Version 2.1.3

OEChem TK 2.1.3

New features

• The InChI code has been updated to the v1.05 source released on January 27, 2017. This code is available from the InChI Trust and was validated against eMolecules and ChEMBL_23 public structure sources.

• InChI is now a fully supported read/write format for chemical structures. New public API points have been added to support this format: OEMolToSTDInChI, OEMolToSTDInChIKey, OEInChIToMol, and OEParseInChI.

Warning

The standard InChI format includes chemical normalization activity that results in round-trip structure alterations to a very high percentage of structures when unnormalized or when arbitrary input chemistry is used. Even the output of OEMolToInChI, which generates a nonstandard InChI and attempts to minimize structure normalizations, results in many changes to input chemical structures.

• OEInChIOptions now supports relative stereo and racemic stereo InChI output as well as control of the timeout condition.

• The default output flavor for writing InChI or InChIKey via OEWriteMolecule has been changed to include the molecule title as well as the InChI information to synchronize behavior with other output formats. Since the InChI identifiers never include white space, there should be no ambiguity for separating the InChI information from the title. If there are third-party readers that have problems with the title, the following output flavor bits are now available to control whether the title is added to the output: OEOFlavor::INCHI::Title and OEOFlavor::INCHIKEY::Title.

• An overload of OEShortestPath has been added to take an atom predicate and return the shortest path between atoms that are not excluded by the predicate.

Minor bug fixes

• OEParseSmiles no longer throws an “Unable to Kekulize SMILES” warning in quiet mode (see also OEParseSmilesOptions).

• OEDeleteEverythingExceptTheFirstLargestComponent has been reimplemented using OEDetermineComponents and no longer returns true for one-component molecules with explicit hydrogens.

• OEWriteMolecule and OEWriteConstMolecule now return the new OEWriteMolReturnCode::NoConformer constant in cases when a multi-conformer molecule is being written without any conformer.

• OEGetSmiStringOrder now has both a const and a non-const version.

• OEGetSmiStringOrder could crash for structures that were modified by deleting atoms. This has been fixed.

• The OESMILESFlag::AllBonds flavor flag had been missing from the OEOFlavor namespace and has been added to the OEOFlavor::SMI, OEOFlavor::ISM, OEOFlavor::CAN and OEOFlavor::USM namespaces.

OESystem TK 2.1.3

New features

• A new parameter has been added to the constructor of OEDots that enables changing the “processed” label in the output lines.

Minor bug fixes

• The function OEGetTag and method OEBase::GetData could segfault when called with a null char * argument in C++ or with an empty argument in the wrapped languages. These have been fixed.

OEBio TK 2.1.3

New features

• OESetupSplitMolComplexOptions now has two additional parameters, siteOverride and modelOverride, that make it easier to configure filters while iterating over binding sites and/or model numbers. The new constant OESplitMolComplexParam::DoNotOverride is used control the behavior of these constants.

• A new atom predicate, OEIsWater, has been added.

• Two new methods, OEInteractionHint::GetDetails and OEInteractionHint::SetDetails, have been added.

• Two new interaction hint types have been added to interaction perceptions: OECovalentInteractionHint and OECationPiInteractionHint. When covalent interactions are present, nearby clash interactions are no longer perceived.

• The OECrystalSymmetryParams class now stores the Z-value parsed from the CRYST1 line of a PDB file.

Minor bug fixes

• GetGroups no longer crashes on Windows in cases where no alternate location group exists.

• Calling the function OEBuildUnitCell on protein molecules had previously consumed large amounts of memory and, as a result, would often crash. This issue has been addressed, and the performance of the function has been improved for molecules of small or medium size.

• Interaction perception for anionic carbonyl groups has been fixed.

• OEIsValidActiveSite now takes into account the non-default parameter ligand component type.

Documentation changes

• An example in Preparing a Protein has been modified to work properly when splitting a ligand from a binding site other than the first one.

OEGrid TK 1.6.0

Minor bug fixes

• OEMaskGridByMolecule no longer segfaults for an empty molecule or for a molecule without 2D coordinates. It now throws a warning and returns false.

• On Windows, UTF8 file and directory names are now correctly supported for toolkit file I/O operations.

Java-specific changes

• The following methods are now wrapped correctly as constCall:

  • OEIsRxnComponentGroup::operator()

  • OEIsReactantGroup::operator()

  • OEIsProductGroup::operator()

Documentation changes

• Read/write examples have been added to demonstrate the use of the InChI structure format.

• Examples of using the preferred OEMolToSTDInChI and OEMolToSTDInChIKey API points when creating standard InChI strings have been updated.

• Examples have been updated to now use OEDeleteEverythingExceptTheFirstLargestComponent rather than the deprecated function OETheFunctionFormerlyKnownAsStripSalts.

• The classes OENearestNbrs and OENbrs, function OEGetNearestNbrs, and namespace OENearestNbrsMethod have been documented.