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::SetValidateKekuleadded to set whether alternative Kekulé forms are enumerated until a valid form is identified before returning a product.
oemolthreadbase::GetMolmethod 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.
Major bug fixes¶
OEPerceiveResidueshad a bug introduced in the 2012.Feb release that could cause crashes or strange data to be written to the
0. Atoms with an atomic number of
0will now be given the name of `` UNK`` (note, the leading space to match PDB style names).
OEAssignAromaticFlagsno longer takes an
OEAroModel, which was a
unsigned short *typedef, but takes an integer from the
OEAroModelnamespace instead. Global constants prepended with
OEAroModel*are now deprecated. This works around a serious bug that would sometimes cause
OEAssignAromaticFlagsto 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.
Code may have to be ported like the following:
OEAroModel m = OEChem::OEAroModelOpenEye; // change the previous line to the following unsigned int = OEChem::OEAroModel::OpenEye; OEAssignAromaticFlags(mol, m);
Minor bug fixes¶
Adding a default constructor for the OELinearColorGradient class that generates a color gradient with no color stop. The
OEColorGradientBase::IsEmptywas added to be able to determine if the object was default constructed. Additionally, the
OEColorGradientBase::GetColorAtmethod will always return the color
OEBlackfor a color gradient with no color stops, i.e.,
OEStringTabsToSpacesfunction added to expand tab characters to 4 space characters.
OEBitVector::FromHexStringperformance has been significantly improved.
Minor bug fixes¶
OEStringTokenizeQuotednow treats consecutive delimiters as blank fields.
OEParseCommandLinewill now call
exit(0)if the internal call to
--helpparameter is found. That is, program execution with the
--helpparameter should not be considered abnormal program termination.
OEGeom3DRotVectorToTransformreturn type changed from
boolto be able to indicate cases when the function can fail.
oeifstream::preadmethod 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::readmethod added to read the entire contents of the stream or throw
std::bad_allocwhenever the system runs out of memory.
oeistream methods that read into
std::stringobjects have been significantly optimized.
OEPlatform::oeifstream::getline that takes a
std::stringwithout a size parameter was arbitrarily capped to only read a line 64K long. The method will now keep reading data provided there is enough memory to allocate for the
OE_CURRENT_FUNCTION macro added that provides a
const char *to the name of the current C++ function.
Major bug fixes¶
OEPlatform::oeifstream::getline would sometimes cause buffer overflows whenever
maxcharacters were actually in the line. The documentation was not very clear what this
maxparameter meant, it used to be the line size, not including the null terminator. Now it means the size of available memory in the
bufferpassed 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
appendmethod in a loop could lead to the process easily running out of a available file descriptors.
OE64BITwere improperly set on 64-bit Windows.