marvinsketch and marvinview: tips and tricks: us ugm 2008

Scientific & technical presentation

MarvinSketch and MarvinView

May 2008

Instead of Introduction

Technical Features

• File types to read/write:

– MOL, SDF, RXN, RDF

(V2000/V3000)

– SMILES, SMARTS/SMIRKS

(recursive)

– XML based format MRV, CML,

InChi, MOL2, XYZ, Gaussian

Cube

– PDB, 1 and 3 letter peptide

– IUPAC Name

• Flexible

– Calculation plugins

– Custom templates

– Custom formatting

– Image export into BMP, JPEG,

PNG, PPM, POV, SVG, EMF,

PDF

• Printing, multipage documents

• 3D models, Java or OpenGL

rendering (with MarvinSpace)

• Available as

– Java (signed) applets

– Applications, deployment with

installer, Java Web Start

– JavaBeans

• System Requirements:

– Java 1.4 (or later version)

platforms (Windows, Mac,

Solaris, Linux/Unix)

Various File Formats

• Molecule source file can be edited

and saved or imported/exported in

different formats

• Possible to insert into a long file of

many compounds at a given

location

• Also possible to read a structure

from a given position of a long file

• Append current structure to an

existing file

ChemAxon Marvin Documents | CML | IUPAC

InChI IUPAC Name | MDL Molfile Extended

Molfile Rxnfile Extended Rxnfile RDfile SDfile |

Peptide sequence | SMILES SMARTS | Tripos

SYBYL molfile Mol2 | Gaussian Cube | PDB |

XYZ

Image Export

• Create raster or vector graphical image from your structure.

OLE component for documents

• Editable molecules in Office

documents

System Compatibility

• 100% pure Java

• .NET integration

– Through JNBridge

• Windows

– 95, 98, Me, NT,

2000, XP, Vista

• Mac OS X

• Unix/Linux

– Linux, Solaris, etc.

Distributions / Marvin Beans

• Marvin Beans

– Desktop applications

(deployment with Installer,

Java Web Start)

– Full API (with JavaBean

support) for developers to use

Marvin components in

applications

– Documentation and examples

• Recommended for end-users

– Easy installation

– Support Java 1.4 capable

platforms (Windows, Mac OS X,

Linux/Unix)

– Command line molecule

converter

– Applications are free for end-

users

• Recommended for developers

– Quick GUI building

– Easy customization

– Direct manipulation of

molecules

• Free for open access, non

commercial websites

• Free for academic research

and teaching

• Free for Evaluation

Distributions / Marvin Applets

• Marvin Applets

– Browser-independent

solution for Marvin

integration into web pages

– Wide range of layout

customization

– API to control the applets

from JavaScript

– Documentation and

examples

• For web developers

– Simple web base

deployment

– Modular architecture

ensures short download

time

– Minimum requirement

(Java 1.4 capable

browsers)

• Free for open access, non

commercial websites

• Free for academic research

and teaching

• Free for Evaluation

Web Browser Compatibility

•Internet Explorer

•Firefox

•Mozilla

•Netscape

•Safari

•Opera

Applet Specific Features

• Using Swing GUI components,

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.

Custom Marvin Applets Layout

Developing with Marvin Beans

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

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.

Molecule Sketching Features

• Drawing molecules, reactions, residues

• Isotopes, charges, radicals

• Stereo features:– tetrahedral (R/S)

– double bond (E/Z)

– diastereomer (Abs/And/Not)

• Reaction (Inv/Ret)

• Templates, aliases, pseudo atoms

• Abbreviated groups, Multiple groups

• Link nodes

• Attached data

• Graphic objects (lines, arrows, boxes, text)

• Curved electron arrows

• Multi-page layout

• Rich compound format:– Fonts

– Colors

– Bond thickness

– Journal drawing styles to load/save

• 3D sketching

Isotopes, Charges, Radicals

Stereo Features, Lone Pairs

Reactions

Templates

Abbreviated and Multiple Groups

Other Sketching Goodies

electron flow arrows

attached data

link nodes

3D sketching

Rich formatting

Configuration setting

ChemDraw configuration

ISIS/Draw configuration

Formatting, customizing

Customizing drawings

• Add graphic objects (lines,

arrows, boxes, text boxes)

• Possible to change font, color,

wire thickness

• Save/load different publication

styles

• Multi-paged documents

MarvinSpace Integration

• Properties calculated by plugins can be visualized using MarvinSpace

Query and General Chemistry Features

• Query design features

– Generic atoms, generic bonds

– Atom lists/not lists

– Query properties: hydrogen

count, connection count,

number of explicit connections,

ring count, smallest ring size,

ring bond count, substitution

count, unsaturation,

aromatic/aliphatic atom

– Topology (ring/chain)

– Reacting center

– R-group queries

– Occurence

– RestH

– If-Then conditions

– Recursive SMARTS

• Basic chemistry functions:

– Aromatization/dearomatization

– Automatic stereo configuration

(R/S, E/Z)

– Automatic reaction component

identification

– Automatic reaction mapping

– Cleaning 2D layout

– 3D geometry optimization

R-group Queries

Structure Cleaning

CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1

3D2D

topology

• Cleaning Options

• 2D

– optional optimization

– wedge bonds cleaning

• 3D– fast clean

– find low energy conformer

– optional hydrogenization

– optional optimization

– generate conformers

Display Conformers

• Using the conformers plugin

one can generate the most

likely 3D structures and select

a suitable one

• The corresponding energies

are also calculated for a given

conformation

Advanced (plugin based) Functions

• Elemental Analysis

• IUPAC Name

• Protonation (pKa, Major Microspecies, Isoelectric Point)

• Partitioning (logP, logD)

• Charge (Charge, Polarizability, Orbital Electronegativity)

• Isomers (Tautomers, Resonance, Stereoisomers)

• Conformation (Conformers, Molecular Dynamics)

• Geometry (Topology analysis, Geometry, Polar surface area (2D), Molecular

Surface Area (3D))

• Markush Enumeration

• Other (H-bond donor/acceptor, Huckel Analysis, Refractivity)

Calculator Plugins

• ChemAxon’s plugin loading

mechanism enables Marvin to

provide access to a wide range

of dynamically loaded calculation

tools

• A set of plugins already provided

by ChemAxon for a separate

license key (single trial is

included in every distributions for

plugins)

• Users can easily add their own

calculator plugins to this

framework

2D & 3D Structure Visualization

• Accurate representation

• Rich visualization options

• Various display modes (wireframe, ball&stick, spacefill, etc.)

- Enable/disable hydrogen visibility (explicit / implicit, on hetero and/or terminal)

- Optional display of stereo information

- Various rotation modes

- Optional valence and reaction error highlighting in sketcher

Further Display Features

• Single structure or table views

• Animated views in viewer

MarvinView Tables

• Display SD files with property

fields

• (Re)customize table layout:

- visible rows/cols

- font size

• (Re)scale molecules in cells

separately or uniformly

Summary

ChemAxon MarvinSketch and MarvinView are

chemically aware, flexible applications enabling the

chemist to draw and display chemical structures and

to perform predictive calculations.

Marvin Beans and Marvin Applets allow developers

to integrate these tools into standalone and web

applications.

Visit other technical presentations

MarvinSketch/View http://www.chemaxon.com/MarvinSketch_View.ppt

MarvinSpace http://www.chemaxon.com/MarvinSpace.ppt

Calculator Plugins http://www.chemaxon.com/Calculator_Plugins.ppt

JChem Base http://www.chemaxon.com/JChem_Base.ppt

JChem Cartridge http://www.chemaxon.com/JChem_Cartridge.ppt

Standardizer http://www.chemaxon.com/Standardizer.ppt

Screen http://www.chemaxon.com/Screen.ppt

JKlustor http://www.chemaxon.com/JKlustor.ppt

Fragmenter http://www.chemaxon.com/Fragmenter.ppt

Reactor http://www.chemaxon.com/Reactor.ppt

Links

• Marvin home page– www.chemaxon.com/marvin

• Full Marvin API:– www.chemaxon.com/marvin/doc/api

• Animated demos and tutorials– www.chemaxon.com/demosite/marvin

• Brochures:– www.chemaxon.com/brochures/MarvinSketch.pdf

– www.chemaxon.com/brochures/MarvinView.pdf