OEChem now supports the creation of InChI. OEChem produces the same InChI as the InChI library provided application for 99.77% of MDDR in the SDF format. The differences fall into two categories:
- Corrupted molecules where the tools have to make arbitrary decisions about how to correctly interpret the data.
- Bond stereo being perceived by the InChI application where bond stereo does not actually exist. OEChem does not assign bond stereo and generates what appears to be a more “correct” InChI for these cases.
The inclusion of InChI support added the following:
In addition, oemolostream will automatically write InChI when using the .inchi file extension.
OEPrepareSearch added that perceives atom and bond properties of a molecule that are necessary to successfully execute a given substructure search. It is now highly recommended to run this function on a molecule before passing the molecule to any of OEChem’s graph matching algorithms.
Several Java API points that pass primitive arrays of doubles or floats were optimized with good results. The following API points that take these primitive array types were optimized: NewConf, SetCoords, and GetCoords.
The following figures should be indicative of the performance increase in the 2013.June release:
- Changed the default input and output molecule file formats for molstreams and molthreads from OEFormat.SMI to OEFormat.ISM.
- OEWriteMDLFile writes MDL enhanced stereo groups.
- OEWriteMDLFile will now automatically write a molecule in the V3000 file format if it has more than 999 atoms or if it has any MDL enhanced stereo group regardless of the given file format flavor.
- OESetMCSExhaustiveSearchTruncationLimit and OEGetMCSExhaustiveSearchTruncationLimit functions added that control how thoroughly the search is performed by the exhaustive MCS search.
- Added the following standard SYBYL atom types: OETriposType.Cu OETriposType.Cooh, OETriposType.Croh, OETriposType.Crth, OETriposType.Fe, OETriposType.Mg, OETriposType.Mn, OETriposType.Mo, OETriposType.Se, OETriposType.Sn, and OETriposType.Zn. Atoms for which no SYBYL atom type exists are still internally handled with the OETriposType.Du type, however when writing these atoms into a MOL2 file their atomic symbol is written to the SYBYL atom type column instead of a string “Du”.
- Added OEGetDimensionFromCoords function that returns the dimension of the molecule from its coordinates.
- Residue information is now retained when reading files with MacroModel formats (.mmod, .mmd, and .dat).
Major bug fixes¶
It used to be possible to perform a substructure search for stereochemistry or hybridization on a molecule that did not yet have those properties perceived. This led to very subtle to detect problems where molecules would not match that were expected to match.
To combat this, the following OESubSearch methods now throw warnings in case some property that is necessary to successfully execute the substructure search has not been perceived yet:
These warnings can be suppressed by calling the OEPrepareSearch function on the molecule first.
It is now thread-safe to copy the same OEMol from multiple threads at the same time. This was caused by some OEMCMolBase methods not actually being const. The following methods were marked as const, but were not actually const, leading to subtle race conditions:
- OEMCMolBase.GetMCMolTitle method added to provide a way to differentiate between a top-level OEMCMolBase title and a conformer title.
- OEMCSSearch.AddConstraint now requires that the constraint is satisfied in all resulting matches. Previously, the documentation stated the following, “Constraints are considered satisfied in subgraphs which do not contain any constrained atoms or bonds in either the pattern or target molecules.” This is no longer the intended behavior.
- OEMCSSearch.AddConstraint now returns false if passed the same pattern atom or bond twice. The user must now use OEMCSSearch.ClearConstraints in order to rebuild a set of constraints.
Minor bug fixes¶
- OE3DToBondStereo function returns false if the molecule dimension is 0, since no cis or trans bonds can be perceived if there are no coordinates.
- Fixed a problem when the max matches value of the OESubSearch was reset to the default value 1024 every time the search was initialized by the OESubSearch.Init method.
- Adjusted the dimension of a molecule to 0 if it is read from either a MDL or an SDF file with no coordinates.
- OE3DToAtomStereo function throws a warning and returns false if any chiral atom of the molecule is not tetrahedral, i.e., if the atom stereo can not be determined from the 3D coordinates, usually because it is flat.
- The following functions and methods throw additional warnings in cases where either the
OE3DToAtomStereo or the OE3DToBondStereo
functions encounter any problems when assigning stereo from coordinates:
- OEPrepareSearch functions
- OEWriteMolecule function when writing the following formats: OEFormat.MDL, OEFormat.SDF OEFormat.ISM, OEFormat.INCHI and OEFormat.INCHIKEY
- OEAbsoluteConfTest.CompareMols method
- OEIsomericConfTest.CompareMols method
- OEAbsCanonicalConfTest.CompareMols method
- OEOmegaConfTest.CompareMols method
- OEDefaultConfTest.CompareMols method
- OESubsetMol now produces correct results when the RGroup flag was true and the molecule contained OEGroupBase objects.
- OEPerceiveChiral function considers hydrogens with different mass as being different i.e. it will recognize the C atom in a molecule “[3H]C(N)F” as a chiral atom, since it has four different neighbors: N, F, H and 3H.
- The first argument of the following methods is not const any longer:
- Improved the performance of the following methods:
- OEAtomBondSet.AddAtom and OEAtomBondSet.AddBond will now return false when the trying to mix atoms from different molecules.
- OEAtomBondSet.HasAtom and OEAtomBondSet.HasBond added for testing for membership.
- The following functors are now properly wrapped in Python, Java, and C#:
- The following functors are now deprecated:
Major bug fixes¶
- Calling OEPlatform::oeofstream::append after OEPlatform::oeofstream::open will no longer hang indefinitely once data is written to it.
Minor bug fixes¶
- The java JVM can run out of memory when trying to free memory. If this is detected, the OpenEye toolkits will print the following message, “JNI::OutOfMemory – the JAVA heap may need to be increased – program terminating”. Please increase the size of the java heap using the -Xmx option.
- Minor internal improvements.