OEChem TK 3.1.0¶
- A new function, OEGetHydrogenCounts, has been added that provides implicit and explicit hydrogen counts in a molecule.
- A new function, OEApplyStateFromRef, has been added that provides the ability to apply a certain state to a molecule. This could be used to apply tautomers to a molecule in 3D or to fix broken valence states using a known state.
- A new function, OERGroupsToHydrogens, has been added that converts R-groups of a molecule to hydrogen atoms.
- A new preliminary namespace, OEFileStringType, has been defined that allows controlling file types in OESimpleAppOptions and OERefInputAppOptions.
- Two new preliminary classes, OEFileStringParameter and OEOutFileStringParameter, have been added to allow better control over file types that can be used in OESimpleAppOptions and OERefInputAppOptions.
- The constructor of the preliminary class OESimpleAppOptions has been modified to take constants defined in OEFileStringType to better control the desired input/output file types.
- A new preliminary class, OERefInputAppOptions, has been added to enable creating an interface to applications and scripts that require a second input, such as a reference or target system.
- A new method, OEResidueCategoryData::AllInDB, has been added that determines if all the specified residue names found in the list are associated with the specified category.
Minor bug fixes¶
- An issue that occurred when a change in the aromaticity model perception would result in double bonds that should have lost their cis/trans parity assignments has been fixed. The bond stereo parities had been incorrectly being retained on aromatic atom endpoints.
- An issue with parsing SMILES with ExtBond couplings that were not honoring the convention that a specified bond order takes precedence over an implicit one, similar to ring closures, has been fixed.
- Extra processing has been added to ensure that a common header corruption for SDF format files throws a warning to indicate a format problem. In general, attempts to skip individual corrupted records in a multi-record file format are employed to ensure that as much of the valid input as possible can be processed. Depending on the type of corruption as well as the specific file format, there is no guarantee that a warning will be emitted for all corrupted records.
- An issue that caused OECopyPDBData and OECopySDData to avoid the copy activity if the source and destination molecules are the same molecule instance, which can cause a crash, has been fixed. The status return will be false, just like a general failure for the copy activity.
- An issue in OEPDBOrderAtoms that caused bad behavior when atoms in a molecule do not have any residue information has been fixed.
OEBio TK 3.1.0¶
- Two new methods, OEDesignUnit::HasTransform and OEDesignUnit::GetTransform, have been added that check whether a valid OETrans object is stored on the OEDesignUnit and retrieve it for use with OETransformDesignUnit.
- A new method, OEMolComplexCategorizer::GetResidueCategoryData, has been added that returns the non-const reference to the OEResidueCategoryData stored in the OEMolComplexCategorizer class.
- A new class, OEReceptor, has been added that represents a receptor as used in OEDocking TK.
- A new class, OEReceptorConstraintFeature, has been added that represents a constraint feature for an OEReceptor.
- A new class, OEReceptorProteinConstraint, has been added that represents a protein constraint for an OEReceptor.
- A new preliminary namespace, OEProteinConstraintType, has been added that defines the valid types for OEReceptorProteinConstraint.
- A new class, OEReceptorCustomConstraints, has been added that represents custom constraints for an OEReceptor.
- Two new methods, OEDesignUnit::HasReceptor and OEDesignUnit::GetReceptor, have been added that check whether a valid OEReceptor object is stored on the OEDesignUnit and retrieve it.
- Several new constants have been added to the namespace OEDesignUnitComponents, related to downstream usage, such as OEMakeReceptor.
Major bug fixes¶
OESystem TK 3.1.0¶
OEPlatform TK 3.1.0¶
OEGrid TK 3.1.0¶
Major bug fixes¶
- A bug in the symmetry operators for the I121 space group has been fixed.
Minor bug fixes¶
- An issue that caused the function OEReadGrid to incorrectly change the OEGridType of grids to the OEGridFileType, where it was being used to read an OEFizzGrid from a file, has been fixed. The OEGridType now remains the same through a round trip grid write and read.
- An issue that caused the function OEReadMTZ to crash when it read large MTZ files and converted them to an OESkewGrid as well as computing the AMIN and AMAX statistics for the resulting OESkewGrid incorrectly has been fixed. The code has been corrected so that the crash no longer happens for large grids; the AMIN and AMAX calculations have also been corrected.
- An issue that caused the script make_design_units.py to crash when reading PDB files using the function OEReadMolecule, when space group numbers that could not be recognized has been fixed. These space group numbers had been preventing the code from reading symmetry correctly from the PDB file. The code has been changed so that incorrect space group numbers result in a warning instead of a fatal crash.
OEMath TK 3.1.0¶
- Two new , OEBox and OESphere, have been added that represent a box and a sphere, respectively.
- The following functions have been added as access functions to the new OEBox class:
- The following functions have been added as access functions to the new OESphere class: