fu (fumodel and fuplot) Programming Guidecbi-society.org/taikai/taikai13/fu-ProgramingGuide-5.pdf9/py2exe-0.6.9.win32-py2.7.exe/ 4-2 Making executable for Windows （ fumodel.exe and

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fu (fumodel and fuplot) Programming Guide

May 30, 2013

ProgrammingProgrammingProgrammingProgramming GuideGuideGuideGuide

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Table of Contents

1. Introduction ... 1

2. Copyright and license ... 1

3. Contributors ... 2

4. Programming environment ... 2

4-1 Installing python and site-packages ... 2

4-2 Making executable for Windows... 3

4-3 Integrated development environment software ... 3

5. Structure and modules of fu ... 3

5-1 Structure of program ... 3

5-2 Modules ... 5

5-3 Class and instance of fu ... 5

(1)Class and instance of fumodel program ... 5

(2)Class and instance of fuplot program ... 6

6. Class and its attributes and methods of fu ... 6

6-1 fuModel class (fumodel.py)...main program of fumodel ... 6

(1)attributes and their default values ... 6

(2) methods ... 7

6-2 fuMole class ... 20


(2)methods ... 20

6-3 Atom class ... 30


(2)methods ... 31

6-4 fuView class ... 32


(2)methods ... 33

6-5 fuCtrlFlag class ... 38

(1)attributes ... 38

(2)methods ... 38

6-6 fuPlot class ... 38

(1)methods ... 38

6-7 FMOProperty class ... 43


(2)methods ... 44

4

6-8 fuGraph class(fugraph) ... 45

(1)methods ... 45

6-9 BarGraph class ... 47

(1)attributes and their defaults ... 47

(2)methods ... 48

6-10 TileGraph class ... 50

(1)attributes and their defaults ... 50

(2)methods ... 51

6-11 MatPlotLib_Frm class ... 53

(1)methods ... 53

6-12 fulib module ... 54

(1) methods ... 54

6-13 Class in fupanel.py module ... 57

7. Miscellaneous ... 58

7-1 Note on sequence number of atoms and 'TER' ... 58

7-2 Types of AddHydrogen ... 58

7-3 Tutorials ... 59

(1) tutorial_01: create window with StatusBar and Menu ... 59

(2) tutorial_02: read PDB file and use PyCrust ... 59

(3) tutorial_03: use of fuView class in fuview.py ... 59

(4) tutorial_04: use of fuMole class in fumole.py

and fuView class in fuView.py ... 59

(5) tutorial_05: use of BarGraph class in fugraph.py ... 60

(6) tutorial_06: use of TileGraph class in fugraph.py ... 60

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1. Introduction

This software is developed to assist modeling of molecules, generation

of FMO[1] input data for GAMESS[2], and visualization of FMO results.

This software is written in Python as a GUI and may be useful to treat

large molecules not only for FMO but also for other large scale

computations. This software is developed by "FMO User Group"[3]. We hope

that this software become a partner in your research.

We thank CMSI[4] for the financial support of this work.

[1] http://www.msg.ameslab.gov/gamess/

[2] http://staff.aist.go.jp/d.g.fedorov/

[3] http://ma.cms-initiative.jp/community

Everyone who is interested in FMO is welcome to join the FMO User

Group.

[4] http://www.cms-initiative.jp/en?set_language=en

2. Copyright and license

The source codes of the program is distributed as public domain software.

The copyright and terms and conditions for use, reproduction, and

distribution are described bellow(The BSD 2-Clause License).

Copyright (c) 2013, FMO User Group. All rights reserved.

TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

Redistribution and use in source and binary forms, with or without

modification, are permitted provided that the following conditions are

met:

• Redistributions of source code must retain the above copyright

notice, this list of conditions and the following disclaimer.

• Redistributions in binary form must reproduce the above copyright

notice, this list of conditions and the following disclaimer in the

documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS

IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED

TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A

PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER

2

OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,

EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,

PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR

PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF

LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING

NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS

This software is used with runtime libraries of python, wxpython and

so on. When you distribute fu with these libraries, you should respect

their corresponding licenses.

3. Contributors

The contributors are listed at the beginning of each module. If you

modify the source codes, please add your name to the contributor list.

4. programming environment

Fu uses python and site-packages, numpy, scipy, wxpython, pyOpenGL,

and MatPlotLib. You have to use consistent versions of python and the

site packages. We started the development of fu at July 2012 and employed

the 32 bit version of python 2.7. The software necessary for the

development of fu is described below for your convenience. Download

this software if necessary.

4-1 Installing python and site-packages

1)Python version2.7, Windows 32bit version

Python 2.7.5 Windows Installer(Windows binary -- does not include

source) in http://www.python.org/download/

2)numpy-1.6.2

numpy-1.6.2-win32-superpack-python2.7.exe in

http://sourceforge.net/projects/numpy/files/NumPy/1.6.2/

3)scipy-0.11.0b1

scipy-0.11.0b1-win32-superpack-python2.7.exe in

http://sourceforge.net/projects/scipy/files/scipy/0.11.0b1/

4)wxPython(wx-2.8-msw-unicode)

wxPython2.8-win32-unicode-py27 in

http://www.wxpython.org/download.php

http://www.python.org/ftp/python/2.7.4/python-2.7.4.msi

http://sourceforge.net/projects/numpy/files/NumPy/1.6.2/numpy-1.6.2-win32-superpack-python2.7.exe/download

http://sourceforge.net/projects/scipy/files/scipy/0.11.0b1/scipy-0.11.0b1-win32-superpack-python2.7.exe/download

3

5)PyOpenGL-3.0.2

PyOpenGL-3.0.2.win32-py2.7.exe in

http://www.lfd.uci.edu/~gohlke/pythonlibs/

6)matplotlib-1.2.0

matplotlib-1.2.0.win32-py2.7.exe in

https://github.com/matplotlib/matplotlib/downloads

7)py2exe（py2exe-0.6.9.win32-py2.7）

py2exe-0.6.9.win32-py2.7 in

http://sourceforge.jp/projects/sfnet_py2exe/downloads/py2exe/0.6.

9/py2exe-0.6.9.win32-py2.7.exe/

4-2 Making executable for Windows（fumodel.exe and fuplot.exe）

After installing software described in 4-1, execute setup.bat

in ./src directory. fumodel.exe and fuplot.exe are created in ./dist

folder.

4-3 Integrated development environment software

We use Eclipse with PyDev installation for the development of fu. The

software is obtained from

http://sourceforge.jp/projects/sfnet_eclipse.mirror/downloads/eclip

se-SDK-3.7.2-win32.zip/. PyDev installation is done in the Help menu

of Eclipse. You may find helpful WEB site for using this software.

5. Structure and modules of fu

Fu consists of two programs: fumodel for structure modeling of molecule

and FMO input generation and fuplot for visualization of FMO output.

5-1 Structure of program

The structure of fumodel is shown in Fig.1.

https://github.com/downloads/matplotlib/matplotlib/matplotlib-1.2.0.win32-py2.7.exe

https://github.com/matplotlib/matplotlib/downloads

http://sourceforge.jp/projects/sfnet_eclipse.mirror/downloads/eclipse-SDK-3.7.2-win32.zip/%E3%81%8B%E3%82%89%E3%83%80%E3%82%A6%E3%83%B3%E3%83%AD%E3%83%BC%E3%83%89%E3%81%97%E3%81%9F%E3%80%82PyDev%E7%B5%84%E3%81%BF%E8%BE%BC%E3%81%BF%E3%81%AFeclipse%E3%81%AE

http://sourceforge.jp/projects/sfnet_eclipse.mirror/downloads/eclipse-SDK-3.7.2-win32.zip/%E3%81%8B%E3%82%89%E3%83%80%E3%82%A6%E3%83%B3%E3%83%AD%E3%83%BC%E3%83%89%E3%81%97%E3%81%9F%E3%80%82PyDev%E7%B5%84%E3%81%BF%E8%BE%BC%E3%81%BF%E3%81%AFeclipse%E3%81%AE

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The structure of fuplot is shown in Fig.2. fuModel class used in this

program is a subset excluding modeling related functions.

fuPlot class

（main program）

Fig.2 Structure of fuplot program

fuModel class

(subset)

draw molecule

fuGraph class

draw graph

control draw

molecule

read files and

set plot item

interface to

PyCrust and

MatPlotLib

fuModel class

（main program）

fuModel_Frm class

（main panel）

fuCtrl class

Fig.1 Structure of fumodel program

fuMole class

structureand display

manupulation

accept andcontrol mouse

and keyboard

input

control menu

and widget

input

child panels

accept input

build and draw

molecule

control drawing

molecule

control child

panels

accept menu and

widget input

display molecule

fuView class

draw molecule

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5-2 Modules

Fu has the following modules.

--- modules for fumodel

fumodel.py ... main module of fumodel including the main program

fuctrl.py ... module to handle menu, mouse and key board input

fumole.py ... module for molecular structure and drawing data

manipulations

fupanel.py ... module includes child panels

fuview.py ... module for molecular model drawing

fulib.py ... global methods

fuconst.py ... global constants

--- modules for fuplot

fuplot.py ... main program of fuplot

fugraph.py ... module for drawing graphs

---

setupmdl.py ... generates fumodel.exe with py2exe

setupplt.py ... generate fuplot.exe with py2exe

（execute setup.bat for generating Windows7 executable）

Beside the above, several tutorial programs (they are not used in fu)

are provided for convenience to study programming with fu (see Sec.7-3)).

5-3 Class and instance of fu

(1)Important class and instance of fumodel program

fumodel (an instance of fuModel class in fumodel.py)

|--- mollst[mol] attribute (mol: an instance of fuMole class

| in fumole.py)

|--- mol[atom] attribute (atom: an instance of Atom class

in fumole.py)

|--- ctrlflag (an instance of CtrlFlag class in fuctrl.py)

|--- frame (an instance of fuModel_Frm class in fumodel.py)

|--- view (an instance of fuView class in fuview.py)

|--- ctrl (an instance of fuCtrl class in fuctrl.py)

|--- menu (an instance of MenuCtrl class in

| fuctrl.py)

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|--- input (an instance of InputCtrl class in

fuctrl.py)

|--- pycrust (an instance of wx.py.crust.CrustFrame)

|--- ctrlwin (an instance of ControlPanel_Frm in fupanel.py)

|--- gmsinputwin (an instance of GamessInput_Frm class in

| fupanel.py)

|--- treewin (an instance of TreeSelector_Frm class in

| fupanel.py)

|--- namewin (an instance of NameSelector_Frm class in

fupanel.py)

(2) Important class and instance of fuplot program

fuplot (instance of fuPlot class in fuplot.py)

|--- fmodatadic[name] attribute (name: an instance of

| FMOProperty class in fuplot.py)

|--- graphname[name] attribute (name: an instance of fuGraph

| class in fuplot.py)

|--- graph (an instance of BarGraph or TileGraph class

in fugraph.py)

|--- molview (an instance of fuModel class in fumodel.py)

|--- mpl (an instance of MatPlotLib_Frm class in fugraph.py)

|--- figure (an in stance of matplotlib.figure)

|--- canvas (an instance of FigureCanvasWxAgg)

|--- pycrust (an instance of wx.py.crust.CrustFrame)

6. Class and its attributes and methods of fu

6-1 fuModel class (fumodel.py)...main program of fumodel

(1)attributes and their default values

curmol=-1 # number of current fuMole instance in mollst[]

# and wrk=mollst[curmol]

mollst=[] # list to store fuMole instance

molnam=[] # name of molecule

files=[] # input file name of molecule

wrkmolnam='' # name of current fuMole instance

mhtdatadic={} # mht data dic {'name0':[mht data...],'name1':[mht

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# data],..}

autoaddhydrogen=True # try to add hydrogen in loaded PDB data

(2) methods

AddBondUseBondLength(): add bond data using bond length

AddBondUseFrameData(): add bond data using molecular frame data

(.mht）

AddChainName(): add/change peptide chain name

AddGroup1H():add one hydrogen to selected atoms

AddGroup2H():add two hydrogens to selected atoms

AddGroup3H():add three hydrogens to selected atoms

AddHydrogenToAAResidue():add hydrogens to selected amino acid

residues

AddHydrogenToCutAA(): add hydrogens at C and N terminus

AddHydrogenToWater():add hydrogens to waters

AddHydrogenUseBondLength():add hydrogen based on atomic

distance

AddHydrogenUseFrameData(): add hydrogens using molecular frame

data(.mht)

AddItemCBoxMol(molnam):add molecule name to combo box list

AssignAAAtomCharge(): assign charge to amino acid residue atoms

AssignIonChg(chg): assign charge to ion

AssignLayer(layer): assign selected atoms to specified layer

layer(int): layer number

AssignLayerUndo():Undo layer assignment(under construction,

15May2013)

AtomAngle(atm0,atm1,atm2): get angle of atoms

atom0(int): sequence number of atom



ret=angle(float): angle between atom0-atom1 and atom2-atom1

AutoAddHydrogen(on): auto addition of hydrogens to polypeptide

and water molecules in reading PDB file

on(True/False): on/off flag

BuildMol(filnam,mol): make fuMole instance from data in PDB file

filename(string): file name

mol(fuMole instance): None except merge molecule

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ChangeAtomColor(item,col): change atom color

item(string): key word, 'by element','by chain',

or 'color pallet'

col(list): color

ChangeBondKind(atmpairlst,bndknd): change bond kind. under

construction(15 May 2013)

ChangeStickBold(bold): change thickness of bond line

bold(int): thickness, default=2

CheckShortContact(mol1,mol2): check short contact between mol1

and mol2

ret=nsht(int): number of short contact

,rmin(float): shortest distance

ClearAllLayer(): cancel all layer assignment

ClearBDA(): remove all BDA points

ClearClipboard():empty clipboard

ClearLayer(layer):cancel layer assignment in specified layer

layer(int): layer number

ConsoleMessage(mess):print message on PyCrust console

CopyMolBitmapToClipboard():copy screen image to clipboard in

bitmap data

CopyMolToClipboard(): copy selected atom data to clipboard

CountEnvSelAtm():count number of environment atoms

ret=nenv(int): number of environment atoms

,lst(list): list of sequence numbers o environment atoms

CreateFrame(parent,fumode,size): create fumodel main panel

DeleteBonds(kind):delete bond kind data

DeleteHydrogens():delete hydrogen atoms in selected

DeleteNonBonded():delete non-bonded atoms

DeleteSelected():delete selected atoms

DeleteTerAtoms():delete 'TER' atom (see Sec7-1))

DeleteVdwBond():delete vdw contact data（trial base)

DeleteWater(): delete waters in selected

DispAtomAngle(atm0,atm1,atm2):display angle on status bar

atom0(int): atom number



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DrawBDAPoint(on): draw BDA points


DrawChainKite(on): in preparation (15 May 2013)

DrawChainTube(on): draw tube peptide chain


DrawDistance(on): draw interatomic distance


DrawFormalCharge(on): draw formal charge


DrawLabelAtm(on,case): draw atom name


case(int): 0 name only, 1 name and atom number

DrawLabelElm(on,case): draw element name

case(int): 0 name only, 1 name and sequence number of atom


DrawLabelFrg(on): draw fragment name


DrawLabelRes(on,case): draw residue name

case(int): 0 name only, 1 name and residue number

on(True/False):on/off flag

DrawLayer(on):draw atoms in layer color

on(Tre/False): on/off flag

DrawMol(updated): draw molecule

updated(True/False): flag to force to make makedispaly list

DrawPlotData(on,save,item,pltcol,ifrg): draw molecule in fuplot

program


save,...: see source codes for details

DrawVdwBond(on): draw vdW bond line (trial base)


FindBondSeqNmb(atm1,atm2): find bond kind between atm1 and atm2

atm1(int): sequence number of atom


ret=nmb(int): bond kind code

FindFragNmb(frgnam):find fragment number

frgnam(string): fragment name

10

ret=ifrg(int): fragment number

FindGrpNmb(ia,grplst): find group atoms(under construction,

15May2013)

ia(int): sequence number of atom

grplst(list): group list containing group atom numbers

ret=igr(int): group number

FindMinMaxXYZ(mol): find min/max coordinates of atoms

mol(fuMole instance): mol instance

ret=xmin,xmax,ymin,ymax,zmin,zmax (all float)

FindRadiusAtoms(radius):find atoms within radius distance from

selected atom(s)

radius(float): radius

ret=nmb(int): number of atoms

,lst(list): atom sequence number list

FindRadiusResidue(radius): find residues within radius distance

from selected atom(s)




FitToScreen(drw): resize and draw molecules in screen

FogEnable(on): Enable/disable Fog


FragmentAARes(case): fragment amino acid residue

case(int): 0 1res/1frg, 1 1res/1frg except GLY, 2

2res/1frg

FragmentNonAARes(): fragment non-amino acid residue

GetFragName(ifrg): get fragment name of ifrg-th fragment

ifrg(int): fragment number

ret=nam(string): fragment name

GetMaxAtmNmb(): get maximum atom number

ret=atmnmb(int): atom number

GetMaxResNmb(): get maximum number of residue

ret=resnmb(int): residue number

GetMouSelMode(): get mouse select mode

GetMouseMoveVector(dif): get mouse migration length

dif(int): mouse migration length

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ret=mov(int): length of mouse move

GetMouseRotMatrix(dif):get matrix of rotation in proportion to

mouse move length

dif(int):mouse move length

ret=rotmat(list,3x3): transformation matrix

GetPntAtm(pos,raspos): get sequence number of clicked atom

pos(lsit,(x,y)): mouse position

raspos(list): raster position of all atoms

ret=nmb(int): sequence number of atom

GetRaspos(ith,raspos): get raster position of i-th atom

ith(int): sequence number of atom

raspos(list): raster position of all atoms

ret=x,y (all int): raster position (x,y)

HideEnvironment(on):hide environment atoms

on(True/Fasle): on/off flag

HideHydrogen(on): hide hydrogen atoms


HideSelected(on): hide selected atoms

on(True/Fasle): on/off flag

HideWater(on): hide water molecules


InputAtomName(a): input name and add it to atom "a"

a(int): sequence number of atom

InputBDABAA(bda,baa): input BDA and BAA atoms and set them

bda(int): sequence number of atom

baa(int):sequence number of atom

ListAtomName():make list of atom name

ret=lst(list): atom name list

ListChainName():make list of peptide chain name

ret=lst(list): chain name list

ListDrawAtom():make draw atom list


,lst(list): draw atom list

ListElement():make list of elements

ret=lst(list): element list

listFragmentName():make fragment name list

12

ret=lst(list): fragment name list

ListGroupName():make group name list (under construction,

15May2013)

ret=lst(list): group name list

ListResidueName():make residue name list

ret=lst(list): residue name list

ListSelectedAtom():make selected atom list

ret=nsel(int): number of atoms


ListTargetAtom():make target atom list

ret=lst(list): atom sequence number list

MakeAtomLabel(atm,nameonly):make atom label

atm(int): sequence number of atom

nameonly(int): 0 name and number, 1 name only

ret=lbl(string): label text

MakeBondedAtomGroupList(lst): make list of bonded atoms

ret=lst(list): atom sequence number list

MakeDrawBDAData(): make data for draw BDA point

ret=drwdat(list): draw data list

MakeDrawDistanceData(): make draw data for distance

ret=disdat(list): draw distance data

MakeEnvByList(lst):set environment atoms according to list

lst(list): atom sequence number list

MakeEnvGrpByRadius(selobj,radius): set atoms to environment

which are within radius distance from selected

object atom(s)

selobj(int): select object


,lst(list): atom sequence numbers list

MakeNewMol(case): make a new fuMole instance with zero atoms

case(key word): 'selected atoms' or 'auto'

MakeNonAAResLst(): make list of non-amino acid residues

ret=reslst(list): list of residue naem + residue number

MakeVdwContact():make vdw contacts(trial base)

ManualBDASetting(on): change mouse mode for manual BDA setting


13

MergeFragments(): merge selected fragments

MergeMol(mol): merge molecule 'mol' with current molecule

mol(fuMole instance): molecule to merge

MergeToCurrrent(filename):merge molecules given by PDB file with

current molecule

filename(string): name of PDB file

MessageStatus(mess,loc,col):print message on status bar

mess(string):message text

loc(int): 0: status bar 0, 1:status bar 1

col(string): wx.color name

MessAtomAngle(atm0,atm1,atm2):print angle on status bar




MessAtomDistance(atm0,atm1):print distance between atom0 and

atom1 on status bar



MessAtomLabel(atm,nameonly):print atom name on status bar

atm(int): atom sequence number

nameonly(True/False): True:nameonly, False:name+number

MessAtomTortion(atm0,atm1,atm2,atm3): print tortion angle of

atm0-1-2-3 on statusbar

NewMolecule(): make new molecule with name of "tempxxx"

OpenAssignLayerPanel():open layer assign panel

OpenAtmChgPanel(): open atom charge input panel

OpenControlPanel():open control panel

OpenGamessPanel():open GAMESS input assistant panel

OpenNameSelector(winpos):open Name/number selector panel

OpenPyCrust():open PyCrust console

OpenTreeSelector(winpos):open Tree selector panel

OrgOrient(pdborg,pdbnew): back molecular orientation to

initial

pdborg(string): original PDB file name

pdbnew(string): new PDB file name

14

ret=err(True/False): True error occurred, False:OK

PasteMolFromClipboard():paste molecules from clipboard

PrintMessage(): print Message on PyCrust console

Quit(): quit program

ReadFiles(filename):read file


RemoveEnvGroup():remove environment atoms

RemoveMol(allmol): delete current or all molecules

allmol(True/False): True: all, False: current

RenameItemCBoxMol(itmnmb,newname):rename molecule name in

ComboBox

itmnmb(int): item number

newname(string): molecule name

RenameMolecule(filename): rename tempxxxx with that created from

file name


ResetItemdicCheck(choosen,check): reset check of checkable menu

item

choosen(string): menu item text

check(True/False): on/off flag

ResetPosAtm(): reset pointed atom list

ResetShowAtom(on): reset atom's show flag


RotateSelected(dif): rotate selected atoms

dif(int): mouse move length

RunScriptCmd(script): run commands in python script

script(string): file name (xxxx.py)

SaveAtomColor(save):backup atom's color data

SaveFragmentAs(filename):write fragment information on file

SaveLayerData(save):backup layer data

SaveRasPosZ(value):backup z-raster position data

SaveShwAtm(value): backup atom's show flag

SelectAABackbone():select backbone of polypeptide

SelectAAResidue(): select amino acid residue

SelectAASideChain():select amino acid side chain

SelectAll(selflg): select/deselect all atoms

15

selflg(True/False): select/deselect flag

SelectAllShowAtom(): select all atoms with show flag-on

SelectAtmNam(atmnam,selflg): select/deselect atom with atmnam

atmnam(string*3): atom name


SelectAtomByAtmNmb(lst,selflg):select/deselect atom with

number of atmnmb

lst(list): list of atom numbers


SelectAtomByList(lst,selflg):select/deselect atoms in lst

lst(list): list of atom sequence numbers


SelectAtomByNamNmb(atmnam,atmnmb,selflg):select/deselect

atom by atom name and number


atmnmb(int): atom number


SelectAtomBySeqNmb(lst,selflg): select/deselect atoms by

sequence number

lst(list): sequence number list


SelectByCircle(newx,newy,centeratm,raspos):select atoms being

in sphere created by mouse drug

newx(int): x position of mouse

newy(int): y position of mouse

centeratm(int): atom sequence number at sphere center

raspos(list): raster positions of all atoms

SelectByClick(pntatmhis,selflg): select/deselect clicked

atom(s)

pntatmhis(list): pointed atom history list


SelectByRadius(selobj,radius,flgval):select/deselect objects

being within radius from selected atoms

selobj(int): atom/residue/fragment flag


flgval(True/False): select/deselect flag

16

ret=nsel(int): number of selected atoms

SelectByRectangle(inix,iniy,newx,newy,raspos):select atoms in

rectangle created by mouse drug

inix(int): initial x position of mouse drug

iniy(int): initial y position of mouse drug

newx(int): current x position of mouse

newy(int): current y position of mouse

raspos(list): raster position list

SelectChainByAtmSeqNmb(a,selflg): select/deselect chain which

has "a" atom

a (int): atom sequence number


SelectChainByList(lst,selflg): select chains in lst

lst(list): chain number list

selflg(True/False):select/deselect flag

ret=nsel(int): number of selected/deselected atoms

SelectChainNam(chanam,selflg): select/deselect chain by name

chanam(string*1): chain name


SelectComplement(): complement select/unselect atoms

SelectElmNam(elmnam,selflg):select/deselect atoms by element

elmnam(string*2): element name


SelectEnv(selflg): select/deselect environment atoms


ret=nsel(int): number of select/deselected atoms

SelectFragByAtmSeqNmb(a,selflg): select/deselect fragment

which has "a" atom



SelectFragNam(frgnam,selflg):select/deselect fragment by name



SelectHydrogen():select hydrogen atoms

SelectNonAARes(res,nmb):select non-amino acid residue(s)

res(string*3): residue name

17

nmb(int): residue number

SelectNonAAResidue(): select non-amino acid residues

SelectNonBonded():select non-bonded atom(s)

SelectRes(resnamlst,resnmblst,selflg):select/deselect

residues in name and number list

resnamlst(list): list of residue name

resnmblst(list): residue number list


SelectResByAtmSeqNmb(a,selflg):select/deselect residue which

has "a" atom



SelectResByNmb(resnmblst,selflg):select/deselect residues in

residue number list

resnamlst(list): list of residue numbers


SelectResidueByList(lst,selflg):select/deselect residues in

"lst"

lst(list): residue list


ret=nsel(int): number of selected/deselected atoms

SelectResNam(resnam,selflg):select/deselect residue by name

resnam(string*3): resdiue name


SelectWater():select water moelcule(s)

SetBDAInAAResidue(target): set BDA in amino acid residue(s)

target(list): atom sequence number list of target

SetBDAWrkMol(resnam,bdalst):set BDA to current molecule

SetBondKind(atm1,atm2,bndknd):set bond kind (not implemented)



bndknd(int): bond kind

SetChainColor()：set chain color

ret=ret(True/False): error flag

SetChoosenColor(col):set col to selected atoms

col(list): color data

18

ret=nmb(int): number of set atoms

SetDeselectAll(): deselect all atoms

ret=nmb(int): number of deselected atoms

SetDrawLabelFragmentName()：set fragment name data for draw

SetDrawVdwBond(on):set vdw bond data for draw


SetElementColor():set element color


SetEnvGrpAtom(ith,on):set ith atom to environment



SetFragmentFMOInp(frgnam,indat,bdabaa):set fragment name,its

atoms,and BAA data


indat(list): atom list in fragment (indat data of FMO input)

bdabaa(list): BDA-BAA list

SetLayerColor():set layer color

SetResidueColor():set residue color


SetSection(rot): set section

rot(int): mouse wheel rotation degree

SetSelectAll(selflg):set select/deselect to all atoms


SetSelectAllAtom(mol,selflg):set select/deselect all atoms for

molecule mol


SetSelectedAtom(ith,selflg):set select/deselect to "i-th" atom



SetSelectRes(resnam,resnmb,selflg):set select/deselect to

residue with reanam and resnmb

resnam(string*3): residue name

resnmb(int): residue number



SetTextFont():set text font

19

SetTurnLst(): set turn list for molecules

SetUpDraw(): set up draw data

SetWrkMol(im): set im-th molecule to current, i.e. wrk

im(int): molecule number

ShowAABackboneOnly(on):set show atom flag on/off to main chain

atoms in polypeptide


ShowAASideChainOnly(on): set show atom flag on/off to side chain

atoms in polypeptide


ShowAllAtom():set show atom flag on to all atoms

ShowDrawModel(model):change molecular model

model(int): 0:line,1:stick,2:stick and ball,3:CPK

ShowSelectedOnly(on):set show atom flag on/off to selected atoms


SwitchMol(name): switch current molecule

TortionAngle(atm0,atm1,atm2,atm3): calsulate tortion angle of

atm0-atm1-atm2-atm3

ret=angle(float): angle in degrees

TranslateSelected(dif):translate selected atoms


UpdateMol(mol):set update flag on for "mol" molecule to force

redraw

mol(fuMole instance)

WriteFiles(filename,save): write PDB data on file


save(True/False): for save/save as

SplitAtTER(molnam,pdbmol)@static method :split molecule at TER

molnam(string): name of molecule

pfdbmol(list): pdb data

ret=namdic(dictionary): name dictionary of generated

molecules

,datdic(dictionary): fuMole instance of generated

molecules

,delcondic(dictionary): deleted bonds list at split

SplitWater(molnam,pdbmol)@static method: split waters in

20

molecule

molnam(string): name of molecule

pdbmol(list): pdb molecule data

ret=namdic(dictionary): dictionary of generated molecule

names

,datdic(dictionary): fuMole instance of generated

molecules

6-2 fuMole class (fumole.py)...Structure and drawing data of molecule


molname='' # name of molecule, made from input file name

inpfile='' # input file name

outfile='' # save file name

inpform='' # pdb,xyz,fmoinp,gmsinp,zmt (only pdb is supported)

remark='' # comment

mol=[] # list of Atom instance

bdadic={} # BDA data for fragments

(2)methods

AddAtomAt(at,elm,coord,atmdatdic)：add one atom at

at(int): sequence number of atom to be added at

elm(string*3): element name

coord(list[x,y,z]): coordinate

atmdatdic(dictionary): atom data, see Atom.SetAtomData

AddBDABond(ia,ib)： add BDA

ia(int): sequence number of bda atom

ib(int): sequence number of baa atom

AddBond(a,b,multi)： add bond data

a(int): sequence number of atom in the bond

b(int): sequence number of partner atom

multi(int): bond kind(1:'single',2:'double',3:'triple',

4:'aromatic',5:'HB',6:'CH/pi',7:'vdw')

AddBondInAARes(resnam,resdat)：add bond data to amino acid residue


resdat(list): residue data created by ExtractAARes method

AddBondUseBL(lst)： add bond data based on distance

lst(list): list of target atoms. if empty, all atoms are

21

subjected

AddBondUseMht(lst,mhtdatadic): add bond data using molecular

frame data(.mht)

lst(list): list of target atoms.

mhtdatadic(dictionary): mht data dictionary

AddGroup1Hydrogen(lst): add one hydrogen to atoms in lst

lst(list): target atom list

AddGroup2Hydrogen(lst):add two hydrogens to atoms in lst


AddGroup3Hydrogen(lst):add three hydrogen to atoms in lst


AddHydrogen(at,nh,coord,hnam): add hydrogen at "at" atom

at(int): sequence number of atom to be attached hydrogen(s)

nh(int): number of hydrogens to attach

coord(list): list of hydrogen atom coordinates,

[[x,y,z],[x,y,z],...]

hnam(list): list of hydrogen atom name, [' 1H ',...]

AddHydrogenToAARes(resnam,resdat,ic): add hydrogens to amino acid

residue atoms


resdat(list): residue data from ExtractAARes method

ic: int, ic >=0 for the second and later residue,

=-1 for the first residue

ret=nh(int): number of attached hydrogens

AddHydrogenToMol(at,hname,htype,bndlst,rhx):add hydrogens to

non-polypeptide

at(int): sequence number of atom to be attached

hydrogen(s)

hname(string*4): atom name of the hydrogen(s)

htype(string*3): type of add hydrogen, See Sec.7,2)

bndlst(list): reference atom list, See Sec.7,2)

rhx(float): H-X bond length

ret=nh(int): number of attached hydrogens

AddHydrogenToNterm(lst): add hydrogens at N terminus


AddHydrogenToPeptideNC(lst): add hydrogens at N and C terminus

22

of polypeptide

lst(list): target atoms list

AddHydrogenToProtein(lst): add hydrogen to protein(polypeptide)


AddHydrogenToWaterMol(lst):add hydrogens to water molecule


AddHydrogenUseBL(lst):add hydrogens based on bond length


AddHydrogenUseMht(lst,mhtdatadic): add hydrogens using molecular

frame data(.mht)


mhtdatadic(dictionary): dictionary of mht data

AssignAAResAtmChg(): add charges to amino acid atoms

ret=err(True/False): error flag

CenterOfMass(lst): calculate center of mass of atom group

lst(list): target atoms

ret=com(list [x,y,z]): center of mass coordinate

,pmi(list [[],...]): principal moment of inertia

vectors

ChangeAtomName(a,atmnam,atmnmb): change atom name

a(int): sequence number of atom to be renamed


atmnmb(int): atom number

CheckBDADup(ia,ib): check duplicate BDA

ia(int): sequence number of BDA

ib(int): sequence number of BAA

ret=dup(True/False)

ClearBDABAA(lst): remove BDA/BAA data


CopyMolInstance(): copy current fuMole instance

ret=cpy(fuMole instance)

CountAARes(): count amino acid residue

ret=nres(int): number of amino acid residues

CountAtomsInRes(resnam,resnmb): count number of atoms in residue



23

ret=natm(int): number of atoms

CountHydrogen(lst): count hydrogen atoms


ret=nh(int): number of hydrogen atoms

CountHydrogenOfAtom(a): count hydrogen of atom a



CountNonAARes(): count non-amino acid residues

ret=nres(int): number of residues

CountResH(resnam,resnmb): count hydrogens in residue


CountWater(lst): count water molecules


ret=nw(int): number of water molecules

CreateBDA(ia,ib): set BDA and BAA

ia(int): sequence number of BDA atom

ib(int): sequence number of BAA atom

CreateFrgConDat(): create connect data for fragmentation.

(See Sec.7,1)

DelAllKindBonds(lst): remove all kind of bond data

DelAtom(ia): delete atom

ia(int): sequence number of atom to delete

DelBDABond(ia,ib):delete BDA-BAA bond data

ia(int): sequence number of BDA atom

ib(int): sequence number of BDA atom

DelBond(a,b): delete bond data


b(int): sequence number of atom

DelFrgBDABond(bdalst,ssblst,con) @static method: delete BDA-BAA

bond in fragmentation data

ret=con(list): connect data list

DelHydrogen(lst): delete hydrogen atoms


DelNonBonded(lst):delete non-bonded atoms


DelVdwBond(lst):delete vdW bond data

24


DelWater(lst): delete water molecules


ExtractAARes(resnam,resnmb): extract amino acid residue data



ret=nresatm(int): number of atoms in the residue

,resdat(list): resdiue data

,resatmdic(list): dictionary of residue atoms

FindAddHTypeBL(a): find add hydrogen type(addhtype, sec7 2))

based on bond length

a(int): sequence number of atom to be attached hydrogen

ret=nh(int): number of hydrogens

,htype(list): addhtype list

,bndlst(list): reference atoms list

,rhx(float): bond length

FindAddHTypeMht(a,mhtdat): find addhtype based on molecular frame

data(mht)

a(int): sequence number of atom to which hydrogen(s) are

attached

mhtdat(string*3): name of mht data

ret=nh: number of hydrogens

,htype(list): addhtype list

,bndlst(list): reference atoms list

,rhxfloat): bond length

FindAtmNamInRes(atmnam,ist,resnam,resnmb): find atom with atmnam

in residue


ist(int): start atom number

reanam(string*3): residiue name


ret=ia(int): >=0 found, <0 not found

FindCalphaInRes(resnam,resnmb): find c-alpha in residue

ret=ic(int): >=0 found, <0 not found

FindCovalentBondedAtom(elmlst,coordlst): find covalent bonded

atoms

25

ret=bndlst(list): bonded atom list

FindItemNmb(lst,b): find item number

lst(list): list to be searched

b(int): number to be searched

ret=found(int): >=0 found, <0 not found

FindMaxAtmNmb(): find maximum atom number

ret=maxatmnmb(int): number

FindMaxResNmb(): find minimum atom number

ret=maxresnmb(int): number

FindNextAtom(ia,atmnam): find next atom

ia(int): start atom number for search

atmnam(string*4): atom name to be searched

ret=nmb(int): >=0 found, <0 not found

FindNmbInGrpLst(ia,grplst): find number in group list

ia(int): number to be found


FindPrevAtom(ia,atmnam): find previous atom

ia(int): the last atom to be searched

atmnam(string*4): atom name to be searched


FindResAtmSeqNmb(resdat,conatm): find sequence number of atom

with name coname

resdat(list): residue data


FindSSBond(idx): find SS bond

idx(list): index list

ret=sslst(list): ss bonded atom list

FrgAARes(lst,case): fragment amino acid residue


case(int): 0:1res/1frg, 1:1res/1frg except GLY, 2:2res/1frg

FrgMergeGly(): merge Gly to neighbor

ret=ndel(int): number of removed fragments

FrgMergeTwoRes(): merge two fragments

ret=ndel(int): number of removed fragments

FrgNonAARes(lst): fragment non-amino acid residue


26

GetBDADicValue(keywd): get BDA dictionary value(BAA atom)

ret=val(int): sequence number of BAA

GetCCAddAtmType1A1(atmlst,r): get Cartesian coordinate of

addhtype 1A1(Sec7,2))

atmlst(list): bonded atmm list

r(float): bond length of H-X


,coord(list): list of coordinates

GetCCAddAtmType1A2(atmlst,r): get cartesian coordinates of

addtype 1A2 (Sec7,2)





GetCCAddAtmType1A3(atmlst,r,bang,trans):get Cartesian

coordinates of addtype 1A3 (Sec7,2)




GetCCAddAtmType2A1(atmlst,r):get Cartesian coordinates of














atmlst(list): bonded atom list



27


GetCCOfWaterHydrogen(cow): get Cartesian coordinates hydrogens

cow(list): coordinates of oxygen atom

ret=chw(list,[x,y,z],...]): coordinate list

GetNumberOfBDA(): get number of BDA

ret=nbda(int): number of BDAs

GetNumberOfFrgConDat(): get number of fragment connect data

ret=ncon(int): number of connect data

InterAtomDistance(a,b): calculate interatomic distance between a

and b


b(int): sequence number of atom

ret=r(float): distance

IsBAAAtom(ia): is ia BAA atom?


ret=ret(True/False)

IsCaAtCterminal(ia): is ia c-alpha in c-terminal residue?


ret=ret(True/False)

MakeAAResDic(): make residue dictionary of amino acid residue

ret=resdic(dictionary): residue dictionary

MakeBDALst(idx): make BDA list


ret=bdalst(list): list of BDA

MakeBondedAtomGroupList(condat): make bonded atom group list

condat(list): connect data list

ret=grplst(list): list of atoms

MakeChainDic(): make dictionary of chains

ret=chaindic(dictionary): chain dictionary

MakeDrawAtomData(lst): make draw atom data


ret=drwdat(list): draw atom data list

MakeDrawBondData(lst): make draw bond data


ret=drwdat(list): draw bond data list

MakeDrawChainTubeData(lst): make draw chain tube data

28


ret=drwdat(list): draw data

MakeElmDic(): make dictionary of element

ret=elmdic(dictionary): element dictionary

MakeFrgAtmLst(grplst,idx): make fragment atom list

grplst(list): group atom list


ret=resnam(string): residue name

,frglst(lsit): fragment atoms list

MakeFrgConDat(idx): make connect data for fragmentation


ret=con(list): connect data list

MakeNonAAResDic(): make dictionary of non-amino acid residues

ret=resdic(dictionary)

MakeSSBond(lst): make SS bond(s)


ret=nss(int): number of SS bonds

MergeFrg(lst): merge fragment


Message(mess,dev,color): print Message on status bar

mess(string): message

dev(int): 0: status bar 0, 1:status bar 1

color(list): text color

RemoveBDA(ia,ib): remove BDA(ia) and BAA(ib)


ib(int): sequence number of atom

RenumberAtmNmb(): renumber atom number

RenumberConDat(): renumber connect data

RenumberIndexForFrg(): renumber index for fragmentation

ret=idx(int): index list

ResetBDADic(): reset dictionary of BDA

SetBDAInAARes(lst): set BDAs in amino acid residue


SetBDAInNonAARes(lst): set BDA in non-amino acid residue


ret=nbda(int): number of BDA

29

SetBndMulti(atom1,atom2,bndmulti): set bond kind



bndmulti(int): bond kind code

SetDefaultAtmRad(lst): set default atom radius to all toms

SetDefaultColor(lst): set default atom color to all atoms

SetDefaultVdwRad(lst): set default vdw radius to all atoms

SetFMOXYZAtoms(inpfile): read atom coordinates from FMO input file

and set them to molecule data

(fuMole.mol)

inpfile(string): file name of FMO input file

SetFragmentName(): set fragment name

SetFragmentUseFMOIndat(frgnam,indat,bdabaa): set fragment data

using data in FMO input

frgnam(list): fragment name list

indat(list): indat data in FMO input

bdabaa(list): BDA-BAA data in FMO input

SetPDBAtoms(pdbmol): set pdb atom data to mol attribute of fuMole

instance

pdbmol(list): pdb molecule data

SetToBDADic(ia,ib): set ia-ib to BDA dictionary


ib(int): sequence number of atom

WriteFrgDat(filfrg): write fragment information on file

filfrg(string): file name

WritePDBMol(filename,parnam,parfilnam,con): write pdb dat on file

filename8string): file name

parnam(string): parent molecule name

parfilnam(string): parent PDB file name

con(True/False): flag for write/don’t-write connect data

AtmNamElm(atmnam) @static method: get element from atom name

ret=elm(string*2): element name

BondAtmGrp(condat,ssblst) @static method: get bonded atom group

condat(list): connect data list

ssblst(list): SS bond list

ret=grplst (list): bonded atom group list

30

GetOrgSeqNmb(ith,idx) @static method: get original sequence

number of i-th atom



ret=nmb(int): atom number in original molecule

MakeFrgTable(frglst) @static method: make fragment table for .frg

file

frglst(list): fragment data list

ret=frgtbl(list): fragment table data

MakeMolName(filnam) @static method: make molecular name

filnam(string): file name

ret=name(string): molecule name(i.e. file name with out

extension)

PrintAtomInPDBForm(): print atom data in PDB 'ATOM' form

ReadFrgDat(filfrg) @static method: read fragment information

file(.frg file)

filfrg(string): file name

ret=resnam(list): residue name list

,bdalst(list): BDA data list

ReadMhtFile(filcon) @static method: read molecular frame

file(.mht file)

filcon(string): file name

ret=resnam(string): residue name

,condat(list): connect data list

ReadPDBMol(filpdb) @static method: read PDB file

filpdeb(string): PDB file name

ret=pdbmol(list): pdb molecule data

6-3 Atom class (fumole.py）...atom data


# data in PDB

seqnmb=-1 # seq number of atoms 0,1,..,natom-1

cc=[] # Cartesian coordinate [x,y,z] in Angstrom

conect=[] # connect data

atmnam='' # atom name

atmnmb=-1 # atom number

31

resnam='' # residue name

resnmb=-1 # residue number

chainnam='' # chain name

altloc=' ' # alternate

elm='' # element name

focc=0 # occupancy

bfc=0 # thrmal factor

charge=0 # atom charge

# additional items to pdb data

bndmulti=[] # bond kind.

extrabnd=[] # extra bonds, H-bond,vdW,CH/pi,...

# draw parameters

color=fuconst.ElmCol['ZZ'] # atom color. default:unknown elm

show=True # show flag

select=False # select flag

model=0 # draw model, 0:line model, 1:stick, 2:ball and stick,

# 3: CPK

atmrad=1.0 # scale factor of atom radius for ball and stick model

vdwrad=1.0 # scale factor of van der Waals radius

thick=2 # bond thickness

# group data

grpnam='' # group name

grpchg=0 # group charg

envflag=False # environment (special group) flag

parnam='' # name of parent molecule

# fragement data

frgnam='' # fragment name, three characters+sequence number

frgchg=0 # fragment atom formal charge used to calulate fragment

charge.

frgbaa=-1 # atom seq numbe of baa. atom with non zero frgbaa is

a bda atom.

layer=1 # FMO layer. 1:1st, n: n-th layer and 11:MM in IMOMM,

12:EFP

frgcondat=[] # connect data for fragment

(2)methods

32

GetAtmDataDic(): get all the attributes in dictionary

ret=atmdatdic(dictionary): attributes dictionary

GetDrwParamDic():get draw parameters in dictionary

ret=paramdic(dictionary)

GetFrgDataDic():get fragment attributes in dictionary

ret=frgdatdic(dictionary)

GetGrpDatDic(): get group attributes in dictionary

ret=grpdatdic(dictionary)

GetPDBDatDic(): get pdb attributes in dictionary

ret=pdbdatdic(dictionary)

GetResDatDic():get residue attributes in dictionary

ret=resdatdic(dictionary)

MakePDBAtom(): make PDB form of atom data

ret(string): s

SetAtomData(atmdatdic):set attributes in dictionary

atmdatdic(dictionary): dictionary of atom attributes

SetDefaultAtmRad():set default atom radius

SetDefaultColor():set default atom color

SetDefaultVdwRad():set default vdw radius

6-4 fuView class (fuview.py)... draw molecular model


getatmpos=True

raspos=[] # raster position of atoms

rasposz=[] # z-position

#

updated=True

# the following data are used for setting center and draw size

atomdata=[]

bonddata=[]

chaintubedata=[]

drawtube=[]

# initial setting

eyepos = [0.0, 0.0, 300.0]

center = [0.0, 0.0, 0.0]

upward = [0.0, 1.0, 0.0]

33

ratio = fuView.DEFAULT_RATIO # angstrom per pixel

DisplayList = None

fog = True

fogscale=5.0

# default parameters

bgcolor = fuView.DEFAULT_BGCOLOR

rad_stick = fuView.DEFAULT_RAD_STICK

rad_ball = fuView.DEFAULT_RAD_BALL

rad_cpk_scale = fuView.DEFAULT_RAD_CPK_SCALE

rad_peptide = fuView.DEFAULT_RAD_PEPTIDE

stereo = fuView.STEREO_OFF

# flags for draw object

atom=False

bond=False

chaintube=False

selectcircle=False

selectrectangle=False

labelelm=False

labelatm=False

labelres=False

labelfrg=False

bdapoint=False

formalchg=False

distance=False

vdwbond=False

sphere=False

(2)methods

CenterMolecular(): get center of molecule

ClearScreen(): clear screen

DrawAtoms(data): draw atoms

data(list): atom data

DrawBDAPoint(drawbdadata): draw BDA points

drawbdadata(list): bda point data

DrawBonds(data): draw bonds

data(list): bond data

DrawChainTube(data): draw chain tube

34

data(list): chain tube data

DrawDistance(data): draw distance label

data(list): distance data

DrawExtraBond(data): draw extra bonds

data(list): extra bond data

DrawLabel(drawdata): draw label

drawdata(list): label data

DrawSelectCircle(): draw circle

DrawSelectRectangle(): draw rectangle

DrawSphere(data): draw sphere

data(list): sphere data

DrawText2(text,font,pos,color): draw text

text(string): text

font(wx.Font)

pos(list[x,y]): position

color(list): color

DrawText3(text,font,pos,color): draw text

text(string): text

font(wx.Font)

pos(list[x,y]): position

color(list): color

FitMolecular(): draw molecule to fit screen

GetAtomRasterPosition(): get raster position of atoms

ret=raspos(list): list of atom raster positions

GetCenter(): get center of drawn atoms

ret=tupple(x,y,z)

GetFogScale(): get fog scale

ret=fog (True/False): on/off flag

,fogscale(float): scale value

GetObjectXYZ(posx,posy): get x,y,z coordinate of raster

positon(posx,posxy)

posx(int): x position

posy(int): y position

ret=x,y,z (all float): x,y,z coordinate

InitGL(): initialize OpenGL

MakeDisplayList(): make display list

35

MouseRotate(dif): rotate molecule in draw


MouseTranslate(dif): translate molecule in draw


OnDraw(): draw event handler

OnEraseBG(): event handler

OnPaint(): paint event handler

OnResize(): size event handler

SetBGColor(): set background color

SetCamera(): set camera

SetDistanceList(data): set draw distance data from list

data(list): drwa data list

ret=distance(list): list of DrawDistanceData instance

SetDrawAtomData(on,data): set draw atom data


data(list): list of DrawAtomData instance

SetDrawAtomList(on,data): set draw atom list


data(list): list of DrawAtomData

SetDrawBDAPonitData(on,data):set draw BDA points data


data(list): DrawBDAPointData

SetDrawBDAPonitList(on,data): set BDA point list


data(list): BDA list

SetDrawBondData(on,data): set draw bond data


data(list): DrawBondData

SetDrawBondList(on,data): set drwa bond list


data(list): draw bond list

SetDrawChainTubeData(on,data): set draw chain tube data


data(list): DrawChainTubeData

SetDrawChainTubeList(on,data): set draw chain tube list


36

data(list): draw tube list

SetDrawDistanceData(on,data):set draw distance data


data(list): DrawDistanceData

SetDrawDistanceList(on,data):set draw distance list


data(list): draw distance list

SetDrawFormalChargeData(on,data):set draw formal charge data


data(list): DrawFormalChargeData

SetDrawFormalChargeList(on,data):set draw formal charge list


data(list): draw formal charge list

SetDrawLabelAtmData(on,data): set draw atom label data


data(list): DrawLabelData

SetDrawLabelAtmList(on,data): set draw atom label list


data(list): draw label list

SetDrawLabelElmData(on,data):set draw element label data



SetDrawLabelElmList(on,data):set draw element name list



SetDrawLabelFrgData(on,data):set draw fragment name data



SetDrawLabelFrgList(on,data):set draw fragment name list



SetDrawLabelList(data):set draw label list


ret=labeldata(list): DrawLabelData

SetDrawLabelResData(on,data): set residue label in

DrawLabelData class instance

37

on(True/False): draw on/off flag

data(list:label,cc,color): residue name data

SetDrawLabelResList(on,data): set residue label in list


data(list): draw label data list

SetDrawNetChargeData(on,data): set net charge data


data(list): charge data for draw

SetDrawNetChargeList(on,data): set net charge list


data(list): charge data list

SetDrawSphereData(on,data): set draw sphere data


data(list): draw sphere data

SetDrawSphereList(on,data): set draw sphere list


data(list): draw sphere list

SetDrawVdwBondData(on,data): set draw vdw bond data


data(list): draw vdw bond data

SetDrawVdwBondList(on,data): set draw vdw bond list


data(list): draw vdw bond list

SetFogScale(on,fogscale): set flag and scale for fog

on(True/False): fog on/off

fogscale(float): fog scale, default=5.0

SetStereoCamera( bCameraLeft, bViewportLeft): set stereo

camera

SetStereoView(stereo): stereo view flag

stereo(True/False)

SetViewAxis(xyz): set view axis

xyz(string,'X','Y' or 'Z'): view axis

Zoom(rot): magnify molecular model drawing

rot(int): degree of magnification

Code2RGB(code)@static method： convert OpenGL RGB code to

38

Windows code

ret=RGB(list[r,g,b])

RGB2Code(RGB)@static method：convert Windows RGB code to OpenGL

code

ret=rgb(list[r,g,b])

6-5 fuCtrlFlag class (fuctrl.py)...cntrol flags

(1)attributes

ctrlflag={} # flag dictionary

(2)methods

GetCtrlFlag(name):

name(string): flag name

ret=(True/False)

RemoveCtrlFlag(name): delete flag


SetCtrlFlag(name,value): set flag value


value(True/False)

6-6 fuPlot class(fuplot.py)...main program

(1)methods

About(): show license on messagebox

AddDerivedDataDic(drvnam,drvcmp): add derived data to

dictionary

drvnam(string): dat aname

drvcmp(list): clist of omponent data

CheckDeriveComp(drvcmp): is component of derived data?

ret=find(True/False): yes/no flag

ConsoleMessage(mess): print message on PyCrust cosole

mess(string): message

ConvertCTChargeForPlot(fmoctchg) @static method: convert ct

charge data for plot

fmoctchg(list): FMO output form of ct charge

ret=ctcharge (list): plot form of ct charge

ConvertGMSMullikenChargeForPlot(mulliken) @static method:

convert GMS Mulliken deta for plot

39

mulliken(list): GMS output form of mulliken

ret=mulchg(list): plot form of mulliken

ConvertMullikenChargeForPlot(fmomulchg) @static method:

convert FMO mulliken data for plot

fmomulchg(list): FMO output form of Mulliken charge

ret=mulchg(list): plot form of Mulliken charge

ConvertOneBodyForPlot(fmoone,layer) @static method: convert

one-body energy data for plot

fmoone(list): FMO output form of one-body energy data

ret=onbody(list): plot form of one-body energy data

ConvertPIEDAForPlot(fmopieda) @static method: convert PIEDA

data for plot

fmopieda(list): PIEDA in FMO output form

ret=pieda(list): PIEDA data in plot form

,ctchg(list): ct charge data in plot form

CreateMatPlotLibFrame(): create MatPlotLib frame

CreatePropertyChoisePanel():create PropertyChoisePanel

CreatePyCrustFrame(): create PyCrust frame

CreateSelectDataPanel():create SelectDataPanel

CreateSplitWindow(): create split window for SelectDataPanel and

PropertyChoisePanel

GetCurrentFMOData(): get current FMOProperty instance

ret=curfmodat(FMOProperty instance):

GetFMOProp(dataname): get FMOProperty instance

dataname(string): data name

ret=fmodat(FMOProperty instance):

GetFMOPropName(fmodatadic,id): get FMO data name

fmodatadic(dictionary of FMOProperty instance):

id(int): data number

ret=dataname(string): data name

GetIDAndName(dataname): get data id and name

dataname(string): data name with id number

ret=id(int): id number of data

,name(string): data name

GetNameAndExt(filename): extract name and extension from file

name

40


ret=err (True/False): error/no error

,name (string): name

,ext(string): extension

GetOpenFiles(curdir,files): get open multiple files

curdir (string): current directory name

files (list): file name list

IsDerivedData(dataname): is this derive data?

dataname(string): plot data name

ret=ret(True/False)

IsDuplicateName(dset,name): is name duplicate?

dset(list): data name list

name(string): name to check duplicate

ret=dup(True/False)

IsFMOProperty(dataname): is data FMO property?

dataname(string): data name

ret=find(True/False)

IsItemInDataDic(item,datadic): is "item" in datadic?

item(string): item name

datadic(dictionary): data dictionary

ret=ret(True/False)

ListFMODataName(): print FMO data name in fmodatadic dictionary

MakeCTChargePlotData(): make CT charge data for plot

ret=ctcharge(list): ct charge plot data

MakeDataList(): make plot data

ret=datalist

MakeDataName(name):

ret=dataname

MakeFMOPropertyDic(curdir,files):

ret=fmodatadic

MakeMullikenPlotData():

ret=mulcharge

MakePIEDAPlotData():

ret=pieda

PlotMenu(): menu of fuplot

PrintFragmentName(): print fragment name

41

PrintMessage(): print message

ReadFMOCTCharge(filename)@static method: read FMO CT charges

filename(string): name of FMO output file

ret=err(True/False): error/no error

,version(string): GAMESS and FMO version

,ctchg(list): list of ct charges

ReadFMOFragStatics(filename) @static method: read FMO fragment

statics in FMO output file


ret=frgstatlist(list): list of FMO statics data

ReadFMOInput(filename)@static method: read FMO input file


,nfrag(int): number of fragments

,icharg(list): icharg data list

,frgnam(list): fragment name list

,indatx(list): indat data list

,bdabaa(list): BDA-BAA data list

ReadFMOIterEnergy(filename)@static method: read FMO iteration

energies



,jter(list): iteration number list

,denergy(list): difference energy list

,ddensity(list): difference density list

ReadFMOKeywrd(filename,keywrd,col1,col2,datcollst) @static

method: read keyword item in FMO output


keyword(string): keyword to be found

col1(int): the first column of keyword in a line

col2(int): the last column of the keyword in a line

datacollst(list): list of data format of keyword items



,valuedic(dictionary): dictionary of keyword items

ReadFMOMulliken(filename) @static method: read Mulliken

charges in FMO output

42




,mulchg(list): list of Mulliken charges

ReadFMOOneBody(filename) @static method: read FMO one-body

energy




,onebody(list): list of one-body energy

ReadFMOPIEDA(filename) @static method: read FMO PIEDA




,pieda(list): PIEDA data list

ReadFMOStatics(filename) @static method: read FMO statics




,prpdic(dictionary): dictionary of FMO properties

ReadFMOXYZ(filename) @static method: read FMOXYZ data

filename(string): file name of FMO input


,geom(list): list of atom coordinates

ReadFrgDistance(filename) @static method: read distances in FMO

output file




,frgdist(list): list of interfragment distances

ReadFrgIterEnergy(filename) @static method: read FMO SCC

energies


ret=errerr(True/False): error/no error


,jter(list): iteration number list

43

,efmo(list): list of efmo

,dele(list): list of delta energy

,deld(list): list of delta density

ReadGMSMulliken(filename) @static method: read Mulliken

charges in GAMESS output file

filename(string): GAMESS output file



,mulchg(list): list of Mulliken charges

ResolveDerivedData(drvnam): resolve derived data

drvnam(string): derived data name

ret=fmodat(list): list of FMOProperty instance

,cmpsign(list): list of sign

RunMethod(method): run method for PyCrust

SavePropChoise(on): save property choice data

SetDataListInSelLB(): set data name in select list box

SetGraphData(pltprp): set graph data

SetPropChoise(): set property choice widgets

Version(): show program version on messagebox

WriteRemark(): write remarks on left panel in main window

6-7 FMOProperty class(fuplot.py)...FMO output data


name=name # data name

outfile=outfil # FMO output file name

inpfile=inpfil # FMO input file name

pdbfile=pdbfil # pdb file name

# property flags

geom=3 # 0:no, 1:output file, 3:input file

pieda=False # =0:pie, =1:pieda

ctchg=False # =0:no data, 1:yes

mulchg=False # 0:not available, 1*yes

espot=False

density=False

orbital=False

# method in FMO

44

fmo=True

nbody=2 # # 2:fmo2, 3:fmo3

corr=0 # flag 0:hf, 1:corr

# property value

prpdic={} # dictionary of FMO property

etfmo2=0 # fmo2,fmo3

etfmo3=0

ecfmo2=0 # fmo2,3

ecfmo3=0 #

# molecule data

natmfrg=[] # natm in each fragment

natm=0 # total natm

nbas=0

nfrg=0

tchg=0 # total charge of while system

nbasfrg=[] # each fragment

frgnam=[] # fragment name

frgchg=[] # fragment charge

indat=[] # indat in FMO input data

bdabaa=[] # bda and baa

jobtitle='' # job comment in output

gamessver='' # GAMESS version

fmover='' # FMO version in GAMESS

# FMO properties list

frgpieda=[] # PIEDA data

frgdist=[] # interfragment distance

ctcharge=[] # CT charge

mulliken=[] # Mulliken population

onebody=[] # one-body energy

(2)methods

SetAttributes(): read FMO attributes in FMO output and set them

to the attributes

GetFMOIterEnergy(): read FMO output to get FMO iterations

ret=iter(int): number of iterations

,de(list): list of energy change

,dd(list): list of density change

45

GetFrgIterEnergy(): read FMO output to get energy change in SCC

ret=iter(list): iteration number for each fragment

,efmo(list): list of total energy

,de(list): list of energy change

,dd(list): list of density change

6-8 fuGraph class(fugraph)...control drawing graph

(1)methods

CreateChildGraphPanel(): create child graph panel

CreateCTChargeCmdPanel(): create control panel for CT charge plot

CreateGraphPanel(): create panels(CreateCTChargeCmdPanel,

CreateMullikenCmdPanel,CreatePIEDACmdPanel)

CreateMullikenCmdPanel(): create controle panel for Mulliken plot

CreatePIEDACmdPanel(): create controle panel for PIEDA plot

DrawChildMolView(): draw moleculr model colored by property

DrawGraph(): draw graph

GetNumberOfPIEDAComponents(): get number of PIEDA components

ret=ncmp(int): number of PIEDA components

GetRankColor(value): get color of function value

value(float): function value

ret=color(list): color

MakeAllCTChergeData(): make plot data for all CT charge

ret=pltdat(list)

MakeAllMullikenData(): make all Mulliken plot data

ret=pltdat(list): list of plot data

MakeDataFor2D(): make 2D plot data

ret=pltdat2d(list): list of 2d plot data

MakeFragmentCTChargeData(ifrg): make CT charge data for plot



MakeFragmentMullikenData(ifrg):make Mulliken plot data for fragment



MakeFragmentPIEDAData(ifrg):make PIEDA plot data for fragment

ifrg(int): number of fragment


46

MakePIEDABondingEnergyData(): make PIEDA bonding energy data


MakePIEDARemarkList(pltdat): make remark data for PIEDA

pltdat(list): list of PIEDA plot data

ret=lst(list): list of PIEDA remarks

MakeRankColorData(): make rank color data for 2D graph

MakeRemarkData(): make remark data in 2D plot

ret=remarkdata(list): list of remark data

MenuGraph(): menu items

PrintData(idat): print data on console

idat(int): data number, i.e. fragment number

PrintMaxData(): print maximum value in data on console

PrintMinData(): print minimum value in data on console

SetFMOProp(pltprp,datnam,molint,piedacmp,mullbody):set FMO

property plot data

pltprp(int): 0 PIEDA, 1 CTCharge, 2: Mulliken

datnam(string): data name

molint(True/False): flag for molecular interaction

piedacmp(list): list of PIEDA component name

mulbody(int): n-body mulliken

SetFMOPropData(natm,nfrg,frgnam,fmoprp,frgdist): set FMO property

natm(int): number of atoms

nfrg(int):number of fragments

frgnam(list): list of fragment names

fmoprp(list): list of FMO poperty data, PIEDA,CTCharge or

Mulliken

frgdist(list): list of fragment distances

SetMolViewFragmentData(pdbfile,indat,bdabaa): set fragment data

for molview draw

pdbfile(string): PDB file name

indat(list): indat data in FMO input data

bdabaa(list): list of bda-baa

SetMullikneBodyWidget(mullbody): set widget for Mulliken

SetPIEDAComponentWidget(piedacmp): set widget for PIEDA components

SetRankColor():Set Rank color

SetWidgetStates():Set widget states

47

SortDataNmb(pltdat): Sort data in ascending data number

pltdat(list): data for plot

ret=order(list): order of data in plot

SortDist(): Sort data in ascending distance


SortLarge(pltdat): Sort data in descending order



SortSmall(pltdat): Sort data in ascending order



6-9 BarGraph class(fugraph.py)...Draw bar graph

(1)attributes and their defaults

fontsize=[6,10] # font size in pixel

fontcolor='black' # font color in wx.color

# set graph size

wplt=self.size[0]; hplt=self.size[1] # plot panel size

# title and axis labels

title='' # title text

xlabel='' # title for x-axis

ylabel='' # title for y-axis

# plot data

ndata=0 # number of data

data=[] # plot data

order=[] # order of data in plot

itemlist=self.SetDefaultItemList() # item list

extradata=False # only 1 extra data is allowed

extradatalabel='' # label of extra data

extposivalue=0.0

maxplotdata=0 # number of plot data; ndata or ndata+1(extra)

begindata=0 # the first sequence number of data to plot

focus=1 # seq. number of data to be drawn with thick frame

# remark

remarklist=[] # remark list

remarkboxsize=[10,8] # tile:[width,height]

48

wremark=0 # 10 width of remark

rank=10 # color rank

# y-axis range

wytitle=30 # width of y-title

wylabel=50 # width of y-label

xunit=12 # unit of x-axis in pixce,barwidth*2+2

barwidth=5 # bar width

hxtitle=20 # x axis title height

hxlabel=30 # height of x-label

# title

htitle=25 # title height

#y range

yrangemin=-50.0 # +/- y max value

yunit=0 # =(yinipos-yendpos)/(2.0*yrange)

# scale out value

scaleoutposi=0.0; scaleoutnega=0.0

(2)methods

ClearGraph(): clear graph

DrawTitle(dc): draw graph title

dc(device context)

DrawAxisLabel(dc): draw x-label

dc(device context)

DrawRemark(dc): draw color remark

dc(device context)

DrawXAxis(dc):draw x-axis

dc(device context)

DrawYAxis(dc):draw y-axis

dc(device context)

FindXpos(value): find x position corresponding to value

value(int): x value

ret=x(int): position

FindYpos(value): find y position corresponding to value

value(float): y value

ret=y(int): position

Plot(on): draw graph

49


PlotItemsInStackBar(dc,ii,x): plot items in stacked bar graph

dc(device context)

ii(int): ii-th item

x(int: position in x-axis

Replot(xmove): replot graph in scrolling graph

xmove(int): mouse move length

SetAxisLabel(xlabel,ylabel): set x and y axis labels

xlabel(string): x-label

ylabel(string): y-label

SetBackgroundColor(color): set background color

color(list,[r,g,b] or wx color, like 'white')

SetDefaultItemList(): set remark list for items to plot

ret=itemlist(list), default=[['1',c1],['2',c2],['3',c3],

['4',c4],['5',c5],['6',c6]],

where ci(i=0-6) is color data

SetData(data,order): set data and plot order

data(list): data in form [[0,value1],[1,value2],..]

order(list): order of data in plot

SetFont(font,fontsize): set font and its size

font(wx.Font): font

fontsize(list): font size in pixels,[width,height]

SetItemNameAndColor(itemlist): set item name and color

itemlist(list): item list in form [['text1',color1],...]

SetPlotSize(wplt,hplt): set graph size

wplt(int): width in pixel, usually equal to panel width

hplt(int): height in pixel, usually equal to panel height

SetRemark(remarkboxsize,remarklist): set remark box size and

remarks

remarkboxsize(list): box size in pixels, [width,height]

remarklist(list): list data for remark

SetRankColor(negacolor,posicolor,negascaleoutcolor,

posiscaleoutcolor): set rank color

regacolor(list): color for negative values

posicolor(list): color for positive values

negascaleoutcolor(list): color for negative values of scale out

50

posiscaleoutcolor(list): color for positive values of scale out

SetTitle(title): set graph title

title(string): title text

SetYRange(ymin,ymax): set y value range

ymin(float): minimum value in y range

ymax(float): maximum value in y range

6-10 TileGraph class(fugraph.py)...draw tile graph

(1)attributes and their defaults

focus=0 # focused fragment number

bgcolor=bgcolor

font = wx.Font(10, wx.FONTFAMILY_DEFAULT, wx.FONTSTYLE_NORMAL,

wx.FONTWEIGHT_NORMAL, False, 'Courier 10 Pitch')

fontsize=[6,8]

fontcolor='black'

# graph size

wplt=self.size[0] # width of graph

hplt=self.size[1] # height of graph

# title and axis labels

title='' # title text

xlabel='' # title for x-axis

ylabel='' # title for y-axis

# plot data

ndata=0 # number of data

data=[] # [[[1,1,value,flag],..[1,n,value,flag]],

# [[2,1,value,flag],..]],.

order=[] # order of data in plot

extradata=False # only 1 extra data is allowed

extradatalabel='' # label of extra data

extposivalue=0.0 # scale out positive value

extnegavalue=0.0 # scale out negative value

maxplotdata=0 # number of plot data; ndata or ndata+1(extra)

xbegindata=0 # the first sequence number of data to plot

ybegindata=0 # the first sequence number of data to plot

# remark

remarklist=[] # list of remark

51

remarkboxsize=[8,8] # remark box size

remarktext='' # remark text

hremark=20 # height of remark

rankposi=10 # rank for positive value

ranknega=10 # rank for negative value

# rank color

posicolor='red' # will be converted to RBG255

negacolor='blue' # will be converted to RGB255

extnegacolor=[0,255,255] # color for scale out negative value,

# 'cyan'

extposicolor=[255,0,152] # color for scale out positive

# value,'magenta'

colorcode1=[255,255,0] # diagonal block color,'yellow'

colorcode2=[255,204,0] # covalent-bonded block color, 'gold'

tilesize=[10,10] # tile size

# x-axis range

wytitle=30 # width of y-title

wylabel=50 # width of y-label

wremark=55 # width of remark

xunit=12 # barwidth*2+2

barwidth=5 # width of bar

hxtitle=20 # height of x-title

hxlabel=30 # height of x-label

# y-axis range

htitle=25 # title height

yrangemin=-50.0

yrangemax=50.0 # +/- y max value

yrange=yrangemax # y value range

scaleoutposi=0.0; scaleoutnega=0.0

(2)methods

ClearGraph(): clear graph

DrawAxisLabel(dc): draw axis label

dc:(device context)

DrawRemark(dc,x,y,remarktext): draw remarks

dc(device context)

52

x(int): x position

y(int): y position

remarktext(string): text data

DrawTitle(dc): draw graph title

dc(device context)

FindXpos(value): find x position corresponding to value

value(int): x value

ret=x(int): x position

FindYpos(value): find y position corresponding to value

value(float): y value

ret=y(int): y position

GetColor(val,code): get color correspond to value

val(float): function value

code(int): 0: color by value, 1: diagonal color, 2: covalent

bonded fragment color

ret=color(list): color data

MakePlotData(): make color plot data

ret=plotdata(list): list of color plot data

Plot(on): draw graph


Replot(xmove,ymove): redraw graph

xmove(int): mouse move length along x axis

ymove(int): mouse move length along y axis

SetAxisLabel(xlabel,ylabel): set axis labels

xlabel(string): x-axis label text

ylabel(string): y-axis label text

SetBackgroundColor(color): set background color

color(list): color data

SetBeginDataNumber(number): set begin data number

number(int): data number

SetData(data,order): set data and order

data(list): plot data

order(list): order list of data to plot

SetFocus(focus): draw rectangle with thick border color

focus(int): current fragment number

SetFont(font,fontsize):set font and font size

53

font(wx.font)

fontsize(list): font size [width,height] in pixels

SetPlotSize(wplt,hplt): set plot region

wplt(int): width of plot panel

hplt(int): height of plot panel

SetRankColor(negacolor,posicolor,extnegacolor,extposicolor,

colorcode1,colorcode2): set color codes

negacolor(list): color for negative value

posicolor(list): color for positive value

extnegacolor(list): color for scale out negative value

extposicolor(list): color for scale out positive value

colorcode1(list): color for self fragment

colorcode2(list): color for covalent bonded fragment

SetRemark(remarkboxsize,remarklist):set remark data

remarkboxsize(list[x,y]): box size

remarklist(list): remark list, see MakePIEDARemarkList

method in fuGraph class

SetRemarkTitle(text): set remark title

text(string): text

SetTitle(title): set title of plot panel

title(string): title text

SetYRange(yrangemin,yrangemax): set y-axis range

yrangemin(float): minimum value in y range

yrangemax(float): maximum value in y range

6-11 MatPlotLib_Frm class(fugraph.py)・・・ Frame for MatPlotLib

(1)methods

Clear(): clear graph

NewPlot(): create subplot (figure.add_subplot(111))

PlotTitle(text): plot title

text(string): title text

PlotXLabel(text): plot x-axis label

text(string): label text

PlotXY(x,y): plot (x,y) data

x(list,[1,2,...]): list if x values

y(list,[1,2,...])：list of y values

54

PlotYLabel(text): plot y-axis label

text(string): label text

6-12 fulib module (fulib.py)・・・ Global methods

(1) methods

AngleT(ra,rb): calculate angle between two vectors

ra(list,[x,y,z]): point vector

rb(list,[x,y,z]): point vector

ret=t(float):angle in radian

AtmNamElm(atmnam):get element from PDB atom name

atmnam(string*4): PDB atom name

ret=elm(string*2): element

ChangeToPreviousDir(dirname,inifile):get directory name in

inifile and change current directory to it

dirname(string): directory of the executable program

inifile(string): file name in which directory name is kept

ret=dir(string): current directory name

ChooseColorPanel(parent):open color picker panel

parent(frame instance): parent frame

CompressIntData(expnint): compress integers

expnint(list): list of integers

ret=cmpint(list): list of compressed integers

CopyBitmapToClipboad(bmp): copy screen image to clipboard

bmp(bitmap): bitmap data of screen image

CovalentBondedAtomList(elm,coord):

elm(list): element list

coord(list): list of coordinates

ret=bndlst(list): bonded atom list

Distance(p1,p2): calculate distance between tow points

p1(list[x,y,z]): point coordinate

p2(list[x,y,z]): point coordinate

ret=r(float): distance between p1 and p2

ExpandIntData(compint): expand packed integers

compint(list):

ret=expnint(list)

ExtractWaters(molnam,pdbmol):

55

ret=watdat,moldat

GetIconFile(exedir,iconname): Get Icon file

exedir(string): directory of exe file

iconname(string): icon name

ret=iconfile(string): file name of icon

GetExeDir(program): get directory of executable program

program(string): program name

ret=dir(string): directory

HSVtoRGB(HSVcol): convert HSV color code to RGB code

HSVcol(list): HSV color

ret=RGBcol(list): RGB color

ListPDBResSeq(pdbmol,skipter,skipwat):

ret=resnamlst

OrientOrg(pdborg,pdbdrv):

ret=pdbdrv

PrintNumericList(filnam,intlst,header,sep,width,colu,nw):

PrintStringList(filnam,strlst,header,sep,width,colu,nw):

RotMatAxi(v,t): return matrix u for rotation by angle "t" (radian)

around vector v.

v(list): axis vector

t(float): angle in radian

ret=u(list): (3x3) transformation matrix

RotMatEul(a,b,c): return rotation matrix u for rotation by (a,b,c)

Euler angles

a(float): angle alpha

b(float): angle beta

c(float): angle gamma


RotMatPnts(refpnt,newpnt): get rotation matrix transforming

reference points to new points

refpnt(list): reference points coordinates

newpnt(list): new coordinates


RotMatX(a): transformation matrix of rotation by angle "a" around

x-axis

a(float): angle in radian

56

ret=ux(list): (3x3) transformation matrix

RotMatY(b):transformation matrix of rotation by angle "b" around

y-axis

b(float): angle in radian

ret=uy(list): (3x3) transformation matrix

RotMatZ(c):transformation matrix of rotation by angle "c" around

z-axis

a(float): angle in radian

ret=uz(list): (3x3) transformation matrix

RotMol(u,cnt,coord): rotate molecule

u(list, 3X3): transformation matrix

cnt(list[x,y,z]): center of rotation

coord(list[x,y,z]):, coordinates

ret=xyz(list[x,y,z]): transformed coordinates

SplitAtTER(mnam,pdbmol): split molecule at TER

mnam(string): name of molecules

pdbmol(list): pdb mol data

ret=molnamdic(dictionary): dictionary of generated molecule

names

,moldatdic(dictionary): dictionary of molecular data

,delcondic(dictionary): dictionary of deleted connect data

SplitRes(molnam,pdbmol): split molecule into residues

molname(string): name of molecule

pdbmol(list): pdb mol data

ret=molnamdic(dictionary): dictionary of molecular names

,moldatdic(dictionary): dictionary of molecular data

StringToInteger(strdata): convert string to integer

strdata(list): string data list

ret=intdata(list): list of integers

TrnMat(ra,ri,rf): get transformation matrix to rotate ri to rf

around axis ra

ra(list[x,y,z]): axial vector for rotation

ri(list[x,y,z]): initial position vector

rf(list[x,y,z]): final position vector

ret=u(list): transformation matrix

WriteDirectoryOnFile(dirname,filename): write directory name on

57

a file

dirname(string):directory name


6-13 Class in fupanel.py module... pop-up panels

class AtomChargeInput_Frm(wx.Frame): atom charge input panel

class ControlPanel_Frm(wx.Frame): control panel

class DeriveDataInput_Frm(wx.Frame): derived data input panel

class GamessInput_Frm(wx.Frame): GAMESS input assistant panel

class GroupJoin_Frm(wx.Frame): Group joint panel

class GroupRename_Frm(wx.Frame): Group rename panel

class LayerAssignPanel_Frm(wx.Frame): layer assignment panel

class NameSelector_Frm(wx.Frame): Name/number select panel

class OpenMultipleFile_Frm(wx.Frame): Open multiple files panel

class RadiusSelector_Frm(wx.Frame): Radius selection panel

class TreeSelector_Frm(wx.Frame): Tree selector panel

class ZMatrixPanel_Frm: Z-matrix panel for change conformation

58

7. Miscellaneous

7-1 Note on sequence number of atoms and 'TER'

It is noted that, in the program atoms are numbered from 0 and in I/O

widgets from 1. The treatment of 'TER's(in PDB ATOM record) is tricky.

Fu keeps all 'TER's without subjecting them to any operation except the

DeleteTerAtoms method of fuModel class. In fragmentation of a molecule,

a complicated code is needed as in SetFragmentName method in fuMole class,

since 'TER' has a sequence number.

7-2 Types of AddHydrogen

Table AddHydrogenType(addhtype)

-------------------------------------------------------------------

addhtype connection of comment

code reference atoms

-------------------------------------------------------------------

|-atom2 H atom and atom1-4 form

1A1 H-atom1-atom3 pseudotetrahedron.

|-atom4 ex. H-CH3 of methane

|-atom2 atom1 is sp2 and H and atom1-3 are in

1A2 H-atom1 a plane. ex. H-C of benzene

|-atom3

1A3 H-atom1-atom2-atom3 H-atom1-atom2-atom3 can be cis

or trans.

ex. H-O-C-C of ethanol

2A1 H-| |-atom2 two H atoms are added at atom1

atom1 H2 and atom2,3 are twisted by

H-| |-atom3 90 degrees. ex. H2 of CH4

2A2 H-| all atoms are in a plane

atom1-atom2-atom3 ex. H2N-C-N(H2)- of arginine

H-|

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3A1 H-| three H atoms are attached at atom1

H-atom1-atom2-atom3 ex. H3N-C-C- of lysine

H-|

-------------------------------------------------------------------

7-3 Tutorials

The following tutorials are provided for help programming with fu.

(1) tutorial_01: create window with StatusBar and Menu

practice: use of wxFrame, wxCreateStatusBar and fuMenu class

in fuctrl.py module.

(2) tutorial_02: read PDB file and use PyCrust

practice: 1)use of ReadPDBData method, a static method of fuModel

class in fumodel.py module.

2)use of PyCrust

usage: 1)Execute 'File'-'Open' command and read PDB file.

2)Then type 'print demo.pdbmol[enter]' in PyCrust

console.

3)Type 'demo.pycrust.shell.run('"print filename:",

demo.filename')'[enter] in PyCrust console.

note: You see that you can access attributes and methods in

running GUI program through python commands in PyCrust

console. That means you can modify data and add

functions interactively, without modifying the source

codes of the program. For execute a python program, type

'execfile('hello.py')'[enter].

(3) tutorial_03: use of fuView class in fuview.py

practice: Draw line model (or CPK model) of CH4 molecule.

usage: The model is rotated and magnified by mouse move with

left button down and mouse wheel rotation, respectively.

(4) tutorial_04: use of fuMole class in fumole.py and fuView class

in fuview.py

practice: Draw molecule created from PDB data.

60

usage: The model is rotated and magnified by mouse move with

left button down and mouse wheel rotation, respectively.

(5) tutorial_05: BarGraph class in fugraph.py

practice: Draw bar graph.

usage: When graph is too large for the panel, a mouse move with

the left button down scrolls the graph.

(6) tutorial_06: TileGraph class in fugraph.py

practice: Draw tile graph.

usage: When graph is too large for the panel, a mouse move with

the left button down scrolls the graph.

Documents

fu (fumodel and fuplot) Programming Guidecbi-society.org/taikai/taikai13/fu-ProgramingGuide-5.pdf9/py2exe-0.6.9.win32-py2.7.exe/ 4-2 Making executable for Windows （ fumodel.exe and