Version 1.7.2¶

OEChem 1.7.2¶

OEPDBIFlag, OEPDBOFlag, OEMDLOFlag, OEMOPACFlag constants namespaces are deprecated.

OEReadMDLQueryFile now sets the title of the query molecule.
OEChem now recognizes the MDL “wavy” bond. An OEBondBase can be queried for its stereo type by querying its generic data for the OEProperty::BondStereo tag. The returned unsigned int will be from the OEBondStereo namespace.
OEChem now supports MDL query file R group definitions. These are lines starting with M RGP. The R group is represented as a OEQAtomBase with a map index the same as the R group number in the file.
OEChem will now correct amidine and guanidinium functional groups where the bonds between C and N are marked as aromatic in MOL2 files.
Significant performance improvement to reading single-conformer molecules from OEB files. Other minor performance improvements were made to OEB as well (including multi-conformer molecules). This speeds up OEDBMol compression and uncompression as well.
Removed OECopyHistory function. OEChem::OEReadHeader is now smart enough to read the header into the OEHeader history if it is already populated with another header’s information.
oemolthreads now support reading and writing OEHeader objects.
Added the oemolthreadbase::PeekMol method.

Fixed a OEReadMDLQueryFile segmentation fault when perceiving aromaticity with spirane rings containing generic atoms.
Fixed a bug where atom parity was ignored when reading a 3D MOL file.
Fixed a memory leak when initializing an OEMCSSearch with its constructor. The workaround in 1.7.0 is to use the OEMCSSearch::Init method instead.
Fixed a memory leak with OEMCSSearch when OEMCSSearch::SetMaxMatches was set to a number lower than the total number of matches found.
Fixed memory leak when creating and destroying multiple OELingoSim objects.
Some OEOFlavor::PDB flavor combinations would generate corrupt data.
OESmilesAtomCount now includes atoms of the form [#6] in its count.
Fixed a bug where map indices on explicit hydrogens would be ignored when generating SMILES. For example, [CH] would get generated even if the hydrogen had a map index specified. Now [H:1][C] will be generated.

Energy set on an OEGraphMol using OEMolBase::SetEnergy would not get written out to OEB files. Energy data will now round-trip through the OEB format.
Automatic conformer combining through the oemolistream::SetConfTest interface will now combine separate single-conformer molecules in an OEB into a multi-conformer molecule similar to the other file formats OEChem supports for that behavior (MOL2, SDF, etc).
OEPerceiveBondOrders is more stable to pre-existing bond orders on the molecule.
Rare non-deterministic bug fixed for sulfur monoxide bug in OEPerceiveBondOrders.
OEChem now recognizes the DU residue name and the mythical DT residue which is synonym for `` T``.
The new overload of OEIsReadable to take a string would return true if there was no periods (‘.’) in the string and the string began with a readable file extension, for example, “MDL-FOO”.
Fixed a bug when OELibraryGen failed to generated products with correct Kekulé-form.

Added the OEGetBitCounts function to efficiently get certain bit counts when comparing two OEBitVector objects. This function is useful for implementing custom fingerprint similarity measures.
Added the OEBitVector::SetData method to allow a rapid method of initializing an OEBitVector with binary data.
Added OEErrorHandler::Verbose method to send OEErrorLevel::Verbose level messages.
Added OESystem::OEHeader::operator bool to test whether the OEHeader has any data in it.
Added OEBoundedBuffer::Peek and OEProtectedBuffer::Peek methods.
Optimized writing generic data attached to an OEBase. This optimized OEDBMol::Compress.
Minor optimization to a common OEChem iterator.

Renamed the OEMakeFP function to OEParseHex to be more explicit about what is does.
Valgrind would throw warnings about a change made in 1.7.0 for thread safety issues. Though this was not a true memory leak the code has been slightly changed to silence this warning.
Fixed an exponential growth bug when adding history to an OEHeader.
Assignment operators for OEMultiGrid now properly copy the titles of the subgrids.

Added the OESetLicenseFile function to allow dynamically setting which OpenEye license file to use.
Added the OEGetCurrentWorkingDirectory function to return the current working directory for the process.
Optimized oeigzstream::seek to only rewind the stream if seeking backwards. Therefore, the optimal way to seek in a gzipped file is in increasing oefpos_t order.
Optimized oeisstream::getbuffer.
Optimized oeosstream::clear.

Revised the oestream::length and oestream::size documentation to be more accurate.
oefpos_t now works for files greater than 4GB on 64-bit windows.
Fixed an infinite loop that would occur from the following code:
```
oeosstream sfs;
sfs.open("foobar");
sfs.write("blah");
```
oeosstream::open will return false. Ignoring the false return value would cause oeosstream::write to loop indefinitely.

Introduced new OEBio classes to manage alternate locations in protein data bank structures along with a new PDB input flavor OEIFlavor::PDB::ALTLOC to retain alternate location atoms on input.

See also

Alternate Locations

The crystal symmetry routines were broken in the 1.7.0 release by a corrupted matrix.
When reading symmetry from external sources (i.e. PDB files or maps) a warning is thrown when reading out of date space groups rather than fail to read symmetry.
Setting space groups will fail unless the most current space group constraints are used.
Added the following space group aliases for older style space groups.
```
I 1 2 1 -> C 1 2 1
P 1-    -> P -1
```

OEMakeGridFromCenterAndExtents added for a grid of an arbitrary template type.

Fixed a rare crash in OEMakeRegularGrid that was caused by floating point round-off error.