scientific & technical presentation marvinsketch and marvinview may 2008

Scientific & technical presentation

MarvinSketch and MarvinView

May 2008

Instead of Introduction

Technical Features

• File types to read/write:– MRV, CDX, SKC– 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 and traditional name

• Flexible– Customizable menu/toolbar– Custom templates– Calculation plugins– 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 1.5 (or later version)

platforms (Windows, Mac, Solaris, Linux/Unix) or

– .NET (Windows)

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 | CDX

CDXML | SKC | MDL Molfile Extended Molfile

Rxnfile Extended Rxnfile RDfile SDfile | Peptide

sequence | IUPAC InChI IUPAC Name |

SMILES SMARTS | Tripos SYBYL molfile Mol2 |

Gaussian Cube | PDB | XYZ

Multirecord file open in MarvinSketch

Converting Images to Structure using OSRA

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 Java or .NET Installer or Java Web Start)

– Full API (with JavaBean or .NET support) for developers to use Marvin components in applications

– Documentation and examples

• Recommended for end-users– Easy installation– Support Java 1.5 or .NET

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 1.5 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

• Easy sketching• Click-drawing, sprout• Templates, aliases,

pseudo atoms• Toolbars, shortcuts

• Stereo features:– tetrahedral (R/S)– double bond (E/Z)– diastereomer

(Abs/And/Not)– Reaction (Inv/Ret)

• Groups– Abbreviated, multiple,

repeating unit, generic, polymer related groups

– On-the-fly expanding

• Bold bonds for projected drawing

• Bracket objects for Sgroups• Attached data• Textboxes• Graphic objects (arrows,

boxes, ellipses, brackets)• Curved electron arrows• Multi-page layout• Rich compound format:

– Fonts, colors, bond thickness– Journal drawing styles to

load/save• 3D sketching

Click-drawing, sprout, on-the-fly expansion

Stereo Features, Lone Pairs

Reactions

Templates

Bold bonds and their juncitons

Brackets as graphical objects

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– R-logic– Position variation– Link node– Recursive SMARTS

• Basic chemistry functions:– Automatic valence check– Automatic lone pair calculation– Automatic stereo configuration

(R/S, E/Z)– Automatic reaction component

identification– Automatic reaction mapping– Conversion between aromatic

and Kekulé form– Cleaning 2D layout– 3D geometry optimizationn

• Structure checker– Automatic error checking– Optional fixes for errors

• Searching in online databases– ChemSpider exact search

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

Structure checker in MarvinSketch GUI

Direct search in ChemSpider

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

Molecule Matrix View

• Display SD files with

property fields

• (Re)customize table

layout: visible rows and

columns; font size

• (Re)scale molecules

in cells separately or

uniformly

Spreadsheet View

• Display structures

and data field in the

same row

• Resizable and

movable columns

• Search and edit in

data fields

• Fast loading and

scrolling of huge

SDFiles

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