OEChem TK 3.2.0¶
Fall 2021
New features¶
A new options class,
OEUniMolecularRxnOptions
, has been added to provide control arguments to the unimolecular reaction APIsOEUniMolecularRxn
andOEGetUniMolecularRxnIter
. The new options class adds support for enabling valence correction, as well as retrieval of altered atom information from the transform for post-processing of the transformed products.Small molecule crystal structures are now writeable as
CIF
files, seeOEWriteCIFFile
for details.Macromolecule files are now writeable as
MMCIF
files, seeOEWriteCIFFile
for details.CIF
andMMCIF
files are now readable usingoemolithread
. This enables their use asOEMolDatabase
as well.The gemmi library used to read and parse
MMCIF
files has been updated to version 0.4.8.New overloads of constructors for the
OESimpleAppOptions
andOERefInputAppOptions
have been added to extend their abilities to be used when no sub-options are involved for an application or when custom file extensions are required.New overloads of constructors for the
OEFileStringParameter
andOEOutFileStringParameter
have been added that accepts file extensions as arguments instead of predefined constants.
Major bug fixes¶
An issue causing missing amide (peptide) bonds when reading protein structures from
MMCIF
files has been fixed.An issue related to incorrect hydrogen atom stripping from stereocenters that are asymmetric by virtue of hydrogen isotope substitutions has been fixed. Isomeric
SMILES
for structures containing hydrogen isotopes on stereogenic centers will now have the atom/bond parity information correctly preserved. A minor consequence of the fix is that a small number of isomericSMILES
with explicit (non-isotopic) hydrogens may haveSMILES
differences due to conversion to a fully hydrogen-suppressedSMILES
form.
Minor bug fixes¶
An issue that could cause a crash during reads of
OEFormat.OEB
format files has been fixed. The read and write ofOEGroupBase
information inOEB
files is now more rigorously checked for invalid objects. Existing corruptedOEB
files will return an error status when read.An issue that could cause overflow in the MDL molecule reader has been fixed.
An issue that caused return of an incorrect default value for
OEPredicateParameter
when it was set to a non-default value has been fixed.
OEBio TK 3.2.0¶
New features¶
The logic identifying aromatic nitrogen atoms has been updated in
OEPlaceHydrogens
, enabling improved hydrogen network optimization as well as the ability to properly distinguish and pick appropriate ligand tautomers in the protein binding site.
Minor bug fixes¶
An issue causing the ligand density coverage (LaD) to change as a result of hydrogen placement in limited circumstances has been fixed.
An issue causing the operator bool on
OEAtomMatchResidue
to return true even if no valid data was provided to the constructor has been fixed.An issue causing an
OEDesignUnit
attached as generic data on molecules to be lost during I/O has been fixed.An issue causing proper backbone verification to fail for capping groups has been fixed.
An issue causing proper backbone verification to fail for non-standard amino acids has been fixed.
An issue causing histidine residues to be in the charged state (HIS+ or HIP) when it clearly was not favorable has been fixed.
The AspDyad mover rule in
OEPlaceHydrogens
has been refined.The class
OEPlaceHydrogensOptions
has been modified to derive fromOEOptions
.
OESystem TK 3.2.0¶
New features¶
OEParameter
classes that accept strings as input values now work with case-insensitive string inputs.A new overload of
OEMultiParameter.SetValue
has been added that acceptsoeifstream
as input.
Minor bug fixes¶
An issue that could cause
OEStringToNumber
to crash has been fixed.
OEPlatform TK 3.2.0¶
Minor internal improvements have been made.
OEGrid TK 3.2.0¶
Minor internal improvements have been made.
OEMath TK 3.2.0¶
New features¶
A new preliminary API class,
OEKernelPLS
, has been added that builds QSAR models from kernelized descriptors using partial least squares (PLS).