>>> mol = OEGraphMol() >>> OESmilesToMol(mol, "c1ccccc1O") True >>> str(OEAtomBondSet(mol.GetAtoms())) ' 0C 1C 2C 3C 4C 5C 6O '
oemolistream, oemolithread, oemolostream, oemolothread now support the Python with statement. This ensures that files are automatically flushed and closed whenever falling out of the with scope. For example:
mol = # some initialized molecule with oemolostream("file.oeb") as ofs: OEWriteMolecule(ofs, mol) # file.oeb is guaranteed to contain the molecule with oemolistream("file.oeb") as ifs: for mol in ifs.GetOEMols(): # do something with mol
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:
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.
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.
.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.
>>> OERed OEColor(r=255,g=0,b=0,a=255) >>> OEGreen OEColor(r=0,g=255,b=0,a=255) >>> OETransparentColor OEColor(r=255,g=255,b=255,a=0)