OEChem TK 4.0.0

New features

  • A new preliminary API that supports generation of atom–atom mapping information for an input reaction has been provided in C++ and Python. See details at OERxnAutomapperOptions, OERxnAutomapper, and OERxnAutomapStatus.

  • A new nondefault input flavor has been added to support the conversion of implicit enhanced stereogroups from a V2000 SD format input file into explicit stereogroups. This allows subsequent export of explicit enhanced stereogroups in formats that support that information, like SDF and CXSMILES. See details at SDF_ForceImp2ExpENHSTE.

  • The explicit chiral-off designation (r) in the CXSMILES appendix is now tolerated when parsing the CXSMILES appendix. This explicit designation is appearing more frequently in vendor structure sets.

  • New overloads of OESimpleAppOptions and OERefInputAppOptions have been added to support applications that do not produce an output file.

  • The MMCIF reader now runs on Gemmi version 0.6.2. It is able to parse and write more sections in MMCIF files.

  • The default OEIFlavor for PDB has been changed to include PDB_DATA by default.

  • The default OEIFlavor for MMCIF has been changed to not include MMCIF_ALTLOC by default, to match the PDB default behavior.

  • Two new OEIFlavor defaults have been added, PDB_SpruceDefault and MMCIF_SpruceDefault, that add ALTLOC in addition to the default flavors for those file formats. These are being used in both the SPRUCE and Make Receptor applications.

  • OEHasAtomName has been extended to take a new optional argument called trimspaces (default=false) to more flexibly match atom names.

  • OEHasChainID has been changed to internally operate on strings instead of characters to support multicharacter chain IDs. The character-based constructor is still available.

Minor bug fixes

  • The SD data format specifies that blank lines are the delimiters between different SD data fields. If an SD file contains blanks within one or more SD data fields, the reader would previously complain about the format error. The reader has been augmented to be more tolerant of this case, but in the process it must strip blank lines from the input SD data to ensure that the SD output does not generate a noncompliant output file. If blank lines are detected in the SD data for a molecule being exported in SD format, a new write status is returned to indicate the blank lines were removed in order to generate a compliant SD output file, and the generated output file will have the noncompliant blank line(s) removed. See details at OEWriteMolReturnCode::InvalidSDData.

  • A minor issue that caused OEGetTorsion to crash if one or more of the atom arguments were null has been fixed.

  • A minor issue that generated an invalid read error from V3000 SD files with nonconsecutively ordered object indices has been fixed. Generally, object indices in V3000 format files can be arbitrarily ordered.

  • A defect that could result in a crash during MCS searching for targets containing single atom fragments has been fixed.

  • An issue that caused OEMolParameter to not be properly transmitted in MPI mode has been fixed.

  • An issue with the assignment operator for OEIsBridgeHead being incorrectly defined has been fixed.

  • New overloads of OESameResidue and OESameChain that take atoms instead of residues have been added. This will prevent the need to get copies of OEResidue objects in wrapped languages, instead of using const references internally.

OEBio TK 4.0.0

New features

  • Two new methods in OEReceptor, GetOuterContourVolume and GetInnerContourVolume, have been added as convenience functions to get the volume of the receptor grid at the set contour level.

  • The function OEUpdateDesignUnit will not fail and return false if passed an empty molecule to update with.

  • The function OEUpdateDesignUnit has been updated to take an optional listIndex parameter if an item in a list molecule needs to be updated (e.g., one of several cofactors).

  • The OEDesignUnit class has been extended with a method ClearComponent to remove or clear a component from a design unit; this method can also take an optional listIndex to remove a specific molecule in a list component (e.g., one of several cofactors).

OESystem TK 4.0.0

New features

  • A new overload of the OEGetColors function has been added that generates a custom color iterator for use in depictions by passing a vector of desired colors.

OEPlatform TK 4.0.0

Minor internal improvements have been made.

OEGrid TK 4.0.0

Minor internal improvements have been made.