Indigo 1.1-beta8

We have released our first version of InChI plugin that allows to load InChI strings and generate InChI and InChIKey for molecules (this version discards stereoinformation, but we are working on it). The plugin is statically linked with the official InChI library and can be loaded on demand, as it is done with IndigoRenderer plugin.

Usage example :

IndigoInchi inchi = new IndigoInchi(indigo);
IndigoObject molecule = indigo.loadMolecule("InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3");
String inchi_string = indigo.getInchi(molecule);

New methods and functionallity:

• InChI support! (without stereochemistry yet)
• mapMolecule(queryReactoinMolecule) to retrieve mapped molecule for the query reaction for the reaction substrcuture match object
• getMolecule(index) to get the reaction molecule

• QueryMolecules can now be constructed with the following methods:

  1. addAtom, resetAtom methods for the QueryMolecule now parses arbitrary SMARTS
  2. addBond method for QueryMolecule
  3. atom.addConstraintOr method has been added
  4. a lot of query atom constraints: atomic-number, charge, isotope, radical, valence, connectivity, total-bond-order, hygrogens, substituents, ring, smallest-ring, ring-bonds, rsite-mask

Fixed:

• Issue with loading molecule attachment points if the bond orders are not marked.
• Better handling of molecules with invalid valence: canonical SMILES, unfoldHydrogens, invalid stereocenters detection. Thanks to Mederich for the bug report: http://groups.google.com/group/indigo-bugs/browse_thread/thread/8f1ac4c1bfcbc346
• Molecule serialization with more than 8 R-groups. Thanks to James Davidson for the bug report: http://tech.knime.org/forum/indigo/changes-to-scaffold-finder-node

Indigo 1.1-beta7

Changelog:

• Fixed bug: render-grid-title-offset options is not initialized.
• Fixed bug: all images are rendered as grid, after grid has been rendered.
• Possible memory issue in IndigoRenderer for Java has been fixed.

Indigo 1.1-beta6

New functionality:

• Indigo.transform(reaction, molecule) method for transformation a molecule according to a rule, specified with a reaction.
  Examples are available here: http://ggasoftware.com/opensource/indigo/concepts/transformation

• New IndigoObject methods for working with reaction atom-to-atom mapping: atomMappingNumber, setAtomMappingNumber, clearAAM

• New IndigoObject methods for working with attachment points: iterateAttachmentPoints, countAttachmentPoints, clearAttachmentPoints.
  See http://ggasoftware.com/opensource/indigo/api#attachment-points for more details

• Other new IndigoObject methods with documentation has been added: changeStereocenterType, addStereocenter, reactingCenter, setReactingCenter, loadSmartsFromFile, loadReactionSmartsFromFile, getSuperatom, getDataSGroup, description, decomposedMoleculeHighlighted, getSubmolecule, addSuperatom

• Smiles saver might throw an exception on a molecule with explicit hydrogens.
  Thanks to Colin Batchelor: http://groups.google.com/group/indigo-bugs/browse_thread/thread/35b240fb402e35c3

Changelog:

• Improvements in the automatic atom-to-atom assignment.
  Thanks to Ernst-Georg Schmid: http://groups.google.com/group/indigo-general/browse_thread/thread/ffe48381a01f7d24
  And to Daniel Lowe: http://groups.google.com/group/indigo-bugs/browse_thread/thread/11373837ba65acd

• Improvements in the molecule decomposition algorithm.

• Python 2.4 support.

• A lot of bugs has been fixed due to some internal inconsistency in explicit hydrogens handing for cis-trans bonds:

  • Substructure matcher result can be incorrect for matching query molecule with cis-trans bonds.
  • Substructure matcher result can be incorrect in case of explicit hydrogens for cis-trans bonds in the target molecule.
  • If a molecule has explicit hydrogens near cis-trans bonds, after been unserialized cis-trans configuration might flip.
  • Canonical SMILES may also produce different results for a molecule with explicit hydrogens and without them.
    

• Better stability of Indigo Java wrapper
  

• Better rendering of a SMARTS query molecules

• Indigo now informs with an exception that both cis- and trans- specification in the SMARTS expression is not supported yet. For example, such SMARTS is not supported yet: */,\[R]=;@[R]/,\*

• Fixed issue with saving query molecules in Molfile format with the atom lists.
  Thanks to Francesca: http://groups.google.com/group/indigo-bugs/browse_thread/thread/b17b468049caf57a

• unfoldHydrogens how works with reaction properly.

• Some fixes of the dearomation algorithm bug arisen during tautomer substructure matching.

• Better support of sgroups in Molfile

• Highlighting is taken into account for the computation of canonical SMILES

• Indigo.countHydrogens method doesn't throw an exception is case of existence of R-groups and pseudoatoms.

• Fixed some issues with loading and saving of polymer repetition in SMILES

• SGroups and R-sites are saving during serialization/unserilization.
  Thanks to Hinnerk Rey: http://groups.google.com/group/indigo-general/browse_thread/thread/1d9bda07b8ac299d

• Faster matching of SMARTS queries with unspecified bonds. This change also improves efficiency for our fingerprints for query molecules.

• Substructure matching counter now property counts queries with explicit hydrogens, like N-[#1].
  Thanks to James Davidson for this bug report: http://tech.knime.org/forum/indigo/substructure-match-counter-question

• Stereocenter parities are now saved into molfile.
  Thanks to Lionel: http://tech.knime.org/forum/indigo/chirality-flags

• R-group iterator now skips R-groups that are empty.

• Molfile loader now accepts left- and right-bounded atom labels.
  Thanks to Ernst-Georg Schmid: http://groups.google.com/group/indigo-bugs/browse_thread/thread/1d2b8a01af98949

• renderGridToBuffer method now support null value as the second parameter.
  Thanks to Mederich: http://groups.google.com/group/indigo-general/browse_thread/thread/b995c53227cf3352

Indigo 1.1-beta5

New functionality:

• Methods for specifing reacting centers on bonds: reaction.reactingCenter(bond), reaction.setReactingCenter(bond, mask)
  All reacting centers types are describes in Indigo namespace for Java and Python, and in ReactingCenter enum for C#.
  Code examples can be found in this thread: http://groups.google.com/group/indigo-bugs/browse_thread/thread/11373837ba65acd

• Method to add stereocenter at atom: atom.addStereocenter(type, atom_index1, atom_index2, atom_index3, atom_index4). Last parameter is optional.
  Code examples can be found in this thread: http://groups.google.com/group/indigo-dev/browse_thread/thread/a164eddce485f053

Note: this new methods have preliminary interface, and interface may be changed in the next version.

Fixed:

• Molecule to Smiles conversion with explicit hydrogens connected to cis-trans bonds.
  Thanks to Colin Batchelor: http://groups.google.com/group/indigo-bugs/browse_thread/thread/35b240fb402e35c3

Indigo 1.1-beta4

New functionality:

• New methods for Indigo: resetAtom, setRSite, isHighlighted for atoms.
  Code example: atom.resetAtom("N"), atom.setRSite("R1, R3"), atom.isHighlighted()
• Reaction product enumerator now supports recursive SMARTS

Fixed:

• Exception during Indigo for Java and Indigo for Python initialization on Mac OS X Lion 10.7
• Different AAM issues. Thanks to Daniel Lowe: http://groups.google.com/group/indigo-bugs/browse_thread/thread/11373837ba65acd
• Exception when calling hasCoord and hasZCoord on a reaction object
• Reaction product enumerator exception when monomers have no name

Indigo 1.1-alpha3

New functionality since Indigo-1.0.0 stable version:

• atomMappingNumber and setAtomMappingNumber methods for atoms to retrieve and change atom-to-atom numbers. New clearAAM method to clear atom-to-atom mapping information. Thanks to Daniel Lowe for pointing out that this functionality is missing. Code examples can be found in this thread: http://groups.google.com/group/indigo-general/browse_thread/thread/d8a413a88b9da834
• addRSite method for adding R-site atoms to the molecule. This method is similar to addAtom.
  Code example: atom = mol.addRSite("R1")

Fixed:

• foldHydrogens on [H][H] and molecules with isotopic hydrogens ([2H]C). Thanks to Daniel Lowe: http://groups.google.com/group/indigo-bugs/browse_thread/thread/2a8416c875aa8fb
• Reaction layout for reactions with empty reactants
• Saving molecule with s-group into molfile format
• Substructure matcher with special query with recursive smarts beginning with hydrogen
• Unbounded memory usage during reaction automapping. Thanks to Daniel Lowe again: http://groups.google.com/group/indigo-bugs/browse_thread/thread/e6a5e0430032e1a6/9dc36a81491283d0
• Indigo Python API module loading on Mac OS X from different directories might cause error messages
• Reaction substructure match throws an exception in some cases when these is no pair of AAM numbers. For example, reactant has AAM number while product hasn't it.