OEChem TK 4.1.0

New features

• We are now able to read and parse the Chem Comp section of mmCIF files.

• We can now force a deterministic sorted order to the enhanced stereo information in generated CXSMILES appendices.

• New overloads of the OESimpleAppOptions constructors have been added to enable their usage when an output parameter is not desired.

• A new value, OEFileStringType.BroodQMol, has been added to OEFileStringType to support molecule files containing BroodQuery.

• The following preliminary API classes have been made permanent.

  • OECreateSubSearchDatabaseOptions

  • OESubSearchDatabase

  • OESubSearchQuery

  • OESubSearchResult

  • OESubSearchScreen

  • OESubSearchScreenTypeBase

  • OEMolRecord

  • OEMolParameter

  • OEFileStringParameter

  • OEMolReaderParameter

  • OEMolWriterParameter

  • OEOutFileStringParameter

  • OEPredicateParameter

  • OEUnAtomPredParameter

  • OEUnBondPredParameter

  • OERefInputAppOptions

  • OESimpleAppOptions

• The following preliminary API functions have been made permanent.

  • OEReadCIFFile

  • OEWriteCIFFile

  • OECreateSubSearchDatabaseFile

  • OEGetSubSearchScreenType

  • OEIsComplementaryScreenType

  • OEIsValidSubSearchDatabase

  • OEIsValidSubSearchScreenString

  • OEMakeSubSearchQueryScreen

  • OEMakeSubSearchTargetScreen

  • OESameSubSearchScreenTypes

  • OEScreen

  • OESubSearchStatusToName

Major bug fixes

• The handling of OESMILESFlag.ExtBonds formatted fragments has been improved to better support explicit cis/trans parity information for the coupling bond.

• Parse multiply referenced enhanced stereogroups correctly from CXSMILES appendices.

• The mapping behavior of *atom and Rgroup atoms for both MDL and SMARTS queries is now synchronized. Rgroups and/or *atoms in queries are now equivalently supported for OEMakeSubSearchQueryScreen.

• Conversion of OERecord to CSV now writes CXSMILES instead of SMILES to ensure enhanced stereo is not dropped.

Minor bug fixes

• Null argument checks have been added to OESuppressHydrogens to avoid causing a crash.

• Any attempt to kekulize partial structures for OEUniMolecularRxn has been fully suppressed when specifically requested, which allows explicit nonaromatic/aromatic transformations for partial ring structures.

• .lst and .list no longer appear as viable input file types in the options in OESimpleAppOptions and OERefInputAppOptions.

OESystem TK 4.1.0

New features

• The following preliminary API classes have been made permanent.

  • OERecord

  • OEOptions

  • OEBoolParameter

  • OEConstParameter

  • OEDoubleParameter

  • OEFloatParameter

  • OEIntParameter

  • OEMultiParameter

  • OEPointerParameter

  • OEPODParameter

  • OEStringParameter

  • OEUIntParameter

• The following preliminary API functions have been made permanent.

  • OEConfigureItf

  • OEConfigureOpts

  • OEUpdateOpts

OEMath TK 4.1.0

New features

• The following preliminary API classes have been made permanent.

  • OEKernelPLS

  • OEMatrix

  • OESquareMatrix

OEBio TK 4.1.0

New features

• A new overload of OESubsetDesignUnit has been added to allow for in-place subsetting of a design unit to avoid generating a copy.

Major bug fixes

• Several issues in OEPlaceHydrogens have been added to address:

  • improved perception and geometry for sp³ secondary amines.

  • improved chelation rules for primary amines.

  • improved chelation rules for phosphate and borate groups.

  • improved chelation rules for sulfonamide groups.

  • improved chelation rules for hydroxamate moieties.

Minor bug fixes

• Null argument checks have been added to OEGetTorsion to avoid causing a crash.

OEGrid TK 4.1.0

Major bug fixes

• A problem in OEReadMTZ has been fixed.

OESystem TK 4.1.0

New features

• The following preliminary API classes have been made permanent.

  • OERecord

  • OEOptions

  • OEBoolParameter

  • OEConstParameter

  • OEDoubleParameter

  • OEFloatParameter

  • OEIntParameter

  • OEMultiParameter

  • OEPointerParameter

  • OEPODParameter

  • OEStringParameter

  • OEUIntParameter

• The following preliminary API functions have been made permanent.

  • OEConfigureItf

  • OEConfigureOpts

  • OEUpdateOpts

OEMath TK 4.1.0

New features

• The following preliminary API classes have been made permanent.

  • OEKernelPLS

  • OEMatrix

  • OESquareMatrix