Whats new in Marvin? GUI features –atom sets, MarvinSpace integration, better customization –AWT is not used anymore File IO –new file types and seeking in files possible Many new API features Plug-ins –new plugins and old ones with extra features

GUI features Atom and bond set customization –color, wire/stick thickness, ball radius, etc. can be set and saved

GUI features Multiple document pages and printer settings

GUI features 3D clean/zoom rotate (Ctrl-3, F6, F7, F8) –MarvinSketch goes 3D with MarvinSpace

GUI features New templates: aromatics, bridged polycycles, bicycles, crown ethers, cycloalkanes, fullerenes - 3D templates

GUI features Abbreviated groups and lone pairs –bond points to the binding atom

GUI features ISIS-like reacting centers –center, make or break, change, make and change, not center –to write queries – reaction search to be implemented

GUI features Default aromatization changed to general New shortcuts for query properties (start typing with a dot) GUI for licence handling: Edit/Preferences/Licences Point-and-type editing for abbreviated groups Extra atom properties from the More window Optionally displaying chiral flags

File IO Save option in MarvinView

File IO New supported types: –Tripos MOL2, InChi –MS BMP and EMF (export only – and to clipboard) –Peptide (1 and 3 letters)

File IO Seeking in files: –API extensions in MolImporter as.skipRecord(), nextDoc(), getRecordCount(), getRecordCountMax(), estimateNumRecords(), seekRecord(int), isRewindable() –Short introduction during workshop

File IO – API features Molecule and document properties with special data types (not only strings) are exported and imported in MRV, SDfiles and RDfiles. –Supported data types: boolean, int, int[], double, double[], Molecule, MDocument, Object, String, ConformersDescriptor.

API features...many new features... MarvinSpace API available –MSpaceEasy Other changes: –MPropertyContainer to store arbitrary data –Molecule.cloneMoleculeWithDocument(): clones the molecule with its non-molecular data (graphics objects).

API features Changes: –CGraph became abstract, MoleculeGraph(parent) and Molecule(parent) constructors removed to avoid confusion with copy constructors. –The implementation of seeking in MolImporter required the extension of the molecule/document import interfaces –see marvin/doc/dev/changes.html

Plug-ins Many new plug-ins: –tautomer, resonance,stereoisomer, conformer, MD, geometry, surface area –old plug-ins are also improved in several cases (pKa, logP, logD, etc.)

Plug-ins Integrated with MarvinSpace and menus are re-arranged