Version 2.2.0

OEChem TK 2.2.0

New features

• Atom and bond expressions of query molecules have been optimized for substructure search. The graphs below show the performance improvement since the 2018.Oct release. Optimization has been turned on for both MDL queries and SMARTS patterns and can be controlled by the following options:

  • OESmartsParseOpts::Optimize when using the OEParseSmarts function

  • OEMDLQueryOpts::Optimize when using the OEReadMDLQueryFile function

  Substructure search performance improvement for MDL queries

  Substructure search performance improvement for SMARTS patterns

• A new OEFormat::OEZ compressed binary format has been added with the .oez extension. This file format only supports multi-conformer molecules derived from the OEMCMolBase class. Each molecule is individually compressed in the file using the Zstandard compression algorithm. See the Compressed Input and Output section for more details.

  Note

  This new file format is not backwards compatible. OpenEye applications and toolkits released before April 2019 will not be able to read or write this file format.

• An OEBitVector object now can be attached as generic data to any OEBase object. Its derived classes now round-trip through the OEB format.

• Multi-conformer molecule overloads have been added to the following existing APIs:

  • OEMDLHasParity

  • OEMDLGetParity

  • OEMDLSetParity

  • OEMDLClearParity

• New input flavors, OEIFlavor::MDL::SuppressEmptyMolSkip, OEIFlavor::SDF::SuppressEmptyMolSkip, and OEIFlavor::RDF::SuppressEmptyMolSkip, have been added to the MDL formats to allow returning empty molecule records. This allows the SD data to be recovered from these records.

• New output flavors, OEOFlavor::MDL::SuppressTimestamps and OEOFlavor::SDF::SuppressTimestamps, have been added to the MDL formats to explicitly suppress timestamps in the file header. This is convenient for generating diffable test files.

• A new OEResidueToString function has been added to convert an OEResidue object into string representation.

• The following new classes have been added to provide alternative ways to access tagged property data in molecules:

  • OEMolPropertyFxn

  • OEMolSDPropertyFxn

  • OEMolGDPropertyFxn

  • OEMolTaggedPropertyFxn

  • OEMolPropertyList

• New predicates, OEIsValidAtomValence and OEIsValidMDLAtomValence, have been added to provide the ability to loop over atoms that satisfy the OpenEye and MDL valence model requirements, respectively.

• The OEMolBase::NewGroup method now also takes an OEAtomBondSet object.

• New OECheckAtomValence and OECheckAtomValences functions have been added that check if an atom or all atoms of a molecule have valid valences.

• A new OELibraryGen::NumPossibleProducts method has been added that returns the number of possible products that can be generated.

• New OEClearSDData and OEClearPDBData function overloads have been added to clear SD or PDB data of multi-conformer molecules.

• A new OEShortestPath overload function has been added that disallows traversing excluded bonds in the path.

• A new OEAtomBondSet::GetParent method has been added.

• A new OEGetResidueIndexFromCode function has been added.

• The OEPDBOrderAtoms function has been updated to take an argument that preserves the PDB residue order. It defaults to false to preserve backwards compatibility.

Major bug fixes

• The number of cases where round-tripping to MDL file format results in stereo information loss has been significantly reduced.

Minor bug fixes

• High-level SMILES readers such as OESmilesToMol and OEReadMolecule now clear cis/trans bond specifications on bonds in small rings (less than 7 members).

• The oemolistream::open and oemolostream::open methods now correctly set the formats for gz filenames.

• A bug that caused a crash when an invalid oemolostream is finalized has been fixed.

• oemolistream::Setgz and oemolostream::Setgz methods are now a no-op if the state of the stream is unchanged.

• An issue that caused the JSON writer to crash with user-specified cis/trans stereo has been fixed.

• The MDL V3000 reader has been fixed and no longer marks “either” double bonds with cis/trans parity.

• The MDL V2000 reader has been fixed and no longer adds “either” double marks to chiral but unspecified cis/trans double bonds.

• OESubsetMol no longer crashes when breaking and adding multiple R-groups to the same atoms.

• Cobalt ions are now assigned a formal charge when being read from the PDB file.

Python-specific changes

• The __str__ method of the OEResidue class now invokes the new OEResidueToString function.

• The OEMolDatabase::GetMoleculeString method has been fixed and now returns bytes.

Documentation changes

• New code snippets have been added to the Substructure Search section to show how to reconstruct matches for the original molecule.

• A new Split molecule file example has been added.

• New code snippets have been added to the OEChemIsLicensed function.

OEBio TK 2.2.0

New features

• A new OEIsCTerminalAtom predicate has been added to identify the C-terminal atom(s) in a protein structure.

• A new OEIsNTerminalAtom predicate has been added to identify the N-terminal atom(s) in a protein structure.

• A new OEAtomMatchResidue predicate has been added to identify residue atoms by RegEx.

• New OEGetResidueAtom functions have been added to provide easy access for specific residue atoms.

• The OEIsBackboneAtom predicate has been updated to take an optional argument to consider the terminal oxygen atom (OXT) as part of the backbone.

• The OEIsWater predicate has been updated to take two optional arguments:

  • to match hydrogen atoms in water molecules

  • to match the water ions \(OH^{-}\) and \(H_{3}O^{+}\)

• A new OEIsStandardProteinResidue overload that takes an atom has been added.

New features (Preliminary)

• The following preliminary APIs have been added to handle design units:

  • OEDesignUnit

  • OEDesignUnitFileType

  • OEIsReadableDesignUnit

  • OEIsWriteableDesignUnit

  • OEReadDesignUnit

  • OEWriteDesignUnit

  • OEDesignUnitComponents

  • OESubsetDesignUnit

  • OEUpdateDesignUnit

  • OEIridiumCategory

  • OEIridiumData

  • OEGetIridiumCategoryName

  • OEGetIridiumCategoryFromName

  • OEStructureQuality

  • OEGetDesignUnitComponentID

  • OEGetDesignUnitComponentName

  The above classes and functions are currently used by Spruce TK for protein handling.

Minor bug fixes

• The OEPlaceHydrogens function has been improved:

  • The OEPlaceHydrogensMoverClass::NH2 mover perception has been updated.

  • The OEPlaceHydrogensMoverClass::COOH mover perception has been updated to only mark the atoms involved in the mover.

Java-specific changes

• The Java example in the Splitting a Macro-molecular Complex Efficiently and Flexibly section has been fixed.

Documentation changes

• A new Interaction Perception chapter has been added.

• Code snippets have been added to the OESetCrystalSymmetry and OEGetCrystalSymmetry functions.

OESystem TK 2.2.0

Minor bug fixes

• The OEMakeMolecularGaussianGrid function now returns false for an empty molecule.

• New code snippets have been added to the OEThrow class to demonstrate how to redirect warning and error messages to a file.

OEPlatform TK 2.2.0

New features

• The following APIs have been rewritten using standard C++11 classes:

  • OEMutex now uses std::mutex.

  • OETryMutex now uses std::try_lock.

  • OELock and OELockSpinlock now use std::lock_guard.

Minor bug fixes

• The OEAddLicenseFromHttp function available in the wrapped languages (Python, Java, and C#) now accepts HTTP responses with a text/plain; charset=utf-8 content type.

OEGrid TK 1.6.3

Minor bug fixes

• The OEReadMTZ function has been updated to read CCP4 alternative space group numbers (e.g., 4005).

• OEReadGrid no longer loses its title beyond the first blank space.

• A potential memory corruption issue with Gaussian volume calculation has been fixed.