- Generic Data handling chapter added.
- All the OEChem examples have been overhauled. Several examples have been removed, new ones have been created and all the examples (across all the languages we support) have been reviewed to bring them up to a similar standard. For the details of example toolkit scripts see the examples summary chapter. Source code is also included in the documentation.
- OEAtomBondSet container added.
- OEIsAtomHybridization functor added.
- OEBase.GetDataIter that takes an unsigned integer added for convenience.
- OEIsMember and OEIsMemberPtr can now be initialized with an OEIterBase pointer.
- OEParseSmiles function will now ignore extra leading spaces in non-strict mode.
- OELibraryGen.SetTitleSeparator will now store an internal copy of the string, fixing issues in wrapped languages.
- OEIs3DFormat function added as a convenience function for the user to determine whether a file format supports 3D coordinates.
- OEMolBase.Clear can now be called on a compressed DBMol and DBMCMol to wipe out the molecule entirely.
- OEIsNonRingAtomDoubleBondedToRing functor added to detect atoms double bonded to a ring. Most users consider atoms double bonded to a ring system as part of the “scaffold”.
- MiniMols can now store coordinates, energy, and dimension. These are stored as generic data, so not particularly “mini”. Just meant to allow MiniMols to be used as a more general purpose molecule implementation.
- Safety precautions to prevent corrupted molecules from being written were placed into the OEB writer for rotor-offset-compressed molecules. These molecules should not be modified, and definitely should not be written if they were modified.
- Both old format and new format PDB hydrogen atom names are now supported. The new PDB naming format is used when new H atom names are assigned. The call OEResidueHydrogens now supports an option to control which style of H atom names is assigned.
- Four new residue types have been defined: OEResidueIndex.NHE (carboxy-terminal amine) OEResidueIndex.NME (carboxy-terminal methyl amine) OEResidueIndex.CIP (AmberFF’s +1 ion) OEResidueIndex.CIM (AmberFF’s -1 ion).
- OENearestNbrs now supports OEFloatArray in
All of the native array wrapper classes like OEFloatArray have two new methods: a constructor that takes a Java array of the same base type, and a toArray method that will return a Java array of the same type.
Major bug fixes¶
- OENearestNbrs fixed in java to not randomly crash due to early garbage collection of the atoms in the returned iterators.
- OENewMolBase, OENewMCMolBase, OENewQMolBase no longer leak the memory of the molecules.
- Fixed a crash in the OEB writer that occurred when very large values were set for the map index or isotope atom properties.
- Fixed a bug with parity bits in SDF files. This would occur if OEPerceiveChiral was called with an aromaticity model other than MDL before the molecule was written. The SDF writer now makes sure to re-perceive chirality based upon the MDL aromaticity model to get the correct parity bits.
- Fixed a memory leak that would occur when reusing a oemolistream for many different files under certain circumstances.
- OEMol.operator= fixed to not duplicate SD data when being assigned from an OEGraphMol.
- The FASTA reader now assigns the proper stereochemistry to the molecules it produces.
- The function OEPerceiveResidues now respects the following data preservation flags: OEPreserveResInfo.Occupancy, OEPreserveResInfo.BFactor, and OEPreserveResInfo.FragmentNumber both individually and implicitly as part of the flag: OEPreserveResInfo.All. Using the flag OEPreserveResInfo.SerialNumber will leave only the serial number of new atoms altered.
Minor bug fixes¶
- OELibraryGen fixed when explicitly defined bonds on the reactant side are not set correctly. This used to generate products with incorrect valence.
- OEMiniMol::Sweep() fixed to properly re-index atoms and bonds after some atoms and bonds were deleted.
- OEKekulize will now fail if the integer bond types are set correctly, i.e., not between 1 and 5 inclusive.
- OEOFlavor.Generic.Default will now be consistent in molstreams for all flavors. The OEIsWriteable function that takes a format and a flavor will now check the generic and specific flavor bits separately.
- OERMSD fixed when dealing with multi-conformer molecules with suppressed hydrogen atoms.
- OERMSD will now check whether the associated OEMatchBase actually belongs to the molecule being passed in.
- OEParseSmiles fixed to not crash when parsing empty strings in strict mode.
- OELibraryGen.GetTitleSeparator method signature changed to return a string directly. The previous signature and function couldn’t operate and didn’t actually do anything.
- OESmartsLexReplace fixed to not give incorrect SMARTS whenever a name appears twice in the bindings vector. Instead, the first pair is used, and a warning is thrown to indicate to the user about there being multiple pairs.
- OEIsHeavy is fixed to not return true for dummy atoms, that is, any atom with an atomic number of 0. OEIsHeavy will only return true if the atomic number is greater than 1.
- oemolithread.openstring crash fixed when used without a valid format being set.
- Atom names perceived for unknown ligand types (OEResidueIndex.UNK and OEResidueIndex.UNL) are now constructed from the element name and an integer.
- OEAddExplicitHydrogens is fixed to produce better hydrogen placement geometries when adding hydrogens to sp3 carbons where the carbon’s existing attachments vary significantly from ideal tetrahedral geometry.
- New OEAltLocationFactory.GetCurrentLocations methods provide a way to determine which alternate locations are selected. A new OEAltLocationFactory.GetGroup method is provided to convert from an OEAltLocation to an OEAltGroup.
- A new OEGetRotamers call that takes an OEResidue is now provided as a convenience.
- A new OEExpandCrystalSymmetry function expands the crystal symmetry of the source molecule into different conformers in the destination molecule.
Minor bug fixes¶
- OERotamer is now properly wrapped in Java.
- Crystal symmetry API is now properly wrapped in Java.
- OEBio::OEHierResidue::GetOEResidue() now returns a reference to a blank residue when the class is uninitialized instead of a reference to random memory.
- Adding OESequenceAlignment.operator bool method. An OESequenceAlignment object is considered invalid until its implementation is set. Both the OEWriteAlignment and the OERMSD functions checks whether the passed alignment is valid and throw a warning if it is not.
Minor bug fixes¶
- OEGetCenterAndExtents fixed to work on a OESkewGrid when it is regular grid, i.e. has no orientation.
- OEErrorHandler.SetOutputStream performance significantly improved to avoid quadratic behavior in certain circumstances.
- OEWriteGrid fixed to actually gzip the output if the file name ends in .gz. Before it would just write the file in the specified format, but never gzip it.
- OEErrorLevel.Default has been changed from OEErrorLevel.Verbose to OEErrorLevel.Info. This allows OEThrow.Verbose to be used for printing more information to the terminal, but it will only appear when OEThrow.SetLevel is called with the OEErrorLevel.Verbose level. In the past, the OEErrorLevel.Verbose level was essentially ignored since it was nearly the same as OEErrorLevel.Info.
- OELinearColorGradient class added to interpolate colors between specified ranges. OEColorStop class added to initialize OELinearColorGradient objects.
- OESystem::OEBkgrdGrey added as a new color for using a light grey background of an image.
- OECopyBaseData convenience function added for copying generic data.
- OEGetTag heavily optimized for multi-threaded use.
Minor bug fixes¶
- OEBitVector.SetData crash fixed where it would try to copy more bytes than the actual size of the given data.
- OEStringToNumber function now allows for new-line characters, \n, to appear after the digits in the string.
- OEBase generic data can now handle an empty std::vector through OEB reading and writing.
- OEStringTokenize now has an additional parameter, concat_delim, that specifies whether consecutive delimiters should be treated as a single delimiter. This is useful for parsing CSV files with empty fields. However, the default behavior is to behave as before, treating consecutive delimiters as a single delimiter.
- OEGridBase.GetXIdx, OEGridBase.GetYIdx, OEGridBase.GetZIdx fixed so that the dimensions are guaranteed to always be within the dimensions of the grid. These methods would sometimes return indices that were outside the range of the dimensions of the grid due to floating point rounding errors.
- unsigned can now be used as the !TYPE in interface files for unsigned int parameters.
- OELinearInterpolate performance has been significantly improved.