Solutions for Cheminformatics

Marvin features and news

Akos Papp

Main original features – 1

• 2D and 3D sketching and viewing– Isotopes, charges, radicals, maps – Stereo features (tetrahedral, double bond, diastereo)– Valence check, lone pairs, implicit hydrogens– Aliases, pseudo-atoms– Attached data– Nice structures (antialiasing)– Rich formatting (fonts, colors, bond thickness) – Recursive SMARTS

Main original features – 2

• Query drawing features– Any atom, atom list/not-list, link nodes– Atom properties (substitution count, aromatic, etc.)– Bond topology (ring, chain)– Reaction topology (reacting center,

inversion/retention)

• Markush structure drawing features

• Groups– Large collection of abbreviated groups– Quick drawing using the keyboard– Custom group creation (R-group, S-group, etc.)

Major original features – 3

• Single step reaction drawing– Automatic component recognition– Automapping Graphics, text boxes, electron flow

arrows

• 2D and 3D structure clean

• Aromatization /dearomatization

• Multipage sketches

• Molecule matrix view in MarvinView

• Customizable menu and toolbar

• ISIS/Draw-like and ChemDraw-like configurations

Major original features – 3

• OLE component for Office documents

• Periodic system ‘Query’ tab containing– Generic query features and periodic table groups

• Dynamic IUPAC name text box

• Name import– From file or from any document through copy/paste

• Creating templates by drag-drawing to toolbar

• Spreadsheet-like view in MarvinView for SD and RDFiles

• Calculator plugins

Calculator plugins - 1

• Elemental analysis

• Protonation (pKa, major microspecies, isoelectric point)

• Partitioning (logP, logD)

• Charge (charge, polarizability, orbital electronegativity)

• Isomers (tautomers, stereoisomers)

• Conformation (conformers, molecular dynamics, 3D alignement)

Calculator plugins – 2

• Geometry (topology analysis, geometry, polar surface area (2D), molecular surface area (3D))

• H-bond donors and acceptors, Huckel analysis, refractivity, resonance, structural frameworks

• Naming– IUPAC name– Traditional name

• Markush enumeration– Sequential, random, library size calculation– Homology group enumeration

Main original technical features

• Import/export of all important molecular file formats– Inter-conversion, automatic recognition

• Image export to the major image file formats

• Visualization with MarvinView and MarvinSpace

• Distributions: Standalone, JWS, Beans, Applets

• Platform and browser independent

• Features are available from API

• Free for Non commercial websites, Academic research and teaching, Evaluation

Developing with Marvin Beans

Additional API is accessible for– Import / Export– Performing

calculations with plugins

– 2D and 3D cleaning of structures

– All operations accessible in the GUIs are also available in the API.

Use Marvin Beans to add MarvinSketch or MarvinView as a graphical component to your standalone application

Applet specific features

• The appropriate version for the browser / JRE is automatically selected

• Signed (trusted) applets enable access to local files, system clipboard and allow printing.

• Applet API accessible from JavaScript to– fetch the current structure

from the applet and send it to the server for further processing.

– change the structure or display options of the applet without reloading the page.

Main new features – 5.2

• Transparent structure painting – Transparent background images (EMF, SVG, PNG)– Transparent OLE object

• MView spreadsheet view speedup

• Marvin initialization speedup in applet version (in 5.2.2)

• Charges can be displayed on brackets

• OLE object improvments– Image properties (colors, implicit H, etc.)– Speed (memory resident OLE server)

• Periodic system coloring schemes

• Reaxys Generics atoms and groups

Future features – 5.3

• .Net version

• Marvin initialization speedup in applet version

• Sprout drawing

• Projected drawing– Bold bonds– Turning structures into projection

• Brackets as graphical objects– Bracket coordinate is automatic by default, but the

the bracket can be moved– Data can be attached to it

Future features – 5.3

• Chemical terms editor in GUI

• Template handling redesign– Load templates from specified directories

• Skc import and export

• Multirecord file (SDFile) import to the same canvas

• Spreadsheet view mode for MView applet

Future features – 5.4

• Marvin Lite (Modular system)

• Structure checker component in GUI

• Enhanced handling of group attachment points– Leaving group definition

• Multistep reaction support– Real arrows with automatic assignment of

reactants

• MarvinView GUI redesign

Thank you