MarvinSketch and MarvinView: Tips And Tricks: US UGM 2008

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Information about MarvinSketch and MarvinView: Tips And Tricks: US UGM 2008

Published on November 5, 2008

Author: ChemAxon



This general presentation on Marvin will summarize the features, and detail the latest additions and improvements. The most important and newest features will be demonstrated, providing tips and tricks for their quicker and easier usage. The list of potential future features will also be presented, including the 'traditional' voting session. For latest developments see:

Scientific & technical presentation MarvinSketch and MarvinView May 2008

Instead of Introduction

Technical Features • File types to read/write: • Printing, multipage documents – MOL, SDF, RXN, RDF • 3D models, Java or OpenGL (V2000/V3000) rendering (with MarvinSpace) – SMILES, SMARTS/SMIRKS • Available as (recursive) – Java (signed) applets – XML based format MRV, CML, InChi, MOL2, XYZ, Gaussian – Applications, deployment with Cube installer, Java Web Start – PDB, 1 and 3 letter peptide – JavaBeans – IUPAC Name • System Requirements: • Flexible – Java 1.4 (or later version) platforms (Windows, Mac, – Calculation plugins Solaris, Linux/Unix) – Custom templates – Custom formatting – Image export into BMP, JPEG, PNG, PPM, POV, SVG, EMF, PDF

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 • Recommended for developers – Desktop applications – Quick GUI building (deployment with Installer, – Easy customization Java Web Start) – Full API (with JavaBean – Direct manipulation of support) for developers to use molecules Marvin components in applications • Free for open access, non – Documentation and examples commercial websites • Recommended for end-users • Free for academic research – Easy installation and teaching – Support Java 1.4 capable • Free for Evaluation platforms (Windows, Mac OS X, Linux/Unix) – Command line molecule converter – Applications are free for end- users

Distributions / Marvin Applets • Marvin Applets • For web developers – Browser-independent – Simple web base solution for Marvin deployment integration into web pages – Modular architecture – Wide range of layout ensures short download customization time – API to control the applets – Minimum requirement from JavaScript (Java 1.4 capable – Documentation and browsers) examples • 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, • Link nodes reactions, residues • Attached data • Isotopes, charges, • Graphic objects (lines, radicals arrows, boxes, text) • Stereo features: • Curved electron arrows – tetrahedral (R/S) • Multi-page layout – double bond (E/Z) – diastereomer • Rich compound format: (Abs/And/Not) – Fonts • Reaction (Inv/Ret) – Colors – Bond thickness • Templates, aliases, – Journal drawing styles to pseudo atoms load/save • Abbreviated groups, • 3D sketching Multiple groups

Isotopes, Charges, Radicals

Stereo Features, Lone Pairs



Abbreviated and Multiple Groups

Other Sketching Goodies electron flow arrows link nodes attached data 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 • Basic chemistry functions: – Generic atoms, generic bonds – Aromatization/dearomatization – Atom lists/not lists – Automatic stereo configuration – Query properties: hydrogen (R/S, E/Z) count, connection count, – Automatic reaction component number of explicit connections, identification ring count, smallest ring size, – Automatic reaction mapping ring bond count, substitution – Cleaning 2D layout count, unsaturation, aromatic/aliphatic atom – 3D geometry optimization – Topology (ring/chain) – Reacting center – R-group queries – Occurence – RestH – If-Then conditions – Recursive SMARTS

R-group Queries

Structure Cleaning • Cleaning Options • 2D CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1 – optional optimization – wedge bonds cleaning topology • 3D – fast clean – find low energy conformer – optional hydrogenization – optional optimization – generate conformers 2D 3D

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 MarvinSpace Calculator Plugins JChem Base JChem Cartridge Standardizer Screen JKlustor Fragmenter Reactor

Links • Marvin home page – • Full Marvin API: – • Animated demos and tutorials – • Brochures: – –

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