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Solutions for Cheminformatics Marvin features and news Akos Papp.

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Presentation on theme: "Solutions for Cheminformatics Marvin features and news Akos Papp."— Presentation transcript:

1 Solutions for Cheminformatics 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 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. Use Marvin Beans to add MarvinSketch or MarvinView as a graphical component to your standalone application

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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