Presentation on theme: "Scientific & technical presentation MarvinSketch and MarvinView"— Presentation transcript:
1Scientific & technical presentation MarvinSketch and MarvinView May 2008
2Instead of Introduction Why Marvin? Marvin is the paranoid robot from The Hitchhikers Guide to The Galaxy.
3Technical Features File types to read/write: Flexible MRV, CDX, SKCMOL, SDF, RXN, RDF (V2000/V3000)SMILES, SMARTS/SMIRKS (recursive)XML based format MRV, CML, InChi, MOL2, XYZ, Gaussian CubePDB, 1 and 3 letter peptideIUPAC and traditional nameFlexibleCustomizable menu/toolbarCustom templatesCalculation pluginsCustom formattingImage export into BMP, JPEG, PNG, PPM, POV, SVG, EMF, PDFPrinting, multipage documents3D models, Java or OpenGL rendering (with MarvinSpace)Available asJava (signed) appletsApplications, deployment with installer, Java Web StartJavaBeansSystem Requirements:Java 1.5 (or later version) platforms (Windows, Mac, Solaris, Linux/Unix) or.NET (Windows)
4Various File FormatsMolecule source file can be edited and saved or imported/exported in different formatsPossible to insert into a long file of many compounds at a given locationAlso possible to read a structure from a given position of a long fileAppend current structure to an existing fileChemAxon 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 | XYZMarvin can import/export molecules from/into several chemical file formats.
10Distributions / 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 applicationsDocumentation and examplesRecommended for end-usersEasy installationSupport Java 1.5 or .NET capable platforms (Windows, Mac OS X, Linux/Unix)Command line molecule converterApplications are free for end-usersRecommended for developersQuick GUI buildingEasy customizationDirect manipulation of moleculesFree for open access, non commercial websitesFree for academic research and teachingFree for EvaluationMarvin is available in the following distributions.
12Web Browser Compatibility Internet ExplorerFirefoxMozillaNetscapeSafariOperaMarvin applets can run in all Java capable browser.
14Custom Marvin Applets Layout You can specify actions to buttons in the Marvin Applets.
15Developing with Marvin Beans Use Marvin Beans to add MarvinSketch or MarvinView as a graphical component to your standalone applicationAdditional 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.Developing with Marvin Beans
16Molecule Sketching Features Easy sketchingClick-drawing, sproutTemplates, aliases, pseudo atomsToolbars, shortcutsStereo features:tetrahedral (R/S)double bond (E/Z)diastereomer (Abs/And/Not)Reaction (Inv/Ret)GroupsAbbreviated, multiple, repeating unit, generic, polymer related groupsOn-the-fly expandingBold bonds for projected drawingBracket objects for SgroupsAttached dataTextboxesGraphic objects (arrows, boxes, ellipses, brackets)Curved electron arrowsMulti-page layoutRich compound format:Fonts, colors, bond thicknessJournal drawing styles to load/save3D sketchingA quick review about Marvin features.
28Customizing drawingsAdd graphic objects (lines, arrows, boxes, text boxes)Possible to change font, color, wire thicknessSave/load different publication stylesMulti-paged documents
29MarvinSpace Integration Properties calculated by plugins can be visualized using MarvinSpace
30Query and General Chemistry Features Query design featuresGeneric atoms, generic bondsAtom lists/not listsQuery properties: hydrogen count, connection count, number of explicit connections, ring count, smallest ring size, ring bond count, substitution count, unsaturation, aromatic/aliphatic atomTopology (ring/chain)Reacting centerR-group queriesR-logicPosition variationLink nodeRecursive SMARTSBasic chemistry functions:Automatic valence checkAutomatic lone pair calculationAutomatic stereo configuration (R/S, E/Z)Automatic reaction component identificationAutomatic reaction mappingConversion between aromatic and Kekulé formCleaning 2D layout3D geometry optimizationnStructure checkerAutomatic error checkingOptional fixes for errorsSearching in online databasesChemSpider exact searchA quick review about Marvin features.
31R-group QueriesR-groups support is useful for query drawing.
32Structure Cleaning You can customize cleaning with various options. Cleaning Options2Doptional optimizationwedge bonds cleaning3Dfast cleanfind low energy conformeroptional hydrogenizationgenerate conformersCC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1topologyYou can customize cleaning with various options.2D3D
33Display ConformersUsing the conformers plugin one can generate the most likely 3D structures and select a suitable oneThe corresponding energies are also calculated for a given conformationBy selecting the Edit->Clean->3D- >Select conformer menu option, you can choose among them.
37Calculator PluginsChemAxon’s plugin loading mechanism enables Marvin to provide access to a wide range of dynamically loaded calculation toolsA 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
382D & 3D Structure Visualization Accurate representationRich visualization optionsVarious display modes (wireframe, ball&stick, spacefill, etc.)Enable/disable hydrogen visibility (explicit / implicit, on hetero and/or terminal)Optional display of stereo informationVarious rotation modesOptional valence and reaction error highlighting in sketcherSeveral display options are common in sketcher and in viewer.
39Further Display Features In viewer, structures can move.Single structure or table viewsAnimated views in viewer
40Molecule Matrix ViewDisplay SD files with property fields(Re)customize table layout: visible rows and columns; font size(Re)scale molecules in cells separately or uniformlyMarvinView application can display property fields of SD files.
41Spreadsheet ViewDisplay structures and data field in the same rowResizable and movable columnsSearch and edit in data fieldsFast loading and scrolling of huge SDFilesMarvinView application can display property fields of SD files.
42SummaryChemAxon 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.
43Visit other technical presentations MarvinSketch/ViewMarvinSpaceCalculator PluginsJChem BaseJChem CartridgeStandardizerScreenJKlustorFragmenterReactor
44Links Marvin home page Full Marvin API: Animated demos and tutorials Full Marvin API:Animated demos and tutorialsBrochures: