Post on 27-Mar-2015
Solutions for Cheminformatics
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– Nice structures (antialiasing)– Rich formatting (fonts, colors, bond thickness) – Recursive SMARTS
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.)
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
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
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)
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
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
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
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.
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
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
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
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
Thank you