Transcript What’s new in Marvin? • GUI features – atom sets, MarvinSpace integration, better customization – AWT is not used anymore • File IO – new file.

What’s 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