Version 1.9.1

OEChem 1.9.1

New features

• OEOmegaConfTest has been created specifically for output from OMEGA. This conftest ignores invertible nitrogen stereochemistry that OMEGA freely adjusts in order to allow these conformers to be read into the same OEMol.

• OELibraryGen.SetValidateKekule added to set whether alternative Kekulé forms are enumerated until a valid form is identified before returning a product.

• OEChem::oemolithread::GetMolData method added to return a generator over all the molecules of a file in their string representation in the source format.

• The oemolthreadbase.GetMol method for oemolithread class will now return chunks of molecule files that can be directly written to files to enable faster tokenization of a molecule file. Before this release, this method would often not return whitespace that was necessary to delineate boundaries between molecules.

• oemolthreadbase.PutMol and oemolthreadbase.GetMol support added to the wrapped languages: Python, Java, and C#.

Major bug fixes

• OEPerceiveResidues had a bug introduced in the 2012.Feb release that could cause crashes or strange data to be written to the OEAtomBase.GetName field whenever OEAtomBase.GetAtomicNum returned 0. Atoms with an atomic number of 0 will now be given the name of `` UNK`` (note, the leading space to match PDB style names).

• OEAssignAromaticFlags no longer takes an OEAroModel, which was a unsigned short * typedef, but takes an integer from the OEAroModel namespace instead. Global constants prepended with OEAroModel* are now deprecated. This works around a serious bug that would sometimes cause OEAssignAromaticFlags to not do anything to the molecule. This may break source-level backwards compatibility for strongly typed languages (C++, Java, and C#) if a global constant prepended with OEAroModel* was stored as a variable.

Python code should continue to work due to dynamic typing. The only change for python is that the following OEAroModel* global constants are now deprecated.

Minor bug fixes

• oemolithread and oemolothread can no longer to be copy constructed. They are heavy weight objects representing real operating system threads and thus should not be copied.

• The MDL V3000 reader now throws a warning that the ENDPTR and ATTACH bond properties will be ignored.

• OEMatch.AddPair now checks whether the atom and bond pairs belong to the same molecule.

• OELibraryGen now allows an aromatic bond to become a triple bond when breaking a ring.

OESystem 1.9.1

New features

• Adding a default constructor for the OELinearColorGradient class that generates a color gradient with no color stop. The OEColorGradientBase.IsEmpty was added to be able to determine if the object was default constructed. Additionally, the OEColorGradientBase.GetColorAt method will always return the color OEBlack for a color gradient with no color stops, i.e., OEColorGradientBase.IsEmpty returns true.

• OEStringTabsToSpaces function added to expand tab characters to 4 space characters.

• OEBitVector.FromHexString performance has been significantly improved.

Minor bug fixes

• OEStringTokenizeQuoted now treats consecutive delimiters as blank fields.

• OEErrorHandler, and thus OEThrow, will no longer record the number of messages that did not actually get through due to the message not meeting the OEErrorHandler.SetLevel threshold.

• OEParseCommandLine will now call exit(0) if the internal call to OECheckHelp returns true that a --help parameter is found. That is, program execution with the --help parameter should not be considered abnormal program termination.

• OEGeom3DRotVectorToTransform return type changed from void to bool to be able to indicate cases when the function can fail.

• OEAnnotation.GetChildren will now work in Python.

• ProcessCommandLineStreams was deprecated, and is now removed.

Documentation fixes

• OEBitVector.FromHexString and OESystem::OEBitVector::ToHexString documentation has been corrected to explain their behavior with respect to bit vector lengths and the handling of non-hexadecimal digits in the translation process.

• OECheckHelp is now documented.

OEPlatform 1.9.1

New features

• oeifstream.pread method added to allow multiple threads to read from a single file.

• oeiofstream class added to support reading and writing to the same open file.

• oeistream.read method added to read the entire contents of the stream or throw std::bad_alloc whenever the system runs out of memory.

• oemultiostream has been added. More than one oeostream can be added to this class for simultaneous output.

• OEFileTempDescriptor added to safely create temporary files without race conditions. OEFileRandomName is now deprecated as it can lead to race conditions in the file names it generates.

Major bug fixes

• OEPlatform::oeifstream::getline would sometimes cause buffer overflows whenever max characters were actually in the line. The documentation was not very clear what this max parameter meant, it used to be the line size, not including the null terminator. Now it means the size of available memory in the buffer passed in, including the null terminator, and the documentation is now more clear on the subject.

• OEPlatform::oeifstream::append will now close the previous file before opening the next file. Before, calling the append method in a loop could lead to the process easily running out of a available file descriptors.

• The macros OE32BIT and OE64BIT were improperly set on 64-bit Windows.

Minor bug fixes

• OEGetHostIdent fixed to work on machines where eth0 was not in use for network traffic.

OEBio 1.9.1

Minor bug fixes

• OESequenceAlignment methods GetBackboneMatch and GetCAlphaMatch now returns OEMatchBase instead of OEMatch.

Documentation fixes

• OERotamer class is now documented for working with frequently observed conformations of amino-acid sidechains .

OEGrid 1.4.2

Major bug fixes

• OEReadGrid no longer leaks memory for CCP4 files.