList< T >:
RbtInteractionNodeList< T >
std::vector< RbtInteractionNode< T > * >
The documentation for this class was generated from the following file:
• RbtInteractionTemplate.h
Generated by Doxygen
5.178 RbtInteractionNodeListMap< T > Class Template Reference 121
5.178 RbtInteractionNodeListMap< T > Class Template Reference
Inheritance diagram for RbtInteractionNodeListMap< T >:
RbtInteractionNodeListMap< T >
std::vector< RbtInteractionNodeList< T > >
The documentation for this class was generated from the following file:
• RbtInteractionTemplate.h
5.179 RbtInteractionNodeListMapConstIter< T > Class TemplateReference
Inheritance diagram for RbtInteractionNodeListMapConstIter< T >:
RbtInteractionNodeListMapConstIter< T >
std::vector< T >::const_iterator
The documentation for this class was generated from the following file:
• RbtInteractionTemplate.h
5.180 RbtInteractionNodeListMapIter< T > Class Template Reference
Inheritance diagram for RbtInteractionNodeListMapIter< T >:
RbtInteractionNodeListMapIter< T >
RbtInteractionNodeListMap< T >::iterator
The documentation for this class was generated from the following file:
• RbtInteractionTemplate.h
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122 Class Documentation
5.181 RbtInvalidRequest Class Reference
Inheritance diagram for RbtInvalidRequest:
RbtInvalidRequest
RbtError
Public Member Functions
• RbtInvalidRequest (const std::string &strFile, int nLine, const std::string &strMessage="")
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtError.h
5.182 RbtLigandError Class Reference
Inheritance diagram for RbtLigandError:
RbtLigandError
RbtError
Public Member Functions
• RbtLigandError (const std::string &strFile, int nLine, const std::string &strMessage="")
Protected Member Functions
• RbtLigandError (const std::string &strName, const std::string &strFile, int nLine, const std::string &str←↩
Message="")
The documentation for this class was generated from the following file:
• RbtLigandError.h
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5.183 RbtLigandFlexData Class Reference 123
5.183 RbtLigandFlexData Class Reference
Inheritance diagram for RbtLigandFlexData:
RbtLigandFlexData
RbtFlexData
RbtParamHandler
RbtSolventFlexData
Public Member Functions
• RBTDLL_EXPORT RbtLigandFlexData (RbtDockingSite ∗pDockSite)
• virtual void Accept (RbtFlexDataVisitor &v)
Static Public Member Functions
• static RBTDLL_EXPORT const std::string & GetTransMode ()
• static RBTDLL_EXPORT const std::string & GetRotMode ()
Static Public Attributes
• static const std::string & _TRANS_STEP
• static const std::string & _ROT_STEP
• static const std::string & _DIHEDRAL_STEP
• static const std::string & _TRANS_MODE
• static const std::string & _ROT_MODE
• static const std::string & _DIHEDRAL_MODE
• static const std::string & _MAX_TRANS
• static const std::string & _MAX_ROT
• static const std::string & _MAX_DIHEDRAL
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtLigandFlexData.h
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124 Class Documentation
5.184 RbtLigandSiteMapper Class Reference
Inheritance diagram for RbtLigandSiteMapper:
RbtLigandSiteMapper
RbtSiteMapper
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtLigandSiteMapper (const std::string &strName="LIGAND_MAPPER")• virtual RbtCavityList operator() ()
Static Public Attributes
• static std::string _CT• static std::string _REF_MOL• static std::string _VOL_INCR• static std::string _SMALL_SPHERE• static std::string _GRIDSTEP• static std::string _RADIUS• static std::string _MIN_VOLUME• static std::string _MAX_CAVITIES
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtLigandSiteMapper.h
5.185 RbtMCStats Class Reference
Public Member Functions
• void Init (double score)• void InitBlock (double score)• void Accumulate (double score, bool bAccepted)• double Mean () const• double Variance () const• double AccRate () const
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5.186 RbtMdlFileSink Class Reference 125
Public Attributes
• double _total
• double _total2
• double _blockInitial
• double _blockFinal
• double _blockMin
• double _blockMax
• double _initial
• double _final
• double _min
• double _max
• int _steps
• int _accepted
The documentation for this class was generated from the following file:
• RbtSimAnnTransform.h
5.186 RbtMdlFileSink Class Reference
Inheritance diagram for RbtMdlFileSink:
RbtMdlFileSink
RbtBaseMolecularFileSink
RbtBaseFileSink
Public Member Functions
• RBTDLL_EXPORT RbtMdlFileSink (const std::string &fileName, RbtModelPtr spModel)
• virtual void Render ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtMdlFileSink.h
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126 Class Documentation
5.187 RbtMdlFileSource Class Reference
Inheritance diagram for RbtMdlFileSource:
RbtMdlFileSource
RbtBaseMolecularFileSource
RbtBaseFileSource RbtBaseMolecularDataSource
Public Member Functions
• RBTDLL_EXPORT RbtMdlFileSource (const std::string &fileName, bool bPosIonisable=true, bool bNeg←↩
Ionisable=true, bool bImplHydrogens=true)• virtual bool isTitleListSupported ()• virtual bool isAtomListSupported ()• virtual bool isCoordinatesSupported ()• virtual bool isBondListSupported ()• virtual bool isDataSupported ()
Protected Member Functions
• virtual void Parse ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtMdlFileSource.h
5.188 RbtModel Class Reference
Public Member Functions
• RBTDLL_EXPORT RbtModel (RbtBaseMolecularFileSource ∗pMolSource)• RBTDLL_EXPORT RbtModel (RbtAtomList &atomList, RbtBondList &bondList)• std::string GetName () const• int GetNumTitles () const• std::vector< std::string > GetTitleList () const• int GetNumAtoms () const• RbtAtomList GetAtomList () const• int GetNumBonds () const• RbtBondList GetBondList () const• int GetNumSegments () const• RbtSegmentMap GetSegmentMap () const
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5.188 RbtModel Class Reference 127
• int GetNumRings () const• RbtAtomListList GetRingAtomLists () const• int GetNumData () const• std::vector< std::string > GetDataFieldList () const• RbtStringVariantMap GetDataMap () const• bool isDataFieldPresent (const std::string &strDataField) const• RBTDLL_EXPORT RbtVariant GetDataValue (const std::string &strDataField) const• RBTDLL_EXPORT void SetDataValue (const std::string &strDataField, const RbtVariant &dataValue)• void ClearDataField (const std::string &strDataField)• RBTDLL_EXPORT void ClearAllDataFields (const std::string &strDataFieldPrefix)• void ClearAllDataFields ()• RbtPseudoAtomPtr AddPseudoAtom (const RbtAtomList &atomList)• void ClearPseudoAtoms ()• void UpdatePseudoAtoms ()• unsigned int GetNumPseudoAtoms () const• RbtPseudoAtomList GetPseudoAtomList () const• unsigned int GetNumTetheredAtoms () const• RbtAtomList GetTetheredAtomList () const• double GetOccupancy () const• bool GetEnabled () const• RBTDLL_EXPORT void SetOccupancy (double occupancy, double threshold=0.5)• void UpdateCoords (RbtBaseMolecularFileSource ∗pMolSource)• void Translate (const RbtVector &vector)• void Rotate (const RbtVector &axis, double thetaDeg)• void Rotate (const RbtVector &axis, double thetaDeg, const RbtCoord ¢er)• RBTDLL_EXPORT void RotateBond (RbtBondPtr spBond, double thetaDeg)• void RotateBond (RbtBondPtr spBond, double thetaDeg, RbtAtomPtr spFixedAtom)• RBTDLL_EXPORT void RotateBond (RbtBondPtr spBond, double thetaDeg, bool bSwap)• void SaveCoords (const std::string &coordName="")• RBTDLL_EXPORT void RevertCoords (const std::string &coordName="")• std::map< std::string, int > GetSavedCoordNames () const• int GetNumSavedCoords () const• int GetCurrentCoords () const• RBTDLL_EXPORT void RevertCoords (int)• RbtCoord GetCenterOfMass () const• void SetCenterOfMass (const RbtCoord &c)• RBTDLL_EXPORT double GetTotalAtomicMass () const• RbtPrincipalAxes GetPrincipalAxes () const• void AlignPrincipalAxes (const RbtPrincipalAxes &alignAxes=RbtPrincipalAxes(), bool bAlignCOM=true)• RBTDLL_EXPORT void SetFlexData (RbtFlexData ∗pFlexData)• RBTDLL_EXPORT RbtFlexData ∗ GetFlexData () const• RBTDLL_EXPORT RbtChromElement ∗ GetChrom () const• bool isFlexible () const• const RbtAtomRList & GetFlexIntns (RbtAtom ∗pAtom) const• RbtBondList GetFlexBonds () const• void SelectFlexAtoms ()• void SelectFlexAtoms (RbtAtom ∗pAtom)• void SetAtomSelectionFlags (bool bSelected=true)• unsigned int GetNumSelectedAtoms ()• RbtAtomList GetSelectedAtomList ()• void SetAtomCyclicFlags (bool bCyclic=true)• unsigned int GetNumCyclicAtoms ()• RbtAtomList GetCyclicAtomList ()• void SetAtomUser1Flags (bool bUser1=true)• void SetAtomUser1Values (double dUser1=0.0)
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128 Class Documentation
• void SetAtomUser2Values (double dUser2=0.0)• unsigned int GetNumHBondAcceptorAtoms ()• RbtAtomList GetHBondAcceptorAtomList ()• unsigned int GetNumHBondDonorAtoms ()• RbtAtomList GetHBondDonorAtomList ()• unsigned int GetNumChargedAtoms ()• RbtAtomList GetChargedAtomList ()• unsigned int GetNumPlanarAtoms ()• RbtAtomList GetPlanarAtomList ()• unsigned int GetNumAtomsWithAtomicNo_eq (int nAtomicNo)• RbtAtomList GetAtomListWithAtomicNo_eq (int nAtomicNo)• unsigned int GetNumAtomsWithFFType_eq (std::string strFFType)• RbtAtomList GetAtomListWithFFType_eq (std::string strFFType)• template<class Predicate >
unsigned int GetNumBonds (const Predicate &pred)• template<class Predicate >
RbtBondList GetBondList (const Predicate &pred)• void SetBondSelectionFlags (bool bSelected=true)• unsigned int GetNumSelectedBonds ()• RbtBondList GetSelectedBondList ()• void SetBondCyclicFlags (bool bCyclic=true)• unsigned int GetNumCyclicBonds ()• RbtBondList GetCyclicBondList ()• void GetMinMaxCoords (RbtCoord &minCoord, RbtCoord &maxCoord, bool bInit=true)• std::map< std::string, int > GetAtomTypeMap ()• std::map< std::string, int > GetBondTypeMap ()
Friends
• class RbtModelMutator
The documentation for this class was generated from the following file:
• RbtModel.h
5.189 RbtModelError Class Reference
Inheritance diagram for RbtModelError:
RbtModelError
RbtError
Public Member Functions
• RbtModelError (const std::string &strFile, int nLine, const std::string &strMessage="")
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5.190 RbtModelMutator Class Reference 129
Protected Member Functions
• RbtModelError (const std::string &strName, const std::string &strFile, int nLine, const std::string &str←↩
Message="")
The documentation for this class was generated from the following file:
• RbtModelError.h
5.190 RbtModelMutator Class Reference
Public Member Functions
• RbtModelMutator (RbtModel ∗pModel, const RbtBondList &rotBonds, const RbtAtomList &tetheredAtoms)
• const RbtAtomRListList & GetFlexIntns () const
• const RbtAtomRListList & GetFlexAtoms () const
• RbtBondList GetFlexBonds () const
The documentation for this class was generated from the following file:
• RbtModelMutator.h
5.191 RbtMOEGrid Class Reference
Public Member Functions
• RbtMOEGrid (RbtMOEGridShape &, RbtMOEGridData &, std::string)
• void SetShape (RbtMOEGridShape &a_shape)
• void SetData (RbtMOEGridData &a_data)
• void SetOutputFileName (std::string &a_filename)
• RBTDLL_EXPORT void CalculateCommonExtents (std::vector< std::string > strPrmFiles)
• void GetDockingSiteExtents (std::string &a_strPrmFile)
• RbtCoord GetMinExtents ()
• RbtCoord GetMaxExtents ()
• RBTDLL_EXPORT long WriteGrid (std::ios_base::openmode mode)
• long ReadGrid ()
The documentation for this class was generated from the following file:
• RbtMOEGrid.h
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130 Class Documentation
5.192 RbtMOEGridPoint Class Reference
Public Member Functions
• RbtMOEGridPoint (std::vector< double >, double)• RbtMOEGridPoint (RbtCoord &, double)• double GetValue ()• const std::vector< double > & GetCoords ()• void SetCoords (double a_val)• void SetValue (double a_val)
The documentation for this class was generated from the following file:
• RbtMOEGrid.h
5.193 RbtMOEGridShape Class Reference
Public Member Functions
• RBTDLL_EXPORT RbtMOEGridShape (std::vector< double >, std::vector< double >, double)• const std::vector< double > & GetOrigin ()• const std::vector< double > & GetExtents ()• const std::vector< int > & GetIExtents ()• double GetStepSize ()• long GetDataSize ()
The documentation for this class was generated from the following file:
• RbtMOEGrid.h
5.194 RbtMOL2FileSource Class Reference
Inheritance diagram for RbtMOL2FileSource:
RbtMOL2FileSource
RbtBaseMolecularFileSource
RbtBaseFileSource RbtBaseMolecularDataSource
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5.195 RbtMOL2Substructure Class Reference 131
Public Member Functions
• RbtMOL2FileSource (const std::string &fileName, bool bImplHydrogens=true)• bool isTitleListSupported ()• bool isAtomListSupported ()• bool isCoordinatesSupported ()• bool isBondListSupported ()• bool isDataSupported ()
Static Public Attributes
• static std::string _CT• static std::string _TRIPOS_DELIM• static unsigned int _TRIPOS_DELIM_SIZE• static std::string _IDS_MOL2_RECDELIM
Protected Member Functions
• virtual void Parse ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtMOL2FileSource.h
5.195 RbtMOL2Substructure Class Reference
Public Member Functions
• RbtMOL2Substructure (const std::string &name, int rr, const std::string &cc, const std::string &ss)• std::string GetName () const• int GetRoot () const• std::string GetChain () const• std::string GetType () const
The documentation for this class was generated from the following file:
• RbtMOL2FileSource.h
5.196 RbtNegChargeConstraint Class Reference
Inheritance diagram for RbtNegChargeConstraint:
RbtNegChargeConstraint
RbtConstraint
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132 Class Documentation
Public Member Functions
• RbtNegChargeConstraint (RbtCoord c, double t)
• void AddAtomList (RbtModelPtr, bool bCheck=true)
Static Public Attributes
• static unsigned int counter
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtConstraint.h
5.197 RbtNmrRestraintFileSource Class Reference
Inheritance diagram for RbtNmrRestraintFileSource:
RbtNmrRestraintFileSource
RbtBaseFileSource
Public Member Functions
• RbtNmrRestraintFileSource (const std::string &fileName)
• unsigned int GetNumNoeRestraints ()
• RbtNoeRestraintNamesList GetNoeRestraintList ()
• unsigned int GetNumStdRestraints ()
• RbtStdRestraintNamesList GetStdRestraintList ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtNmrRestraintFileSource.h
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5.198 RbtNmrSF Class Reference 133
5.198 RbtNmrSF Class Reference
Inheritance diagram for RbtNmrSF:
RbtNmrSF
RbtBaseInterSF RbtBaseIdxSF
RbtBaseSF RbtBaseSF
RbtBaseObject RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtNmrSF (const std::string &strName="NMR")
Static Public Attributes
• static std::string _CT• static std::string _FILENAME• static std::string _QUADRATIC
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupScore ()• virtual double RawScore () const• void ParameterUpdated (const std::string &strName)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtNmrSF.h
5.199 RbtNoeEndAtoms Class Reference
Public Member Functions
• RbtNoeEndAtoms (const RbtNoeEndNames &n, const RbtAtomList &atomList)• bool isOK () const
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134 Class Documentation
Public Attributes
• RbtAtomList atoms• Rbt::eNoeType type
The documentation for this class was generated from the following file:
• RbtNoeRestraint.h
5.200 RbtNoeEndNames Class Reference
Public Member Functions
• bool isOK () const
Public Attributes
• std::vector< std::string > names• Rbt::eNoeType type
The documentation for this class was generated from the following file:
• RbtNoeRestraint.h
5.201 RbtNoeRestraintAtoms Class Reference
Public Member Functions
• RbtNoeRestraintAtoms (const RbtNoeRestraintNames &n, const RbtAtomList &atomList)• bool isOK () const• bool isSimple () const
Public Attributes
• RbtNoeEndAtoms from• RbtNoeEndAtoms to• double maxDist
The documentation for this class was generated from the following file:
• RbtNoeRestraint.h
Generated by Doxygen
5.202 RbtNoeRestraintNames Class Reference 135
5.202 RbtNoeRestraintNames Class Reference
Public Member Functions
• bool isOK () const
Public Attributes
• RbtNoeEndNames from• RbtNoeEndNames to• double maxDist
The documentation for this class was generated from the following file:
• RbtNoeRestraint.h
5.203 RbtNoFileInDir Class Reference
Inheritance diagram for RbtNoFileInDir:
RbtNoFileInDir
RbtFileError
RbtError
Public Member Functions
• RbtNoFileInDir (const std::string &strFile, int nLine, const std::string &strMessage="")
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFileError.h
5.204 RbtNonBondedGrid Class Reference
Inheritance diagram for RbtNonBondedGrid:
RbtNonBondedGrid
RbtBaseGrid
Generated by Doxygen
136 Class Documentation
Public Member Functions
• RbtNonBondedGrid (const RbtCoord &gridMin, const RbtCoord &gridStep, unsigned int NX, unsigned intNY, unsigned int NZ, unsigned int NPad=0)
• RbtNonBondedGrid (std::istream &istr)
• RbtNonBondedGrid (const RbtNonBondedGrid &)
• RbtNonBondedGrid (const RbtBaseGrid &)
• RbtNonBondedGrid & operator= (const RbtNonBondedGrid &)
• RbtNonBondedGrid & operator= (const RbtBaseGrid &)
• virtual void Print (std::ostream &ostr) const
• virtual void Write (std::ostream &ostr) const
• virtual void Read (std::istream &istr)
• const RbtAtomRList & GetAtomList (unsigned int iXYZ) const
• const RbtAtomRList & GetAtomList (const RbtCoord &c) const
• void SetAtomLists (RbtAtom ∗pAtom, double radius)
• void ClearAtomLists ()
• void UniqueAtomLists ()
Static Public Attributes
• static std::string _CT
Protected Member Functions
• void OwnPrint (std::ostream &ostr) const
• void OwnWrite (std::ostream &ostr) const
• void OwnRead (std::istream &istr)
The documentation for this class was generated from the following file:
• RbtNonBondedGrid.h
5.205 RbtNonBondedHHSGrid Class Reference
Inheritance diagram for RbtNonBondedHHSGrid:
RbtNonBondedHHSGrid
RbtBaseGrid
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5.206 RbtNullTransform Class Reference 137
Public Member Functions
• RbtNonBondedHHSGrid (const RbtCoord &gridMin, const RbtCoord &gridStep, unsigned int NX, unsignedint NY, unsigned int NZ, unsigned int NPad=0)
• RbtNonBondedHHSGrid (std::istream &istr)• RbtNonBondedHHSGrid (const RbtNonBondedHHSGrid &)• RbtNonBondedHHSGrid (const RbtBaseGrid &)• RbtNonBondedHHSGrid & operator= (const RbtNonBondedHHSGrid &)• RbtNonBondedHHSGrid & operator= (const RbtBaseGrid &)• virtual void Print (std::ostream &ostr) const• virtual void Write (std::ostream &ostr) const• virtual void Read (std::istream &istr)• const HHS_SolvationRList & GetHHSList (unsigned int iXYZ) const• const HHS_SolvationRList & GetHHSList (const RbtCoord &c) const• void SetHHSLists (HHS_Solvation ∗pHHS, double radius)• void ClearHHSLists (void)
Static Public Attributes
• static std::string _CT
Protected Member Functions
• void OwnPrint (std::ostream &ostr) const• void OwnWrite (std::ostream &ostr) const• void OwnRead (std::istream &istr)
The documentation for this class was generated from the following file:
• RbtNonBondedHHSGrid.h
5.206 RbtNullTransform Class Reference
Inheritance diagram for RbtNullTransform:
RbtNullTransform
RbtBaseTransform
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtNullTransform (const std::string &strName="NULL")• virtual void Update (RbtSubject ∗theChangedSubject)
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138 Class Documentation
Static Public Attributes
• static std::string _CT
Protected Member Functions
• virtual void Execute ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtNullTransform.h
5.207 RbtObserver Class Reference
Inheritance diagram for RbtObserver:
RbtObserver
RbtBaseObject
RbtBaseSF RbtBaseTransform RbtFilter RbtSiteMapper
RbtBaseIdxSF
RbtBaseInterSF
RbtBaseIntraSF
RbtDihedralSF
RbtPolarSF
RbtSFAgg
RbtVdwSF
RbtBaseBiMolTransform
RbtBaseUniMolTransform
RbtNullTransform
RbtTransformAgg
RbtLigandSiteMapper
RbtSphereSiteMapper
Public Member Functions
• virtual void Update (RbtSubject ∗theChangedSubject)=0
• virtual void Deleted (RbtSubject ∗theDeletedSubject)=0
The documentation for this class was generated from the following file:
• RbtObserver.h
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5.208 RbtParameterFileSource Class Reference 139
5.208 RbtParameterFileSource Class Reference
Inheritance diagram for RbtParameterFileSource:
RbtParameterFileSource
RbtBaseFileSource
Public Member Functions
• RbtParameterFileSource (const char ∗fileName)• RBTDLL_EXPORT RbtParameterFileSource (const std::string &fileName)• RBTDLL_EXPORT std::string GetTitle ()• std::string GetVersion ()• unsigned int GetNumParameters ()• RBTDLL_EXPORT std::vector< std::string > GetParameterList ()• double GetParameterValue (const std::string &strParamName)• RBTDLL_EXPORT std::string GetParameterValueAsString (const std::string &strParamName)• bool isParameterPresent (const std::string &strParamName)• int GetNumSections ()• std::vector< std::string > GetSectionList ()• std::string GetSection () const• RBTDLL_EXPORT void SetSection (const std::string &strSection="")
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtParameterFileSource.h
5.209 RbtParamHandler Class Reference
Inheritance diagram for RbtParamHandler:
RbtParamHandler
RbtBaseObject RbtFlexData RbtWorkSpace
RbtBaseSF RbtBaseTransform RbtFilter RbtSiteMapper RbtLigandFlexData RbtReceptorFlexData RbtBiMolWorkSpace
RbtBaseIdxSF
RbtBaseInterSF
RbtBaseIntraSF
RbtDihedralSF
RbtPolarSF
RbtSFAgg
RbtVdwSF
RbtBaseBiMolTransform
RbtBaseUniMolTransform
RbtNullTransform
RbtTransformAgg
RbtLigandSiteMapper
RbtSphereSiteMapper
RbtSolventFlexData
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140 Class Documentation
Public Member Functions
• unsigned int GetNumParameters () const• RbtVariant GetParameter (const std::string &strName) const• bool isParameterValid (const std::string &strName) const• std::vector< std::string > GetParameterNames () const• RbtStringVariantMap GetParameters () const• RBTDLL_EXPORT void SetParameter (const std::string &strName, const RbtVariant &vValue)• virtual void Print (std::ostream &s) const
Protected Member Functions
• void AddParameter (const std::string &strName, const RbtVariant &vValue)• void DeleteParameter (const std::string &strName)• void ClearParameters ()• virtual void ParameterUpdated (const std::string &strName)
The documentation for this class was generated from the following file:
• RbtParamHandler.h
5.210 RbtParser Class Reference
Public Member Functions
• RbtParser (const RbtParser &)• RbtFilterExpressionPtr Parse (RbtTokenIterPtr, RbtContextPtr)
Static Public Attributes
• static std::string _CT
The documentation for this class was generated from the following file:
• RbtParser.h
5.211 RbtPdbFileSource Class Reference
Inheritance diagram for RbtPdbFileSource:
RbtPdbFileSource
RbtBaseMolecularFileSource
RbtBaseFileSource RbtBaseMolecularDataSource
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5.212 RbtPharmaSF Class Reference 141
Public Member Functions
• RbtPdbFileSource (const char ∗fileName)• RbtPdbFileSource (const std::string fileName)• virtual bool isTitleListSupported ()• virtual bool isAtomListSupported ()• virtual bool isCoordinatesSupported ()• virtual bool isBondListSupported ()
Protected Member Functions
• virtual void Parse ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtPdbFileSource.h
5.212 RbtPharmaSF Class Reference
Inheritance diagram for RbtPharmaSF:
RbtPharmaSF
RbtBaseInterSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtPharmaSF (const std::string &strName="PHARMA")• virtual void ScoreMap (RbtStringVariantMap &scoreMap) const
Static Public Attributes
• static std::string _CT• static std::string _CONSTRAINTS_FILE• static std::string _OPTIONAL_FILE• static std::string _NOPT• static std::string _WRITE_ERRORS
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142 Class Documentation
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupScore ()• virtual double RawScore () const• void ParameterUpdated (const std::string &strName)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtPharmaSF.h
5.213 RbtPlane Class Reference
Public Member Functions
• RbtPlane (const RbtVector &v, double d)• RbtPlane (const RbtCoord &c0, const RbtCoord &c1, const RbtCoord &c2)• double D () const• RbtVector VNorm () const• void Normalise ()
Friends
• std::ostream & operator<< (std::ostream &s, const RbtPlane &plane)
The documentation for this class was generated from the following file:
• RbtPlane.h
5.214 RbtPMFDirSource Class Reference
Inheritance diagram for RbtPMFDirSource:
RbtPMFDirSource
RbtDirectorySource
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5.215 RbtPMFGridSF Class Reference 143
Public Member Functions
• RbtPMFDirSource (const std::string &)• virtual void ReadFiles (std::vector< std::vector< RbtPMFValue >> ∗aVect, std::vector< std::string > ∗a←↩
NameVect, std::vector< RbtPMFValue > ∗aSlopeVect)• virtual void ParseLines (std::vector< std::string > anStrVect, std::vector< RbtPMFValue > ∗aValueVect)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtPMFDirSource.h
5.215 RbtPMFGridSF Class Reference
Inheritance diagram for RbtPMFGridSF:
RbtPMFGridSF
RbtBaseInterSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtPMFGridSF (const std::string &strName="PMFGRID")
Static Public Attributes
• static std::string _CT• static std::string _GRID• static std::string _SMOOTHED
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupScore ()• virtual double RawScore () const• unsigned int GetCorrectedType (RbtPMFType aType) const
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144 Class Documentation
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtPMFGridSF.h
5.216 RbtPMFIdxSF Class Reference
#include <RbtPMFIdxSF.h>
Inheritance diagram for RbtPMFIdxSF:
RbtPMFIdxSF
RbtBaseInterSF RbtBaseIdxSF RbtAnnotationHandler
RbtBaseSF RbtBaseSF
RbtBaseObject RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtPMFIdxSF (const std::string &strName="PMF")• virtual ∼RbtPMFIdxSF ()• virtual void Update (RbtSubject ∗theChangedSubject)
Static Public Attributes
• static std::string _CT• static std::string _PMFDIR• static std::string _CC_CUTOFF• static std::string _SLOPE
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupScore ()• virtual double RawScore (void) const• double GetLinearCloseRangeValue (double aDist, RbtPMFType aRecType, RbtPMFType aLigType) const
Additional Inherited Members
5.216.1 Detailed Description
RbtPMFIdxSF class for PMF scoring.
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5.216 RbtPMFIdxSF Class Reference 145
5.216.2 Constructor & Destructor Documentation
5.216.2.1 RbtPMFIdxSF()
RbtPMFIdxSF::RbtPMFIdxSF (
const std::string & strName = "PMF" )
The only one constructor
5.216.2.2 ∼RbtPMFIdxSF()
virtual RbtPMFIdxSF::∼RbtPMFIdxSF ( ) [virtual]
The virtual destructor
5.216.3 Member Function Documentation
5.216.3.1 GetLinearCloseRangeValue()
double RbtPMFIdxSF::GetLinearCloseRangeValue (
double aDist,
RbtPMFType aRecType,
RbtPMFType aLigType ) const [protected]
Estimate value for short distances instead of using plateau in PMFs
5.216.3.2 RawScore()
virtual double RbtPMFIdxSF::RawScore (
void ) const [protected], [virtual]
RawScore(void) returning with the actual PMF score
Implements RbtBaseSF.
5.216.3.3 SetupLigand()
virtual void RbtPMFIdxSF::SetupLigand ( ) [protected], [virtual]
determine PMF types for all ligand atoms
Implements RbtBaseInterSF.
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146 Class Documentation
5.216.3.4 SetupReceptor()
virtual void RbtPMFIdxSF::SetupReceptor ( ) [protected], [virtual]
Setting up receptor means atom typing for all the receptor atoms and create RbtNonBondedGrid for NN
Implements RbtBaseInterSF.
5.216.3.5 SetupScore()
virtual void RbtPMFIdxSF::SetupScore ( ) [protected], [virtual]
Setting up scores
Implements RbtBaseInterSF.
5.216.3.6 Update()
virtual void RbtPMFIdxSF::Update (
RbtSubject ∗ theChangedSubject ) [virtual]
Observer functionalities pure virtual, so it must be overloaded.
Reimplemented from RbtBaseInterSF.
5.216.4 Member Data Documentation
5.216.4.1 _CT
std::string RbtPMFIdxSF::_CT [static]
This string serves as a name for the weight factor of the PMF score. Should be read from the .prm file.
5.216.4.2 _PMFDIR
std::string RbtPMFIdxSF::_PMFDIR [static]
String pointing to the dir with PMF tables
The documentation for this class was generated from the following file:
• RbtPMFIdxSF.h
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5.217 RbtPMFValue Struct Reference 147
5.217 RbtPMFValue Struct Reference
#include <RbtPMF.h>
Public Attributes
• float distance• float density
5.217.1 Detailed Description
Basic data type to represent distance-value pairs of the PMF function
The documentation for this struct was generated from the following file:
• RbtPMF.h
5.218 RbtPolarIdxSF Class Reference
Inheritance diagram for RbtPolarIdxSF:
RbtPolarIdxSF
RbtBaseInterSF RbtBaseIdxSF RbtPolarSF
RbtBaseSF RbtBaseSF RbtBaseSF RbtAnnotationHandler
RbtBaseObject RbtBaseObject RbtBaseObject
RbtRequestHandler
RbtObserver
RbtParamHandler
RbtRequestHandler
RbtObserver
RbtParamHandler
RbtRequestHandler
RbtObserver
RbtParamHandler
Public Member Functions
• RBTDLL_EXPORT RbtPolarIdxSF (const std::string &strName="POLAR")• virtual void ScoreMap (RbtStringVariantMap &scoreMap) const
Static Public Member Functions
• static RBTDLL_EXPORT std::string & GetIncr ()
Static Public Attributes
• static std::string _CT• static std::string _INCR• static std::string _ATTR• static std::string _THRESHOLD_POS• static std::string _THRESHOLD_NEG
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148 Class Documentation
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupSolvent ()• virtual void SetupScore ()• virtual double RawScore () const• void ClearReceptor ()• void ClearLigand ()• void ClearSolvent ()• void DeleteList (RbtInteractionCenterList &icList)• void ParameterUpdated (const std::string &strName)
The documentation for this class was generated from the following file:
• RbtPolarIdxSF.h
5.219 RbtPolarIntraSF Class Reference
Inheritance diagram for RbtPolarIntraSF:
RbtPolarIntraSF
RbtBaseIntraSF RbtPolarSF
RbtBaseSF RbtBaseSF RbtAnnotationHandler
RbtBaseObject RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtPolarIntraSF (const std::string &strName="POLAR")
Static Public Attributes
• static std::string _CT• static std::string _ATTR
Protected Member Functions
• virtual void SetupScore ()• virtual double RawScore () const• virtual void HandleRequest (RbtRequestPtr spRequest)• void ClearModel ()• void ParameterUpdated (const std::string &strName)
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5.220 RbtPolarSF Class Reference 149
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtPolarIntraSF.h
5.220 RbtPolarSF Class Reference
Inheritance diagram for RbtPolarSF:
RbtPolarSF
RbtBaseSF RbtAnnotationHandler
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
RbtPolarIdxSF RbtPolarIntraSF
Classes
• struct f1prms
Static Public Attributes
• static std::string _CT• static std::string _INCR• static std::string _R12FACTOR• static std::string _R12INCR• static std::string _DR12MIN• static std::string _DR12MAX• static std::string _A1• static std::string _DA1MIN• static std::string _DA1MAX• static std::string _A2• static std::string _DA2MIN• static std::string _DA2MAX• static std::string _INCMETAL• static std::string _INCHBD• static std::string _INCHBA• static std::string _INCGUAN• static std::string _GUAN_PLANE• static std::string _ABS_DR12• static std::string _LP_OSP2• static std::string _LP_PHI• static std::string _LP_DPHIMIN• static std::string _LP_DPHIMAX• static std::string _LP_DTHETAMIN• static std::string _LP_DTHETAMAX
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150 Class Documentation
Protected Member Functions
• RbtInteractionCenterList CreateAcceptorInteractionCenters (const RbtAtomList &atomList) const• RbtInteractionCenterList CreateDonorInteractionCenters (const RbtAtomList &atomList) const• void BuildIntraMap (const RbtInteractionCenterList &ICList1, const RbtInteractionCenterList &ICList2, Rbt←↩
InteractionListMap &intns) const• void BuildIntraMap (const RbtInteractionCenterList &ICList, RbtInteractionListMap &intns) const• double IntraScore (const RbtInteractionCenterList &posList, const RbtInteractionCenterList &negList, const
RbtInteractionListMap &prtIntns, bool attr) const• void Partition (const RbtInteractionCenterList &posList, const RbtInteractionCenterList &negList, const
RbtInteractionListMap &intns, RbtInteractionListMap &prtIntns, double dist=0.0) const• f1prms GetRprms () const• f1prms GetA1prms () const• f1prms GetA2prms () const• double PolarScore (const RbtInteractionCenter ∗intn, const RbtInteractionCenterList &intnList, const f1prms
&Rprms, const f1prms &A1prms, const f1prms &A2prms) const• void OwnParameterUpdated (const std::string &strName)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtPolarSF.h
5.221 RbtPopulation Class Reference
Public Member Functions
• RBTDLL_EXPORT RbtPopulation (RbtChromElement ∗pChr, int size, RbtBaseSF ∗pSF)• int GetMaxSize () const• int GetActualSize () const• RBTDLL_EXPORT RbtGenomePtr Best () const• double GetScoreMean () const• double GetScoreVariance () const• const RbtGenomeList & GetGenomeList () const• RbtBaseSF ∗ GetSF () const• void SetSF (RbtBaseSF ∗pSF)• RBTDLL_EXPORT void GAstep (int nReplicates, double relStepSize, double equalityThreshold, double
pcross, bool xovermut, bool cmutate)• RBTDLL_EXPORT RbtGenomePtr RouletteWheelSelect () const• void Print (std::ostream &) const
Static Public Attributes
• static std::string _CT
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5.222 RbtPosChargeConstraint Class Reference 151
Friends
• std::ostream & operator<< (std::ostream &, const RbtPopulation &)
The documentation for this class was generated from the following file:
• RbtPopulation.h
5.222 RbtPosChargeConstraint Class Reference
Inheritance diagram for RbtPosChargeConstraint:
RbtPosChargeConstraint
RbtConstraint
Public Member Functions
• RbtPosChargeConstraint (RbtCoord c, double t)• void AddAtomList (RbtModelPtr, bool bCheck=true)
Static Public Attributes
• static unsigned int counter
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtConstraint.h
5.223 RbtPrincipalAxes Class Reference
Public Attributes
• RbtCoord com• RbtVector axis1• RbtVector axis2• RbtVector axis3• double moment1• double moment2• double moment3
The documentation for this class was generated from the following file:
• RbtPrincipalAxes.h
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152 Class Documentation
5.224 RbtPRMFactory Class Reference
Public Member Functions
• RBTDLL_EXPORT RbtPRMFactory (RbtParameterFileSource ∗pParamSource)• RBTDLL_EXPORT RbtPRMFactory (RbtParameterFileSource ∗pParamSource, RbtDockingSite ∗pDS)• int GetTrace () const• void SetTrace (int iTrace)• RbtDockingSite ∗ GetDockingSite () const• void SetDockingSite (RbtDockingSite ∗pDS)• RBTDLL_EXPORT RbtModelPtr CreateReceptor ()• RBTDLL_EXPORT RbtModelPtr CreateLigand (RbtBaseMolecularFileSource ∗pSource)• RBTDLL_EXPORT RbtModelList CreateSolvent ()
Static Public Attributes
• static const std::string & _CT• static const std::string & _REC_SECTION• static const std::string & _REC_FILE• static const std::string & _REC_TOPOL_FILE• static const std::string & _REC_COORD_FILE• static const std::string & _REC_NUM_COORD_FILES• static const std::string & _REC_FLEX_DISTANCE• static const std::string & _REC_DIHEDRAL_STEP• static const std::string & _LIG_SECTION• static const std::string & _SOLV_SECTION• static const std::string & _SOLV_FILE
The documentation for this class was generated from the following file:
• RbtPRMFactory.h
5.225 RbtPseudoAtom Class Reference
Inheritance diagram for RbtPseudoAtom:
RbtPseudoAtom
RbtAtom
Public Member Functions
• RbtPseudoAtom (const RbtAtomList &atomList, int nAtomId=-1, std::string strAtomName="PSEUDO")• virtual std::ostream & Print (std::ostream &s) const• unsigned int GetNumAtoms () const• RbtAtomList GetAtomList () const• void UpdateCoords ()
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5.226 RbtPsfFileSink Class Reference 153
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtPseudoAtom.h
5.226 RbtPsfFileSink Class Reference
Inheritance diagram for RbtPsfFileSink:
RbtPsfFileSink
RbtBaseMolecularFileSink
RbtBaseFileSink
Public Member Functions
• RBTDLL_EXPORT RbtPsfFileSink (const std::string &fileName, RbtModelPtr spModel)• virtual void Render ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtPsfFileSink.h
5.227 RbtPsfFileSource Class Reference
Inheritance diagram for RbtPsfFileSource:
RbtPsfFileSource
RbtBaseMolecularFileSource
RbtBaseFileSource RbtBaseMolecularDataSource
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154 Class Documentation
Public Member Functions
• RbtPsfFileSource (const std::string &fileName, const std::string &strMassesFile=Rbt::GetRbtFile←↩
Name("data", "masses.rtf"), bool bImplHydrogens=true)• virtual bool isTitleListSupported ()• virtual bool isAtomListSupported ()• virtual bool isCoordinatesSupported ()• virtual bool isBondListSupported ()
Protected Member Functions
• virtual void Parse ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtPsfFileSource.h
5.228 RbtQuat Class Reference
Public Member Functions
• RbtQuat (double s1, double vx, double vy, double vz)• RbtQuat (double s1, const RbtVector &v1)• RbtQuat (const RbtVector &axis, double phi)• RbtQuat (const RbtQuat &quat)• RbtQuat & operator= (const RbtQuat &quat)• void operator+= (const RbtQuat &quat)• void operator-= (const RbtQuat &quat)• void operator∗= (const double &d)• void operator/= (const double &d)• double Length () const• RbtQuat Unit () const• double Dot (const RbtQuat &quat) const• RbtQuat Conj () const• RbtCoord Rotate (const RbtCoord &w) const
Public Attributes
• double s• RbtVector v
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5.229 RbtRand Class Reference 155
Friends
• std::ostream & operator<< (std::ostream &s, const RbtQuat &quat)• bool operator== (const RbtQuat &quat1, const RbtQuat &quat2)• bool operator!= (const RbtQuat &quat1, const RbtQuat &quat2)• RbtQuat operator+ (const RbtQuat &quat1, const RbtQuat &quat2)• RbtQuat operator- (const RbtQuat &quat1, const RbtQuat &quat2)• RbtQuat operator- (const RbtQuat &quat)• RbtQuat operator∗ (const RbtQuat &quat1, const RbtQuat &quat2)• RbtQuat operator∗ (const RbtQuat &quat, const double &d)• RbtQuat operator∗ (const double &d, const RbtQuat &quat)• RbtQuat operator/ (const RbtQuat &quat, const double &d)
The documentation for this class was generated from the following file:
• RbtQuat.h
5.229 RbtRand Class Reference
Public Member Functions
• RBTDLL_EXPORT void Seed (int seed=0)• void SeedFromRandomDevice ()• RBTDLL_EXPORT int GetSeed ()• RBTDLL_EXPORT double GetRandom01 ()• int GetRandomInt (int nMax)• RbtVector GetRandomUnitVector ()• double GetGaussianRandom (double, double)• double GetCauchyRandom (double, double)
The documentation for this class was generated from the following file:
• RbtRand.h
5.230 RbtRandLigTransform Class Reference
Inheritance diagram for RbtRandLigTransform:
RbtRandLigTransform
RbtBaseUniMolTransform
RbtBaseTransform
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
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156 Class Documentation
Public Member Functions
• RbtRandLigTransform (const std::string &strName="RANDLIG")
Static Public Attributes
• static std::string _CT• static std::string _TORS_STEP
Protected Member Functions
• virtual void SetupTransform ()• virtual void Execute ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtRandLigTransform.h
5.231 RbtRandPopTransform Class Reference
Inheritance diagram for RbtRandPopTransform:
RbtRandPopTransform
RbtBaseBiMolTransform
RbtBaseTransform
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RBTDLL_EXPORT RbtRandPopTransform (const std::string &strName="RANDPOP")
Static Public Attributes
• static std::string _CT• static std::string _POP_SIZE• static std::string _SCALE_CHROM_LENGTH
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5.232 RbtRealGrid Class Reference 157
Protected Member Functions
• virtual void SetupTransform ()• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupSolvent ()• virtual void Execute ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtRandPopTransform.h
5.232 RbtRealGrid Class Reference
Inheritance diagram for RbtRealGrid:
RbtRealGrid
RbtBaseGrid
RbtFFTGrid
Public Member Functions
• RBTDLL_EXPORT RbtRealGrid (const RbtCoord &gridMin, const RbtCoord &gridStep, unsigned int NX,unsigned int NY, unsigned int NZ, unsigned int NPad=0)
• RBTDLL_EXPORT RbtRealGrid (std::istream &istr)• RbtRealGrid (const RbtRealGrid &)• RbtRealGrid (const RbtBaseGrid &)• RbtRealGrid & operator= (const RbtRealGrid &)• RbtRealGrid & operator= (const RbtBaseGrid &)• virtual void Print (std::ostream &ostr) const• virtual void Write (std::ostream &ostr) const• virtual void Read (std::istream &istr)• float ∗ GetGridData ()• double GetTolerance () const• void SetTolerance (double tol)• double GetValue (const RbtCoord &c) const• double GetValue (unsigned int iX, unsigned int iY, unsigned int iZ) const• double GetValue (unsigned int iXYZ) const• RBTDLL_EXPORT double GetSmoothedValue (const RbtCoord &c) const• void SetValue (const RbtCoord &c, double val)• void SetValue (unsigned int iX, unsigned int iY, unsigned int iZ, double val)• void SetValue (unsigned int iXYZ, double val)• RBTDLL_EXPORT void SetAllValues (double val)
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158 Class Documentation
• void ReplaceValue (double oldVal, double newVal)• void ReplaceValueRange (double oldValMin, double oldValMax, double newVal)• void SetSphere (const RbtCoord &c, double radius, double val, bool bOverwrite=true)• void SetSurface (const RbtCoord &c, double innerRad, double outerRad, double val, bool bOverwrite=true)• void CreateSurface (double oldVal, double adjVal, double newVal)• bool isValueWithinSphere (const RbtCoord &c, double radius, double val)• void SetAccessible (double radius, double oldVal, double adjVal, double newVal, bool bCenterOnly=true)• unsigned int Count (double val) const• unsigned int CountRange (double valMin, double valMax) const• double MinValue () const• double MaxValue () const• unsigned int FindMinValue () const• unsigned int FindMaxValue () const• RBTDLL_EXPORT void PrintInsightGrid (std::ostream &s) const
Static Public Attributes
• static std::string _CT
Protected Member Functions
• void OwnPrint (std::ostream &ostr) const• void OwnWrite (std::ostream &ostr) const• void OwnRead (std::istream &istr)
The documentation for this class was generated from the following file:
• RbtRealGrid.h
5.233 RbtReceptorFlexData Class Reference
Inheritance diagram for RbtReceptorFlexData:
RbtReceptorFlexData
RbtFlexData
RbtParamHandler
Public Member Functions
• RBTDLL_EXPORT RbtReceptorFlexData (RbtDockingSite ∗pDockSite)• virtual void Accept (RbtFlexDataVisitor &v)
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5.234 RbtRequest Class Reference 159
Static Public Attributes
• static const std::string & _FLEX_DISTANCE• static const std::string & _DIHEDRAL_STEP
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtReceptorFlexData.h
5.234 RbtRequest Class Reference
Inheritance diagram for RbtRequest:
RbtRequest
RbtSFDisableRequest RbtSFEnableRequest RbtSFPartitionRequest RbtSFSetParamRequest
Public Member Functions
• RbtRequestID GetID () const• unsigned int GetNumParameters () const• RbtVariantList GetParameters () const• RbtRequest (RbtRequestID id)• void AddParameter (const RbtVariant &v)
The documentation for this class was generated from the following file:
• RbtRequest.h
5.235 RbtRequestHandler Class Reference
Inheritance diagram for RbtRequestHandler:
RbtRequestHandler
RbtBaseObject
RbtBaseSF RbtBaseTransform RbtFilter RbtSiteMapper
RbtBaseIdxSF
RbtBaseInterSF
RbtBaseIntraSF
RbtDihedralSF
RbtPolarSF
RbtSFAgg
RbtVdwSF
RbtBaseBiMolTransform
RbtBaseUniMolTransform
RbtNullTransform
RbtTransformAgg
RbtLigandSiteMapper
RbtSphereSiteMapper
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160 Class Documentation
Public Member Functions
• virtual void HandleRequest (RbtRequestPtr spRequest)
The documentation for this class was generated from the following file:
• RbtRequestHandler.h
5.236 RbtRingAromaticConstraint Class Reference
Inheritance diagram for RbtRingAromaticConstraint:
RbtRingAromaticConstraint
RbtConstraint
Public Member Functions
• RbtRingAromaticConstraint (RbtCoord c, double t)• void AddAtomList (RbtModelPtr, bool bCheck=true)
Static Public Attributes
• static unsigned int counter
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtConstraint.h
5.237 RbtRotSF Class Reference
Inheritance diagram for RbtRotSF:
RbtRotSF
RbtBaseInterSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
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5.238 RbtSAIdxSF Class Reference 161
Public Member Functions
• RbtRotSF (const std::string &strName="ROT")
Static Public Attributes
• static std::string _CT• static std::string _INCNH3• static std::string _INCOH
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupScore ()• virtual double RawScore () const• void ParameterUpdated (const std::string &strName)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtRotSF.h
5.238 RbtSAIdxSF Class Reference
Inheritance diagram for RbtSAIdxSF:
RbtSAIdxSF
RbtBaseInterSF RbtBaseIdxSF RbtAnnotationHandler
RbtBaseSF RbtBaseSF
RbtBaseObject RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RBTDLL_EXPORT RbtSAIdxSF (const std::string &strName="SAIdxSF")• virtual void ScoreMap (RbtStringVariantMap &scoreMap) const• virtual void HandleRequest (RbtRequestPtr spRequest)
Static Public Attributes
• static std::string _CT• static std::string _INCR
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162 Class Documentation
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupSolvent ()• virtual void SetupScore ()• virtual double RawScore (void) const• void ClearReceptor (void)• void ClearLigand (void)• void ClearSolvent (void)• double GetASP (RbtHHSType::eType, double) const• double GetP_i (RbtHHSType::eType) const• double GetR_i (RbtHHSType::eType) const• void PrintWeightMatrix () const
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtSAIdxSF.h
5.239 RbtSetupPMFSF Class Reference
Inheritance diagram for RbtSetupPMFSF:
RbtSetupPMFSF
RbtBaseInterSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtSetupPMFSF (const std::string &strName="SETUP_PMF")
Static Public Attributes
• static std::string _CT
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5.240 RbtSetupPolarSF Class Reference 163
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupScore ()• virtual double RawScore () const• void SetupReceptorPMFTypes (void)• void SetupLigandPMFTypes (void)• RbtPMFType GetPMFfor_lC (RbtAtomPtr)• RbtPMFType GetPMFfor_lN (RbtAtomPtr)• RbtPMFType GetPMFfor_lO (RbtAtomPtr)• RbtPMFType GetPMFfor_lS (RbtAtomPtr)• RbtPMFType GetPMFfor_rC (RbtAtomPtr)• RbtPMFType GetPMFfor_rN (RbtAtomPtr)• RbtPMFType GetPMFfor_rO (RbtAtomPtr)• RbtPMFType GetPMFfor_rS (RbtAtomPtr)• bool IsChargedNitrogen (RbtAtomPtr)
Additional Inherited Members
5.239.1 Member Function Documentation
5.239.1.1 GetPMFfor_lC()
RbtPMFType RbtSetupPMFSF::GetPMFfor_lC (
RbtAtomPtr ) [protected]
Routines to figure out complex PMF types
The documentation for this class was generated from the following file:
• RbtSetupPMFSF.h
5.240 RbtSetupPolarSF Class Reference
Inheritance diagram for RbtSetupPolarSF:
RbtSetupPolarSF
RbtBaseInterSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
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164 Class Documentation
Public Member Functions
• RBTDLL_EXPORT RbtSetupPolarSF (const std::string &strName="SETUP_POLAR")
Static Public Attributes
• static std::string _CT• static std::string _RADIUS• static std::string _NORM• static std::string _POWER• static std::string _CHGFACTOR• static std::string _GUANFACTOR
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupSolvent ()• virtual void SetupScore ()• virtual double RawScore () const
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtSetupPolarSF.h
5.241 RbtSetupSASF Class Reference
Inheritance diagram for RbtSetupSASF:
RbtSetupSASF
RbtBaseInterSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtSetupSASF (const std::string &strName="SETUP_SA")
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5.242 RbtSFAgg Class Reference 165
Static Public Attributes
• static std::string _CT
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupScore ()• virtual double RawScore () const• void SetupReceptorSATypes (void)• void SetupLigandSATypes (void)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtSetupSASF.h
5.242 RbtSFAgg Class Reference
Inheritance diagram for RbtSFAgg:
RbtSFAgg
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RBTDLL_EXPORT RbtSFAgg (const std::string &strName="SCORE")• virtual void ScoreMap (RbtStringVariantMap &scoreMap) const• virtual void Add (RbtBaseSF ∗)• virtual void Remove (RbtBaseSF ∗)• virtual bool isAgg () const• virtual unsigned int GetNumSF () const• virtual RbtBaseSF ∗ GetSF (unsigned int iSF) const• virtual void Register (RbtWorkSpace ∗)• virtual void Unregister ()• virtual void Update (RbtSubject ∗theChangedSubject)• virtual void HandleRequest (RbtRequestPtr spRequest)• virtual void Print (std::ostream &s) const
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166 Class Documentation
Static Public Attributes
• static std::string _CT
Protected Member Functions
• virtual double RawScore () const
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtSFAgg.h
5.243 RbtSFDisableRequest Class Reference
Inheritance diagram for RbtSFDisableRequest:
RbtSFDisableRequest
RbtRequest
Public Member Functions
• RbtSFDisableRequest (const std::string &sfName)
The documentation for this class was generated from the following file:
• RbtSFRequest.h
5.244 RbtSFEnableRequest Class Reference
Inheritance diagram for RbtSFEnableRequest:
RbtSFEnableRequest
RbtRequest
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5.245 RbtSFFactory Class Reference 167
Public Member Functions
• RbtSFEnableRequest (const std::string &sfName)
The documentation for this class was generated from the following file:
• RbtSFRequest.h
5.245 RbtSFFactory Class Reference
Public Member Functions
• virtual RbtBaseSF ∗ Create (const std::string &strSFClass, const std::string &strName)• virtual RbtSFAgg ∗ CreateAggFromFile (RbtParameterFileSourcePtr spPrmSource, const std::string &str←↩
Name, const std::string &strSFClasses=std::string())
The documentation for this class was generated from the following file:
• RbtSFFactory.h
5.246 RbtSFPartitionRequest Class Reference
Inheritance diagram for RbtSFPartitionRequest:
RbtSFPartitionRequest
RbtRequest
Public Member Functions
• RbtSFPartitionRequest (double dist)• RbtSFPartitionRequest (const std::string &sfName, double dist)
The documentation for this class was generated from the following file:
• RbtSFRequest.h
5.247 RbtSFSetParamRequest Class Reference
Inheritance diagram for RbtSFSetParamRequest:
RbtSFSetParamRequest
RbtRequest
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168 Class Documentation
Public Member Functions
• RbtSFSetParamRequest (const std::string ¶mName, const RbtVariant ¶mValue)• RbtSFSetParamRequest (const std::string &sfName, const std::string ¶mName, const RbtVariant
¶mValue)
The documentation for this class was generated from the following file:
• RbtSFRequest.h
5.248 RbtSimAnnTransform Class Reference
Inheritance diagram for RbtSimAnnTransform:
RbtSimAnnTransform
RbtBaseBiMolTransform
RbtBaseTransform
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RBTDLL_EXPORT RbtSimAnnTransform (const std::string &strName="SIMANN")
Static Public Member Functions
• static RBTDLL_EXPORT std::string & GetStartT ()• static RBTDLL_EXPORT std::string & GetFinalT ()• static RBTDLL_EXPORT std::string & GetBlockLength ()• static RBTDLL_EXPORT std::string & GetNumBlocks ()• static RBTDLL_EXPORT std::string & GetStepSize ()• static RBTDLL_EXPORT std::string & GetPartitionDist ()• static RBTDLL_EXPORT std::string & GetPartitionFreq ()
Static Public Attributes
• static std::string _CT• static std::string _START_T• static std::string _FINAL_T• static std::string _BLOCK_LENGTH• static std::string _SCALE_CHROM_LENGTH• static std::string _NUM_BLOCKS• static std::string _STEP_SIZE• static std::string _MIN_ACC_RATE• static std::string _PARTITION_DIST• static std::string _PARTITION_FREQ• static std::string _HISTORY_FREQ
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5.249 RbtSimpleSolvationParameters Struct Reference 169
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupTransform ()• void MC (double t, int blockLen, double stepSize)• virtual void Execute ()
The documentation for this class was generated from the following file:
• RbtSimAnnTransform.h
5.249 RbtSimpleSolvationParameters Struct Reference
Public Attributes
• double p• double r
The documentation for this struct was generated from the following file:
• RbtSetupSASF.h
5.250 RbtSimplexCostFunction Class Reference
Public Types
• typedef double DataType• typedef Eigen::VectorXd ParameterType
Public Member Functions
• RbtSimplexCostFunction (RbtBaseSF ∗pSF, RbtChromElementPtr chrom)• double operator() (const ParameterType ¶meters)
Public Attributes
• unsigned long int nCalls = 0
The documentation for this class was generated from the following file:
• RbtSimplexCostFunction.h
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170 Class Documentation
5.251 RbtSimplexTransform Class Reference
Inheritance diagram for RbtSimplexTransform:
RbtSimplexTransform
RbtBaseBiMolTransform
RbtBaseTransform
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RBTDLL_EXPORT RbtSimplexTransform (const std::string &strName="SIMPLEX")
Static Public Member Functions
• static RBTDLL_EXPORT std::string & GetMaxCalls ()• static RBTDLL_EXPORT std::string & GetNCycles ()• static RBTDLL_EXPORT std::string & GetStepSize ()
Static Public Attributes
• static std::string _CT• static std::string _MAX_CALLS• static std::string _NCYCLES• static std::string _STOPPING_STEP_LENGTH• static std::string _PARTITION_DIST• static std::string _STEP_SIZE• static std::string _CONVERGENCE
Protected Member Functions
• virtual void SetupTransform ()• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupSolvent ()• virtual void Execute ()
The documentation for this class was generated from the following file:
• RbtSimplexTransform.h
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5.252 RbtSiteMapper Class Reference 171
5.252 RbtSiteMapper Class Reference
Inheritance diagram for RbtSiteMapper:
RbtSiteMapper
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
RbtLigandSiteMapper RbtSphereSiteMapper
Public Member Functions
• RbtModelPtr GetReceptor () const• virtual RbtCavityList operator() ()=0• virtual void Update (RbtSubject ∗theChangedSubject)
Static Public Attributes
• static std::string _CT
Protected Member Functions
• RbtSiteMapper (const std::string &strClass, const std::string &strName)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtSiteMapper.h
5.253 RbtSiteMapperFactory Class Reference
Public Member Functions
• virtual RbtSiteMapper ∗ Create (const std::string &strMapperClass, const std::string &strName)• virtual RbtSiteMapper ∗ CreateFromFile (RbtParameterFileSourcePtr spPrmSource, const std::string &str←↩
Name)
The documentation for this class was generated from the following file:
• RbtSiteMapperFactory.h
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172 Class Documentation
5.254 RbtSolventFlexData Class Reference
Inheritance diagram for RbtSolventFlexData:
RbtSolventFlexData
RbtLigandFlexData
RbtFlexData
RbtParamHandler
Public Member Functions
• RbtSolventFlexData (RbtDockingSite ∗pDockSite)• virtual void Accept (RbtFlexDataVisitor &v)
Static Public Attributes
• static const std::string & _OCCUPANCY• static const std::string & _OCCUPANCY_STEP
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtSolventFlexData.h
5.255 RbtSphereSiteMapper Class Reference
Inheritance diagram for RbtSphereSiteMapper:
RbtSphereSiteMapper
RbtSiteMapper
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
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5.256 RbtStdRestraintAtoms Class Reference 173
Public Member Functions
• RbtSphereSiteMapper (const std::string &strName="SPHERE_MAPPER")• virtual RbtCavityList operator() ()
Static Public Attributes
• static std::string _CT• static std::string _VOL_INCR• static std::string _SMALL_SPHERE• static std::string _LARGE_SPHERE• static std::string _GRIDSTEP• static std::string _CENTER• static std::string _RADIUS• static std::string _MIN_VOLUME• static std::string _MAX_CAVITIES
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtSphereSiteMapper.h
5.256 RbtStdRestraintAtoms Class Reference
Public Member Functions
• RbtStdRestraintAtoms (const RbtStdRestraintNames &n, const RbtAtomList &atomList)• bool isOK () const• bool isSimple () const
Public Attributes
• RbtNoeEndAtoms from• double maxDist
The documentation for this class was generated from the following file:
• RbtNoeRestraint.h
5.257 RbtStdRestraintNames Class Reference
Public Member Functions
• bool isOK () const
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174 Class Documentation
Public Attributes
• RbtNoeEndNames from• double maxDist
The documentation for this class was generated from the following file:
• RbtNoeRestraint.h
5.258 RbtStringContext Class Reference
Inheritance diagram for RbtStringContext:
RbtStringContext
RbtContext
Public Member Functions
• RbtStringContext (SmartPtr< std::ifstream > ifile)• RbtStringContext (const RbtStringContext &c)• void Assign (std::string key, RbtReturnType val)• void Assign (int i, RbtReturnType val)• double Get (RbtModelPtr lig, std::string name)• double Get (RbtModelPtr rec, RbtDockingSitePtr site, std::string name)• double Get (RbtBaseSF ∗spSF, std::string name, RbtModelPtr lig)• const RbtVble & GetVble (std::string key)• const RbtVble & GetVble (int key)• void SetVble (int key, const RbtVble &v)• void UpdateLigs (RbtModelPtr lig)• void UpdateSite (RbtModelPtr rec, RbtDockingSitePtr site)• void UpdateScores (RbtBaseSF ∗spSF, RbtModelPtr lig)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtContext.h
5.259 RbtStringTokenIter Class Reference
Inheritance diagram for RbtStringTokenIter:
RbtStringTokenIter
RbtTokenIter
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5.260 RbtStringTooLong Class Reference 175
Public Member Functions
• RbtStringTokenIter (const RbtStringTokenIter &)• RbtStringTokenIter (const istreamPtr, RbtContextPtr)• void copy (const RbtStringTokenIter &)• void Next (RbtContextPtr)• RbtTokenPtr Current ()
Static Public Attributes
• static std::string _CT
The documentation for this class was generated from the following file:
• RbtStringTokenIter.h
5.260 RbtStringTooLong Class Reference
Inheritance diagram for RbtStringTooLong:
RbtStringTooLong
RbtFileError
RbtError
Public Member Functions
• RbtStringTooLong (const std::string &strFile, int nLine, const std::string &strMessage="")
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtFileError.h
5.261 RbtSubject Class Reference
Inheritance diagram for RbtSubject:
RbtSubject
RbtWorkSpace
RbtBiMolWorkSpace
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176 Class Documentation
Public Member Functions
• virtual void Attach (RbtObserver ∗)• virtual void Detach (RbtObserver ∗)• virtual void Notify ()
The documentation for this class was generated from the following file:
• RbtSubject.h
5.262 RbtTetherSF Class Reference
Inheritance diagram for RbtTetherSF:
RbtTetherSF
RbtBaseInterSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtTetherSF (const std::string &strName="TETHER")
Static Public Attributes
• static std::string _CT• static std::string _REFERENCE_FILE
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupScore ()• virtual double RawScore () const• void ParameterUpdated (const std::string &strName)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtTetherSF.h
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5.263 RbtToken Class Reference 177
5.263 RbtToken Class Reference
Public Member Functions
• RbtToken (const RbtVble &)• RbtToken (RbtCommands)• RbtToken (const RbtToken &)• const RbtVble & GetVble () const• bool IsVble ()• bool IsLog ()• bool IsExp ()• bool IsAdd ()• bool IsSub ()• bool IsMul ()• bool IsDiv ()• bool IsAnd ()• bool IsIf ()
Static Public Attributes
• static std::string _CT
The documentation for this class was generated from the following file:
• RbtToken.h
5.264 RbtTokenIter Class Reference
Inheritance diagram for RbtTokenIter:
RbtTokenIter
RbtCellTokenIter RbtStringTokenIter
Public Member Functions
• virtual void Next (RbtContextPtr)=0• virtual RbtTokenPtr Current ()=0
The documentation for this class was generated from the following file:
• RbtTokenIter.h
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178 Class Documentation
5.265 RbtTransformAgg Class Reference
Inheritance diagram for RbtTransformAgg:
RbtTransformAgg
RbtBaseTransform
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RBTDLL_EXPORT RbtTransformAgg (const std::string &strName="DOCK")
• virtual void Add (RbtBaseTransform ∗)
• virtual void Remove (RbtBaseTransform ∗)
• virtual bool isAgg () const
• virtual unsigned int GetNumTransforms () const
• virtual RbtBaseTransform ∗ GetTransform (unsigned int iTransform) const
• virtual void Register (RbtWorkSpace ∗)
• virtual void Unregister ()
• virtual void Update (RbtSubject ∗theChangedSubject)
• virtual void HandleRequest (RbtRequestPtr spRequest)
• virtual void Print (std::ostream &s) const
Static Public Attributes
• static std::string _CT
Protected Member Functions
• virtual void Execute ()
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtTransformAgg.h
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5.266 RbtTransformFactory Class Reference 179
5.266 RbtTransformFactory Class Reference
Public Member Functions
• virtual RbtBaseTransform ∗ Create (const std::string &strTransformClass, const std::string &strName)• virtual RbtTransformAgg ∗ CreateAggFromFile (RbtParameterFileSourcePtr spPrmSource, const std::string
&strName, const std::string &strTransformClasses=std::string())
The documentation for this class was generated from the following file:
• RbtTransformFactory.h
5.267 RbtTriposAtomType Class Reference
Classes
• struct info
Public Types
• enum eType {UNDEFINED = 0, Al, Br, C_cat,C_1, C_1_H1, C_2, C_2_H1,C_2_H2, C_3, C_3_H1, C_3_H2,C_3_H3, C_ar, C_ar_H1, Ca,Cl, Du, F, H,H_P, I, K, Li,LP, N_1, N_2, N_3,N_4, N_am, N_ar, N_pl3,Na, O_2, O_3, O_co2,P_3, S_2, S_3, S_o,S_o2, Si, MAXTYPES }
Public Member Functions
• eType operator() (RbtAtom ∗pAtom, bool useExtendedTypes=false) const• RBTDLL_EXPORT std::string Type2Str (eType) const• int Type2Hybrid (eType) const• int Type2AtomicNo (eType) const• RBTDLL_EXPORT eType Str2Type (const std::string &) const
The documentation for this class was generated from the following file:
• RbtTriposAtomType.h
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180 Class Documentation
5.268 RbtVariant Class Reference
Public Member Functions
• RbtVariant (int i)• RbtVariant (double d)• RbtVariant (const std::string &s)• RbtVariant (const char ∗c)• RbtVariant (const std::vector< std::string > &sl)• RbtVariant (bool b)• RbtVariant (const RbtCoord &c)• RbtVariant (const std::vector< double > &dl, int maxCols, int precision)• RbtVariant & operator= (int i)• RbtVariant & operator= (double d)• RbtVariant & operator= (const std::string &s)• RbtVariant & operator= (const char ∗c)• RbtVariant & operator= (const std::vector< std::string > &sl)• RbtVariant & operator= (bool b)• RbtVariant & operator= (const RbtCoord &c)• void operator+= (const RbtVariant &v)• operator int () const• operator unsigned int () const• operator double () const• operator std::string () const• operator std::vector< std::string > () const• operator bool () const• operator RbtCoord () const• double Double () const• std::string String () const• std::vector< std::string > StringList () const• bool Bool () const• RbtCoord Coord () const• unsigned int Size () const• bool isEmpty () const
Friends
• std::ostream & operator<< (std::ostream &s, const RbtVariant &v)
The documentation for this class was generated from the following file:
• RbtVariant.h
5.269 RbtVble Class Reference
Public Types
• enum VbleType { CTE, LIG, SCORE, SITE }
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5.270 RbtVdwGridSF Class Reference 181
Public Member Functions
• RbtVble (std::string s, RbtReturnType val=0.0)• RbtVble (const RbtVble &v)• void SetValue (RbtReturnType val)• RbtReturnType GetValue () const• RbtVble & operator= (const RbtVble &v)• void SetName (std::string nm)• std::string GetName () const• bool IsLig ()• bool IsScore ()• bool IsSite ()
Static Public Attributes
• static std::string _CT
The documentation for this class was generated from the following file:
• RbtVble.h
5.270 RbtVdwGridSF Class Reference
Inheritance diagram for RbtVdwGridSF:
RbtVdwGridSF
RbtBaseInterSF
RbtBaseSF
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RbtVdwGridSF (const std::string &strName="VDW")
Static Public Member Functions
• static RBTDLL_EXPORT std::string & GetCt ()
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182 Class Documentation
Static Public Attributes
• static std::string _CT• static std::string _GRID• static std::string _SMOOTHED
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupSolvent ()• virtual void SetupScore ()• virtual double RawScore () const• void ParameterUpdated (const std::string &strName)
The documentation for this class was generated from the following file:
• RbtVdwGridSF.h
5.271 RbtVdwIdxSF Class Reference
Inheritance diagram for RbtVdwIdxSF:
RbtVdwIdxSF
RbtBaseInterSF RbtBaseIdxSF RbtVdwSF
RbtBaseSF RbtBaseSF RbtBaseSF RbtAnnotationHandler
RbtBaseObject RbtBaseObject RbtBaseObject
RbtRequestHandler
RbtObserver
RbtParamHandler
RbtRequestHandler
RbtObserver
RbtParamHandler
RbtRequestHandler
RbtObserver
RbtParamHandler
Public Member Functions
• RBTDLL_EXPORT RbtVdwIdxSF (const std::string &strName="VDW")• virtual void ScoreMap (RbtStringVariantMap &scoreMap) const
Static Public Attributes
• static std::string _CT• static std::string _THRESHOLD_ATTR• static std::string _THRESHOLD_REP• static std::string _ANNOTATION_LIPO• static std::string _ANNOTATE• static std::string _FAST_SOLVENT
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5.272 RbtVdwIntraSF Class Reference 183
Protected Member Functions
• virtual void SetupReceptor ()• virtual void SetupLigand ()• virtual void SetupSolvent ()• virtual void SetupScore ()• virtual double RawScore () const• double InterScore () const• double ReceptorScore () const• double SolventScore () const• double ReceptorSolventScore () const• double LigandSolventScore () const• void ParameterUpdated (const std::string &strName)
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtVdwIdxSF.h
5.272 RbtVdwIntraSF Class Reference
Inheritance diagram for RbtVdwIntraSF:
RbtVdwIntraSF
RbtBaseIntraSF RbtVdwSF
RbtBaseSF RbtBaseSF RbtAnnotationHandler
RbtBaseObject RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler RbtParamHandler RbtObserver RbtRequestHandler
Public Member Functions
• RBTDLL_EXPORT RbtVdwIntraSF (const std::string &strName="VDW")• virtual void HandleRequest (RbtRequestPtr spRequest)
Static Public Attributes
• static std::string _CT
Protected Member Functions
• virtual void SetupScore ()• virtual double RawScore () const• void ParameterUpdated (const std::string &strName)
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184 Class Documentation
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtVdwIntraSF.h
5.273 RbtVdwSF Class Reference
Inheritance diagram for RbtVdwSF:
RbtVdwSF
RbtBaseSF RbtAnnotationHandler
RbtBaseObject
RbtParamHandler RbtObserver RbtRequestHandler
RbtVdwIdxSF RbtVdwIntraSF
Static Public Member Functions
• static RBTDLL_EXPORT std::string & GetEcut ()
Static Public Attributes
• static std::string _CT• static std::string _USE_4_8• static std::string _USE_TRIPOS• static std::string _RMAX• static std::string _ECUT• static std::string _E0
Protected Member Functions
• void OwnParameterUpdated (const std::string &strName)• double VdwScore (const RbtAtom ∗pAtom, const RbtAtomRList &atomList) const• double VdwScoreEnabledOnly (const RbtAtom ∗pAtom, const RbtAtomRList &atomList) const• double MaxVdwRange (const RbtAtom ∗pAtom) const• double MaxVdwRange (RbtTriposAtomType::eType t) const• void BuildIntraMap (const RbtAtomRList &atomList, RbtAtomRListList &intns) const• void BuildIntraMap (const RbtAtomRList &atomList1, const RbtAtomRList &atomList2, RbtAtomRListList
&intns) const• void Partition (const RbtAtomRList &atomList, const RbtAtomRListList &intns, RbtAtomRListList &prtIntns,
double dist=0.0) const
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5.274 RbtWorkSpace Class Reference 185
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtVdwSF.h
5.274 RbtWorkSpace Class Reference
Inheritance diagram for RbtWorkSpace:
RbtWorkSpace
RbtSubject RbtParamHandler
RbtBiMolWorkSpace
Public Member Functions
• RbtWorkSpace (unsigned int nModels=2)• RBTDLL_EXPORT std::string GetName () const• RBTDLL_EXPORT void SetName (const std::string &)• RBTDLL_EXPORT unsigned int GetNumModels () const• RBTDLL_EXPORT RbtModelList GetModels () const• RBTDLL_EXPORT RbtModelPtr GetModel (unsigned int iModel) const• void SetModel (unsigned int iModel, RbtModelPtr spModel)• RbtModelList GetModels (unsigned int iModel) const• void AddModels (RbtModelList modelList)• void SetModels (unsigned int iModel, RbtModelList modelList)• void RemoveModels (unsigned int iModel)• RbtMolecularFileSinkPtr GetSink () const• RBTDLL_EXPORT void SetSink (RbtMolecularFileSinkPtr)• virtual void Save (bool bSaveScores=true)• RbtMolecularFileSinkPtr GetHistorySink () const• RBTDLL_EXPORT void SetHistorySink (RbtMolecularFileSinkPtr)• virtual void SaveHistory (bool bSaveScores=true)• RBTDLL_EXPORT RbtBaseSF ∗ GetSF () const• RBTDLL_EXPORT void SetSF (RbtBaseSF ∗)• RbtBaseTransform ∗ GetTransform () const• RBTDLL_EXPORT void SetTransform (RbtBaseTransform ∗)• virtual void Run ()• void SetPopulation (RbtPopulationPtr population)• RbtPopulationPtr GetPopulation () const• void ClearPopulation ()• RBTDLL_EXPORT RbtDockingSitePtr GetDockingSite () const• RBTDLL_EXPORT void SetDockingSite (RbtDockingSitePtr spDockSite)• RbtFilterPtr GetFilter () const• RBTDLL_EXPORT void SetFilter (RbtFilterPtr spFilter)
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186 Class Documentation
Static Public Attributes
• static std::string _CT• static std::string _NAME
Additional Inherited Members
The documentation for this class was generated from the following file:
• RbtWorkSpace.h
5.275 RbtNM::RelativeValueCriterion< DataType > Class TemplateReference
Public Member Functions
• RelativeValueCriterion (DataType ftol)• template<class State >
bool operator() (const State &state)
The documentation for this class was generated from the following file:
• RbtNMCriteria.h
5.276 Rbt::RestoreHHS Class Reference
Public Member Functions
• void operator() (HHS_Solvation ∗pHHS)
The documentation for this class was generated from the following file:
• RbtSATypes.h
5.277 Rbt::RotateAtomUsingQuat Class Reference
Public Member Functions
• RotateAtomUsingQuat (const RbtQuat &qq)• void operator() (RbtAtom ∗pAtom)
The documentation for this class was generated from the following file:
• RbtAtom.h
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5.278 Rbt::RotateAtomUsingQuatIfSelected Class Reference 187
5.278 Rbt::RotateAtomUsingQuatIfSelected Class Reference
Public Member Functions
• RotateAtomUsingQuatIfSelected (const RbtQuat &qq)• void operator() (RbtAtom ∗pAtom)
The documentation for this class was generated from the following file:
• RbtAtom.h
5.279 Rbt::SaveHHS Class Reference
Public Member Functions
• void operator() (HHS_Solvation ∗pHHS)
The documentation for this class was generated from the following file:
• RbtSATypes.h
5.280 SearchTest Class Reference
Inheritance diagram for SearchTest:
SearchTest
Test
Protected Member Functions
• void SetUp () override• void TearDown () override• double rmsd (const RbtCoordList &rc, const RbtCoordList &c)
Protected Attributes
• RbtAtomList m_atomList• RbtBiMolWorkSpacePtr m_workSpace• RbtSFAggPtr m_SF
The documentation for this class was generated from the following files:
• SearchTest.h• SearchTest.cxx
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188 Class Documentation
5.281 Rbt::SelectAtom Class Reference
Public Member Functions
• SelectAtom (bool bb)• void operator() (RbtAtom ∗pAtom)
The documentation for this class was generated from the following file:
• RbtAtom.h
5.282 Rbt::SelectFlexAtoms Class Reference
Public Member Functions
• void operator() (RbtAtom ∗pAtom)
The documentation for this class was generated from the following file:
• RbtAtom.h
5.283 Rbt::SelectInteractionCenter Class Reference
Public Member Functions
• SelectInteractionCenter (bool bb)• void operator() (RbtInteractionCenter ∗pIC)
The documentation for this class was generated from the following file:
• RbtInteractionGrid.h
5.284 RbtNM::Simplex< DataType, ParameterType, Function, Criterion >
Class Template Reference
#include <RbtNMSimplex.h>
Public Member Functions
• Simplex (const Criterion &criterion)• void Optimize (Function &fun)• const ParameterType & GetBestParameters () const• DataType GetBestValue () const• void SetStartPoint (const ParameterType &point)• void SetDelta (DataType delta)• void SetDelta (ParameterType deltas)
5.284.1 Detailed Description
template<class DataType, class ParameterType, class Function, class Criterion>class RbtNM::Simplex< DataType, ParameterType, Function, Criterion >
The Nelder-Mead Simplex algorithm Complies to a simple and standard interface
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5.285 Singleton< singleton_type > Class Template Reference 189
Parameters
DataType is the type of inner values to consider
ParameterType is the type of ParameterType (Eigen if possible)
Function is the type of Function to optimize
Criterion is the type of the stopping Criterion
5.284.2 Member Function Documentation
5.284.2.1 GetBestParameters()
template<class DataType , class ParameterType , class Function , class Criterion >
const ParameterType& RbtNM::Simplex< DataType, ParameterType, Function, Criterion >::GetBest←↩
Parameters ( ) const [inline]
Retrieves the best parameters
5.284.2.2 GetBestValue()
template<class DataType , class ParameterType , class Function , class Criterion >
DataType RbtNM::Simplex< DataType, ParameterType, Function, Criterion >::GetBestValue ( )
const [inline]
Retrieves the best final value
The documentation for this class was generated from the following file:
• RbtNMSimplex.h
5.285 Singleton< singleton_type > Class Template Reference
Static Public Member Functions
• static singleton_type & instance ()
Protected Types
• enum action { DESTROY, CREATE, GET }
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190 Class Documentation
Static Protected Member Functions
• static singleton_type ∗ object (const action &a)
The documentation for this class was generated from the following file:
• Singleton.h
5.286 SmartPtr< T > Class Template Reference
Public Member Functions
• SmartPtr (T ∗pT)• SmartPtr (const SmartPtr< T > &sp)• template<class T2 >
SmartPtr (const SmartPtr< T2 > &sp)• const SmartPtr< T > & operator= (const SmartPtr< T > &sp)• template<class T2 >
const SmartPtr< T > & operator= (const SmartPtr< T2 > &sp)• bool Null () const• unsigned ∗ GetCountPtr () const• T ∗ Ptr ()• const T ∗ Ptr () const• void SetNull ()• T ∗ operator-> ()• const T ∗ operator-> () const• T & operator∗ ()• const T & operator∗ () const• operator T∗ () const
The documentation for this class was generated from the following file:
• RbtSmartPointer.h
5.287 RbtNM::State< DataType, ParameterType > Struct TemplateReference
#include <RbtNMState.h>
Public Attributes
• ParameterType bestParameters• DataType bestValue• ParameterType currentParameters• DataType currentValue• ParameterType formerParameters• DataType formerValue• long iteration
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5.288 Rbt::TranslateAtom Class Reference 191
5.287.1 Detailed Description
template<class DataType, class ParameterType>struct RbtNM::State< DataType, ParameterType >
Optimization state for an optimizer
The documentation for this struct was generated from the following file:
• RbtNMState.h
5.288 Rbt::TranslateAtom Class Reference
Public Member Functions
• TranslateAtom (const RbtVector &vv)• void operator() (RbtAtom ∗pAtom)
The documentation for this class was generated from the following file:
• RbtAtom.h
5.289 Rbt::TranslateAtomIfSelected Class Reference
Public Member Functions
• TranslateAtomIfSelected (const RbtVector &vv)• void operator() (RbtAtom ∗pAtom)
The documentation for this class was generated from the following file:
• RbtAtom.h
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192 Class Documentation
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Chapter 6
File Documentation
6.1 RbtCSVFileSink.h File Reference
#include "RbtBaseMolecularFileSink.h"#include "RbtElementFileSource.h"
Classes
• class RbtCSVFileSink
Typedefs
• typedef SmartPtr< RbtCSVFileSink > RbtCSVFileSinkPtr
6.1.1 Detailed Description
Outputs RbtModel(s) to CSV files.
194 File Documentation
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Index
_CTRbtPMFIdxSF, 146
_PMFDIRRbtPMFIdxSF, 146
∼RbtPMFIdxSFRbtPMFIdxSF, 145
CharmmType, 21
EvaluateVisitor, 22
FilterAddExp, 23FilterAndExp, 23FilterDivExp, 24FilterExpExp, 24FilterIfExp, 25FilterLogExp, 25FilterMulExp, 26FilterSubExp, 26FilterVbleExp, 27
GetBestParametersRbtNM::Simplex< DataType, ParameterType,
Function, Criterion >, 189GetBestValue
RbtNM::Simplex< DataType, ParameterType,Function, Criterion >, 189
GetLinearCloseRangeValueRbtPMFIdxSF, 145
GetPMFfor_lCRbtSetupPMFSF, 163
HHS_Solvation, 28
OccupancyTest, 50
PrettyPrintVisitor, 52PrintVisitor, 52
RawScoreRbtPMFIdxSF, 145
Rbt::CyclicAtom, 22Rbt::GenomeCmp_Score, 27Rbt::InitHHS, 29Rbt::InteractionCenterCmp, 29Rbt::InvertSelectAtom, 30Rbt::isAtom_12Connected, 30Rbt::isAtom_13Connected, 30Rbt::isAtom_eq, 31Rbt::isAtomAnionic, 31Rbt::isAtomBridgehead, 31
Rbt::isAtomCationic, 32Rbt::isAtomCharged, 32Rbt::isAtomCyclic, 33Rbt::isAtomEnabled, 33Rbt::isAtomExtended, 33Rbt::isAtomGuanidiniumCarbon, 34Rbt::isAtomHBondAcceptor, 34Rbt::isAtomHBondDonor, 35Rbt::isAtomicNo_eq, 35Rbt::isAtomId_eq, 35Rbt::isAtomInsideCuboid, 36Rbt::isAtomInsideSphere, 37Rbt::isAtomIonic, 37Rbt::isAtomLipophilic, 37Rbt::isAtomMetal, 38Rbt::isAtomName_eq, 38Rbt::isAtomNearCoordList, 39Rbt::isAtomNegCharged, 39Rbt::isAtomPlanar, 39Rbt::isAtomPosCharged, 40Rbt::isAtomPtr_eq, 40Rbt::isAtomRNA, 41Rbt::isAtomSelected, 41Rbt::isBond_eq, 41Rbt::isBondAmide, 42Rbt::isBondCyclic, 42Rbt::isBondPtr_eq, 43Rbt::isBondRotatable, 43Rbt::isBondSelected, 43Rbt::isBondToNH3, 44Rbt::isBondToOH, 44Rbt::isCavityNearCoord, 45Rbt::isCoordinationNumber_eq, 45Rbt::isFFType_eq, 46Rbt::isGenome_eq, 46Rbt::isHHSSelected, 46Rbt::isHHSType_eq, 47Rbt::isHybridState_eq, 47Rbt::isInteractionCenterSelected, 48Rbt::isInteractionD_lt, 48Rbt::isPiAtom, 48Rbt::isSegmentName_eq, 49Rbt::isSubunitId_eq, 49Rbt::isSubunitName_eq, 50Rbt::OverlapHHS, 51Rbt::OverlapVariableHHS, 51Rbt::PartitionHHS, 51Rbt::RbtAnn_Cmp_AtomId2, 54Rbt::RbtAtomPtrCmp_AtomicNo, 59
196 INDEX
Rbt::RbtAtomPtrCmp_AtomId, 59Rbt::RbtAtomPtrCmp_AtomName, 59Rbt::RbtAtomPtrCmp_Ptr, 59Rbt::RbtBondPCmp_BondId, 76Rbt::RbtCavityPtrCmp_Distance, 79Rbt::RbtCavityPtrCmp_Volume, 79Rbt::RestoreHHS, 186Rbt::RotateAtomUsingQuat, 186Rbt::RotateAtomUsingQuatIfSelected, 187Rbt::SaveHHS, 187Rbt::SelectAtom, 188Rbt::SelectFlexAtoms, 188Rbt::SelectInteractionCenter, 188Rbt::TranslateAtom, 191Rbt::TranslateAtomIfSelected, 191RbtAlignTransform, 53RbtAnnotation, 54RbtAnnotationHandler, 55RbtAromIdxSF, 55RbtAssert, 56RbtAtom, 57RbtBadArgument, 60RbtBadReceptorFile, 60RbtBaseBiMolTransform, 61RbtBaseFileSink, 61RbtBaseFileSource, 62RbtBaseGrid, 63RbtBaseIdxSF, 65RbtBaseInterSF, 66RbtBaseIntraSF, 67RbtBaseMolecularDataSource, 68RbtBaseMolecularFileSink, 68RbtBaseMolecularFileSource, 69RbtBaseObject, 71RbtBaseSF, 72RbtBaseTransform, 73RbtBaseUniMolTransform, 74RbtBiMolWorkSpace, 75RbtBond, 76RbtCavity, 77RbtCavityFillSF, 77RbtCavityGridSF, 78RbtCavityGridSF::HeavyAtomFactory, 28RbtCellContext, 79RbtCellTokenIter, 80RbtCharmmDataSource, 81RbtCharmmTypesFileSource, 81RbtChrom, 81RbtChromDihedralElement, 82RbtChromDihedralRefData, 83RbtChromElement, 84RbtChromFactory, 85RbtChromOccupancyElement, 86RbtChromOccupancyRefData, 87RbtChromPositionElement, 87RbtChromPositionRefData, 88RbtChromTest, 89RbtCommands, 90
RbtConstraint, 90RbtConstSF, 92RbtContext, 92RbtCoord, 93RbtCrdFileSink, 94RbtCrdFileSource, 95RbtCSVFileSink, 95RbtCSVFileSink.h, 193RbtDihedral, 96RbtDihedral::prms, 53RbtDihedralIntraSF, 96RbtDihedralSF, 97RbtDihedralTargetSF, 98RbtDirectorySource, 98RbtDirIsNotAccessible, 99RbtDockingError, 100RbtDockingSite, 100RbtDockingSite::isAtomInRange, 36RbtElementData, 101RbtElementFileSource, 101RbtEnvNotDefined, 102RbtError, 102RbtEuler, 103RbtFFTGrid, 104RbtFFTPeak, 105RbtFileError, 105RbtFileMissingParameter, 106RbtFileParseError, 106RbtFileReadError, 107RbtFileWriteError, 107RbtFilter, 108RbtFilterExpression, 109RbtFilterExpressionVisitor, 110RbtFlexAtomFactory, 110RbtFlexData, 111RbtFlexDataVisitor, 111RbtGATransform, 112RbtGenome, 113RbtHBAConstraint, 113RbtHBDConstraint, 114RbtHeavyConstraint, 114RbtHHSType, 115RbtHydroAliphaticConstraint, 116RbtHydroAromaticConstraint, 116RbtHydroConstraint, 117RbtInteractionCenter, 117RbtInteractionGrid, 118RbtInteractionGridTemplate< T >, 119RbtInteractionGridTemplatePtr< T >, 120RbtInteractionNode< T >, 120RbtInteractionNodeList< T >, 120RbtInteractionNodeListMap< T >, 121RbtInteractionNodeListMapConstIter< T >, 121RbtInteractionNodeListMapIter< T >, 121RbtInvalidRequest, 122RbtLigandError, 122RbtLigandFlexData, 123RbtLigandSiteMapper, 124
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INDEX 197
RbtMCStats, 124RbtMdlFileSink, 125RbtMdlFileSource, 126RbtModel, 126RbtModelError, 128RbtModelMutator, 129RbtMOEGrid, 129RbtMOEGridPoint, 130RbtMOEGridShape, 130RbtMOL2FileSource, 130RbtMOL2Substructure, 131RbtNegChargeConstraint, 131RbtNM::AndCriteria< Criteria1, Criteria2 >, 21RbtNM::IterationCriterion, 50RbtNM::RelativeValueCriterion< DataType >, 186RbtNM::Simplex< DataType, ParameterType, Function,
Criterion >, 188GetBestParameters, 189GetBestValue, 189
RbtNM::State< DataType, ParameterType >, 190RbtNmrRestraintFileSource, 132RbtNmrSF, 133RbtNoeEndAtoms, 133RbtNoeEndNames, 134RbtNoeRestraintAtoms, 134RbtNoeRestraintNames, 135RbtNoFileInDir, 135RbtNonBondedGrid, 135RbtNonBondedHHSGrid, 136RbtNullTransform, 137RbtObserver, 138RbtParameterFileSource, 139RbtParamHandler, 139RbtParser, 140RbtPdbFileSource, 140RbtPharmaSF, 141RbtPlane, 142RbtPMFDirSource, 142RbtPMFGridSF, 143RbtPMFIdxSF, 144
_CT, 146_PMFDIR, 146∼RbtPMFIdxSF, 145GetLinearCloseRangeValue, 145RawScore, 145RbtPMFIdxSF, 145SetupLigand, 145SetupReceptor, 145SetupScore, 146Update, 146
RbtPMFValue, 147RbtPolarIdxSF, 147RbtPolarIntraSF, 148RbtPolarSF, 149RbtPolarSF::f1prms, 22RbtPopulation, 150RbtPosChargeConstraint, 151RbtPrincipalAxes, 151
RbtPRMFactory, 152RbtPseudoAtom, 152RbtPsfFileSink, 153RbtPsfFileSource, 153RbtQuat, 154RbtRand, 155RbtRandLigTransform, 155RbtRandPopTransform, 156RbtRealGrid, 157RbtReceptorFlexData, 158RbtRequest, 159RbtRequestHandler, 159RbtRingAromaticConstraint, 160RbtRotSF, 160RbtSAIdxSF, 161RbtSetupPMFSF, 162
GetPMFfor_lC, 163RbtSetupPolarSF, 163RbtSetupSASF, 164RbtSFAgg, 165RbtSFDisableRequest, 166RbtSFEnableRequest, 166RbtSFFactory, 167RbtSFPartitionRequest, 167RbtSFSetParamRequest, 167RbtSimAnnTransform, 168RbtSimpleSolvationParameters, 169RbtSimplexCostFunction, 169RbtSimplexTransform, 170RbtSiteMapper, 171RbtSiteMapperFactory, 171RbtSolventFlexData, 172RbtSphereSiteMapper, 172RbtStdRestraintAtoms, 173RbtStdRestraintNames, 173RbtStringContext, 174RbtStringTokenIter, 174RbtStringTooLong, 175RbtSubject, 175RbtTetherSF, 176RbtToken, 177RbtTokenIter, 177RbtTransformAgg, 178RbtTransformFactory, 179RbtTriposAtomType, 179RbtTriposAtomType::info, 29RbtVariant, 180RbtVble, 180RbtVdwGridSF, 181RbtVdwIdxSF, 182RbtVdwIntraSF, 183RbtVdwSF, 184RbtWorkSpace, 185
SearchTest, 187SetupLigand
RbtPMFIdxSF, 145SetupReceptor
RbtPMFIdxSF, 145
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198 INDEX
SetupScoreRbtPMFIdxSF, 146
Singleton< singleton_type >, 189SmartPtr< T >, 190
UpdateRbtPMFIdxSF, 146
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