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Marvin features and news

Marvin features and news. Akos Papp. Main original features – 1. 2D and 3D sketching and viewing Isotopes, charges, radicals, maps Stereo features (tetrahedral, double bond, diastereo) Valence check, lone pairs, implicit hydrogens Aliases, pseudo-atoms Attached data

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Marvin features and news

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  1. Marvin features and news Akos Papp

  2. Main original features – 1 • 2D and 3D sketching and viewing • Isotopes, charges, radicals, maps • Stereo features (tetrahedral, double bond, diastereo) • Valence check, lone pairs, implicit hydrogens • Aliases, pseudo-atoms • Attached data • Nice structures (antialiasing) • Rich formatting (fonts, colors, bond thickness) • Recursive SMARTS

  3. Main original features – 2 • Query drawing features • Any atom, atom list/not-list, link nodes • Atom properties (substitution count, aromatic, etc.) • Bond topology (ring, chain) • Reaction topology (reacting center, inversion/retention) • Markush structure drawing features • Groups • Large collection of abbreviated groups • Quick drawing using the keyboard • Custom group creation (R-group, S-group, etc.)

  4. Major original features – 3 • Single step reaction drawing • Automatic component recognition • Automapping Graphics, text boxes, electron flow arrows • 2D and 3D structure clean • Aromatization /dearomatization • Multipage sketches • Molecule matrix view in MarvinView • Customizable menu and toolbar • ISIS/Draw-like and ChemDraw-like configurations

  5. Major original features – 3 • OLE component for Office documents • Periodic system ‘Query’ tab containing • Generic query features and periodic table groups • Dynamic IUPAC name text box • Name import • From file or from any document through copy/paste • Creating templates by drag-drawing to toolbar • Spreadsheet-like view in MarvinView for SD and RDFiles • Calculator plugins

  6. Calculator plugins - 1 • Elemental analysis • Protonation (pKa, major microspecies, isoelectric point) • Partitioning (logP, logD) • Charge (charge, polarizability, orbital electronegativity) • Isomers (tautomers, stereoisomers) • Conformation (conformers, molecular dynamics, 3D alignement)

  7. Calculator plugins – 2 • Geometry (topology analysis, geometry, polar surface area (2D), molecular surface area (3D)) • H-bond donors and acceptors, Huckel analysis, refractivity, resonance, structural frameworks • Naming • IUPAC name • Traditional name • Markush enumeration • Sequential, random, library size calculation • Homology group enumeration

  8. Main original technical features • Import/export of all important molecular file formats • Inter-conversion, automatic recognition • Image export to the major image file formats • Visualization with MarvinView and MarvinSpace • Distributions: Standalone, JWS, Beans, Applets • Platform and browser independent • Features are available from API • Free for Non commercial websites, Academic research and teaching, Evaluation

  9. 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.

  10. Applet specific features • 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.

  11. Main new features – 5.2 • Transparent structure painting • Transparent background images (EMF, SVG, PNG) • Transparent OLE object • MView spreadsheet view speedup • Marvin initialization speedup in applet version (in 5.2.2) • Charges can be displayed on brackets • OLE object improvments • Image properties (colors, implicit H, etc.) • Speed (memory resident OLE server) • Periodic system coloring schemes • Reaxys Generics atoms and groups

  12. Future features – 5.3 • .Net version • Marvin initialization speedup in applet version • Sprout drawing • Projected drawing • Bold bonds • Turning structures into projection • Brackets as graphical objects • Bracket coordinate is automatic by default, but the the bracket can be moved • Data can be attached to it

  13. Future features – 5.3 • Chemical terms editor in GUI • Template handling redesign • Load templates from specified directories • Skc import and export • Multirecord file (SDFile) import to the same canvas • Spreadsheet view mode for MView applet

  14. Future features – 5.4 • Marvin Lite (Modular system) • Structure checker component in GUI • Enhanced handling of group attachment points • Leaving group definition • Multistep reaction support • Real arrows with automatic assignment of reactants • MarvinView GUI redesign

  15. Thank you

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