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   ...
Various File Formats
 •      Molecule source file can be edited
        and saved or imported/exported in
        differen...
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,
 ...
Distributions / Marvin Beans

•   Marvin Beans                       •   Recommended for developers
    – Desktop applicat...
Distributions / Marvin Applets

• Marvin Applets                  • For web developers
   – Browser-independent           ...
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 automat...
Custom Marvin Applets Layout
Developing with Marvin Beans

•   Use Marvin Beans to add MarvinSketch or MarvinView as a graphical
    component to your ...
Molecule Sketching Features

• Drawing molecules,     • Link nodes
  reactions, residues    • Attached data
• Isotopes, ch...
Isotopes, Charges, Radicals
Stereo Features, Lone Pairs
Reactions
Templates
Abbreviated and Multiple Groups
Other Sketching Goodies




               electron flow arrows


                                                      li...
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,
 ...
MarvinSpace Integration

•   Properties calculated by plugins can be visualized using MarvinSpace
Query and General Chemistry Features

•    Query design features                •   Basic chemistry functions:
      – Gen...
R-group Queries
Structure Cleaning

                                    •   Cleaning Options
                                    •       2...
Display Conformers

•   Using the conformers plugin
    one can generate the most
    likely 3D structures and select
    ...
Advanced (plugin based) Functions

•   Elemental Analysis

•   IUPAC Name

•   Protonation (pKa, Major Microspecies, Isoel...
Calculator Plugins

•   ChemAxon’s       plugin  loading
    mechanism enables Marvin to
    provide access to a wide rang...
2D & 3D Structure Visualization

•   Accurate representation
•   Rich visualization options
•   Various display modes
    ...
Further Display Features




•   Single structure or table
    views
•   Animated views in viewer
MarvinView Tables



      • Display SD files with property
      fields

      • (Re)customize table layout:
            ...
Summary

ChemAxon        MarvinSketch   and    MarvinView   are
chemically aware, flexible applications enabling the
chemi...
Visit other technical presentations

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

MarvinSpace      ...
Links


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

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

• Animat...
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MarvinSketch and MarvinView: Tips And Tricks: US UGM 2008

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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: http://www.chemaxon.com/product/marvin_land.html

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MarvinSketch and MarvinView: Tips And Tricks: US UGM 2008

  1. 1. Scientific & technical presentation MarvinSketch and MarvinView May 2008
  2. 2. Instead of Introduction
  3. 3. 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
  4. 4. 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
  5. 5. Image Export • Create raster or vector graphical image from your structure.
  6. 6. OLE component for documents • Editable molecules in Office documents
  7. 7. 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.
  8. 8. 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
  9. 9. 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
  10. 10. Web Browser Compatibility •Internet Explorer •Firefox •Mozilla •Netscape •Safari •Opera
  11. 11. 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.
  12. 12. Custom Marvin Applets Layout
  13. 13. 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.
  14. 14. 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
  15. 15. Isotopes, Charges, Radicals
  16. 16. Stereo Features, Lone Pairs
  17. 17. Reactions
  18. 18. Templates
  19. 19. Abbreviated and Multiple Groups
  20. 20. Other Sketching Goodies electron flow arrows link nodes attached data 3D sketching
  21. 21. Rich formatting
  22. 22. Configuration setting ChemDraw configuration ISIS/Draw configuration
  23. 23. Formatting, customizing
  24. 24. 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
  25. 25. MarvinSpace Integration • Properties calculated by plugins can be visualized using MarvinSpace
  26. 26. 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
  27. 27. R-group Queries
  28. 28. 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
  29. 29. 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
  30. 30. 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)
  31. 31. 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
  32. 32. 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
  33. 33. Further Display Features • Single structure or table views • Animated views in viewer
  34. 34. 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
  35. 35. 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.
  36. 36. 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
  37. 37. 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

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