Version 2.0.1

OEChem 2.0.1

New features

• OEMolBase::SetCoords will now reset the atom and bond stereo perception flags, OEPerceived::AtomStereo and OEPerceived::BondStereo respectively. This can force reperception of the stereo information from the new coordinates by other functions that may need it. For example, a later call to OEWriteMolecule will now automatically call OE3DToAtomStereo.

• OECopyMol function added to make a copy of a molecule and return the atom or bond associations between the source and destination molecules.

• OEMolBase::ClearBase method added to allow clearing generic data on the OEMolBase without destroying the molecule itself.

• OEUniMolecularRxn::SetValidateKekule method added to allow skipping the Kekule validation step after the reaction is applied. Note, this allows OEUniMolecularRxn to return radicals, leaving clean up to the user.

• OESuppressHydrogens can now suppress hydrogens at specific heavy atom sites.

• OENthAtom predicate’s 2nd argument now defaults to 0 to be easier to use.

• OEGetMolDatabaseIdxFileName added to generate index file names from database file names using the same rules as OECreateMolDatabaseIdx and Save.

Major bug fixes

• OEMMFFAtomType will no longer crash whenever an unbonded sulfur with a single implicit hydrogen is encountered.

• OEAssignAromaticFlags now invokes the OEFindRingAtomsAndBonds function, when necessary. If no ring atoms are detected in the molecule, the OEAssignAromaticFlags functions returns after setting all atoms and bonds of the molecule to be non-aromatic.

• The OESubSearch class now throws a warning in the following two cases:

  • If there are only explicit hydrogens in the pattern, but the target has only implicit hydrogens.

  • If there are only implicit hydrogens in the pattern, but the target has only explicit hydrogens.

  These warnings are necessary in order to avoid substructure match failures that are the result of mismatched hydrogen representation.

• The OEGetFileType function now returns OEFormat::UNDEFINED for file extensions that contain extra characters after the known file extension. For example, ismama used to inappropriately return OEFormat::ISM. The only exception is if the extra characters are preceded by “.”. Therefore, the following strings are still considered valid: sdf.gz, sdf.bin, and sdf.zip.

• V3000 entries with a broken atom or bond block will no longer crash, the reader will now throw a warning and skip the molecule.

• OEMDLPerceiveBondStereo function will no longer clear wavy bonds, OEBondStereo::Wavy, since this property can not be re-perceived from other information. The MDL bond stereo can be removed by calling the new OEMDLClearBondStereo function.

• OEWriteMDLFile no longer has a subtle race condition that could lead to incorrect time stamps being written in the header. The race condition was caused by the use of the standard C library localtime function.

• OEChem::oemolithread::open will no longer crash when given an empty .csv file.

• OEReadMDLReactionQueryFile previously incorrectly required “M END” lines between reactant and product blocks. These lines are no longer required and will be ignored if they are encountered. This change allows reaction query files to be read that are generated by ChemDraw and the Accelrys Enterprise Platform.

Minor bug fixes

• OEMolDatabase::GetTitle will no longer return a corrupted title for multi-molecule .mol2 files.

• OEGenerate2DCoordinates will now handle a molecule as a reaction if any of its atoms have a reaction role other than OERxnRole::None. Previously, only molecules that returned true from OEMolBase::IsRxn would be handled as reactions.

• OEChem 2.0.0, the previous release, introduced automatic 2D coordinate generation when writing to the following file formats: OEFormat::SDF, OEFormat::MDL, and OEFormat::CDX. However, coordinate generation will only occur if OEMolBase::GetDimension does not return 2 or 3, indicating that the molecule already contains coordinates. OEWriteMolecule will now throw a warning message if coordinates are detected on the molecule and OEMolBase::SetDimension was not appropriately called. Users should either call OEMolBase::SetDimension to the appropriate dimensionality of the molecule, or clear the molecule’s coordinates.

  Note

  .cdx files will still automatically generate 2D coordinates from 3D molecules since .cdx is a 2D molecule format only.

• OEAssignAromaticFlags used to only set atoms to non-aromatic if no ring bonds were found. Bond aromaticity will now be cleared as well if no ring atoms are found.

• OECreateMolDatabaseIdx will no longer crash whenever called inside a directory without write permissions.

• OEChem::oemolostream::seekp removed since it did not do anything.

• OESmartsLexReplace argument is now const since the function does not need to alter the vector.

• Removed unbounded stack allocations.

• The partial support for CPSS-style rxnfiles has been entirely removed as this format is documented as obsolete in the CTfile format specification.

• OEAddExplicitHydrogens no longer has the rare chance of using uninitialized memory when sprouting hydrogens in 3D.

• OEReadMDLQueryFile will now interpret ![N,O,S] as ![N,O,S,H] to be consistent with MDL matching behavior.

• OEOmegaConfTest::CompareMols, OEIsomericConfTest::CompareMols, OEAbsoluteConfTest::CompareMols will all now return true if the only difference between the bonds of the two molecules is whether the Bgn and End bonds have been swapped.

Documentation fixes

• All examples should now use OESmilesToMol instead of OEParseSmiles. OESmilesToMol is the preferred safer method for parsing SMILES.

• Simplified the documentation for the basic molecule class hierarchy. Previously, documentation was spread between the base class and the concrete classes. The base class sections should now be the canonical place to look for specific method documentation.

  • For OEGraphMol methods, see the OEMolBase section

  • For OEMol methods, see the OEMCMolBase section

  • For OEQMol methods, see the OEMolBase section

• Added documentation for OEConfBase and OEMCMolBase classes that are instantiations of OEChem::OEConfBaseT and OEChem::OEMCMolBaseT template classes, respectively.

• Added missing documentation for the OEConfBase and OEMCMolBase classes.

• Generated new images for the Explicit Hydrogens section of the Substructure Search with MDL Queries chapter

• Memory leak fixed in NewConfFromCoords documentation example.

• Corrected a link to the CTfile format document from Accelrys, Inc.

• OEProperty namespace formatting fixed in PDF files to actually be readable.

• OEOmegaConfTest added to the conformer test section for Input and Output.

OEBio 2.0.1

Major bug fixes

• OESetRotamer can properly set rotamers with angles of 0.0. Previously the angle was silently left unchanged.

OESystem 2.0.1

New features

• OEInterface can now report all the OpenEye toolkit libraries being used by specifying --help versions on the command line.

• OEParseCommandLine now accepts an argument for specifying the program’s version number. This version number will be printed whenever --version is found on the command line.

• OEMemPoolMode::Spinlocked memory pool mode added to provide a more efficient mutual exclusion mechanism than mutexes for the small object caches.

• Added the following functions to provide predefined sets of colors:

  • OEGetColors

  • OEGetContrastColors

  • OEGetDeepColors

  • OEGetLightColors

  • OEGetVividColors

• Added the following colors:

  • OESystem::OEBrass

  • OESystem::OECopper

  • OESystem::OEGold (the original color was renamed to OESystem::OEMandarin)

  • OESystem::OESilver

  • OESystem::OEPewter

Minor bug fixes

• Removed unbounded stack allocations.

• SetDate no longer has a subtle race condition due to the use of the standard C library localtime function.

• OEMakeString used to be limited by an internal buffer to only output strings with less than 8192 characters. The function will now allow any output size string to be created.

Documentation fixes

• Added missing documentation for the following colors:

  • OESystem::OEGreenBlue

  • OESystem::OEGreenTint

OEPlatform 2.0.1

New features

• OESpinlock and OELockSpinlock classes added to provide mutual exclusion to cheap sections of code with less overhead than OEMutex.

• OELocalTime added as a cross platform thread safe equivalent to the standard C library localtime function.

• OECurrentTime overload added to return the current time in a standard C library struct tm object in a thread safe manner.

Major bug fixes

• OEGetPlatformInfo will now return Windows versions for Windows Vista through Windows 8.1.

• OEGetProcessorInfo would previously only show Pentium III for newer chips on Windows. The function will now interrogate the chip using the cpuid instruction.

• OECurrentTime is now thread safe. The function was not thread safe due to the standard C library localtime and asctime functions not being thread safe. This was causing writing files to the following file formats to not be thread safe: .svg, .ps.

• OEFile::DirContents will no longer leak memory by leaving open a DIR * object.

Minor bug fixes

• OEGetTimeOfDay will now return a bool instead of an int to more clearly show when the function fails.

• OEOnce::GetValue method is now provided on all platforms.

Documentation fixes

• The following functions are not available in Python, Java, or C# and are only documented in the C++ documentation:

  • OECurrentTime

  • OECycleTime

  • OEGetTimeOfDay

  • OELocalTime

  • OESleep

OEGrid 1.4.6

New Features

• OEMakeMolecularGaussianGrid now has an overload to allow a grid with existing dimensions, mid-point, and spacing to be filled. Previously, the grid size would always be recreated based upon the size of the molecule.

Major bug fixes

• Better support for output of non crystallographic grids to CCP4 file. Now the CCP4 ARMS value is set to 1.0 and the CCP4 MEAN is set to 0.0 to prevent scaling and offsetting in CCP4 map visualizers. Additionally, the spacegroup is now output as 146 (H3) as opposed to the nonstandard 1146 (R3) to facilitate viewing in MOE. Please note that values appearing outside of the specified unit cell will be incorrect.

Documentation fixes

• Adding missing OEMTZMapType namespace to the documentation.

• OEChem release notes for 2.0.0 and 1.9.3 had the OEGrid version slightly wrong. The OEGrid version numbers have been corrected to 1.4.5 and 1.4.4 respectively.