Published on November 5, 2008
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
Web Browser Compatibility •Internet Explorer •Firefox •Mozilla •Netscape •Safari •Opera
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
Configuration setting ChemDraw configuration ISIS/Draw configuration
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
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 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
... US UGM 2008. Combinatorial Markush structure handling at ChemAxon: ... MarvinSketch and MarvinView: Tips And Tricks: US UGM 2008. J Chem Edu 2008 85 1083.
2008 European User Group Meeting Program May 7th and 8th, ... tips and tricks. ... The new system uses MarvinView and MarvinSketch, ...
MarvinSketch and MarvinView: Tips And Tricks: US UGM 2008. ... US UGM 2008. AP European History Exam format, tips and tricks. HFM Tips and Tricks.
2008 US User Group Meeting ... features, tips and tricks. György Pirok ... Robots, fish and integration at first US UGM.
Scientific & technical presentation MarvinSketch and MarvinView May 2008. ... Scientific & technical presentation MarvinSketch and MarvinView May 2008 :
Since the last US UGM several new features ... The development of the .Net version of MarvinSketch and MarvinView ... What's new? Tips & Tricks ...
June, 2007 David Spender*, Erika Biró What's new in Marvin and development discussion.
November 2008. 2 Migration ... MarvinSketch MarvinView MarvinSpace ... Java Solutions for Cheminformatics - Platform independent. software for chemistry.