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There are no significant changes to OEPlatform in this release.
OECheckHelp that prevents displaying
on-line help for ``HIDDEN'' command line interface options.
OEInterface::GetInterface that would fail
to find the correct interface by name.
OEInterface::DeleteInterface.
We now return false if we failed to delete the given interface.
ToLast method on some
kinds of iterators (specifically, OEPredVectorPtrIters).
OECartesianToInternal and OEInternalToCartesian and the
functions OECalcCartesianCoord and OECalcInternalCoord
are now publicly available.
OECanonicalOrderAtoms
or OECanonicalOrderBonds is called with less then two atoms.
OEGetSmallestSubtree to correctly return the smallest
set of atoms on either side of a given bond when the molecule contains
disconnected components.
OEGraphMolParameter, to avoid
using OEIsomericConfTest when loading single conformer molecules.
OEMCMolBase::DeleteConf that could occasionally
result in that multi-conformer molecule's active conformer being corrupted.
OEMDLPerceiveBondStereo to preferentially place the
wedge or hash bond on the bond to an explicit hydrogen, for chiral stereo
centers of degree three.
OEMDLPerceiveParity to support chiral
atoms with two heavy atom neighbors and an explicit hydrogen. These
aren't supported by MDL software (including ISIS/Draw) but this allows
OEChem to convert X[N@H]Y to an MDL mol file and back to isomeric
SMILES without loss of information.
OEMDLStereoFromParity to set OEChem's
atomic chirality for the MDL stereo parity flag for both degree three
and degree four atom stereo centers.
OEMiniAtom::Copy where duplicating an
atom would preserve the explicit degree of the original, as returned by
OEAtomBase::GetExplicitDegree.
OEMiniBond::SetOrder and
OEMiniBond::SetIntType that would incorrectly reset the
aromaticity and in-ring flags of a bond as a side-effect.
OEMiniMol::Copy.
oemolostream::openstring to allow an oemolostream
to be reused multiple times, rather than constructed and destructed for each
use.
OEPerceiveSymmetry would previously segmentation fault on some
platforms if passed a molecule with no atoms. This routine has now been
idiot-proofed.
OEReadPDBFile to handle PDB files
deposited at RCSB, upto July 2004. For example, correctly handling
the hetero atoms of the ``NZQ'' residue of pdb1oj7.ent.
OERMSD has been addressed.
A change to OERMSD for OEChem 1.3 unexpectedly resulted in a
significant drop in superposition speed. This has now been resolved and
OERMSD is as fast as (or faster than) it was in OEChem 1.2.
OESetComment is now correctly
marked as const. This value is never modified by this function.
OESetTorsion has been improved such
that we now return false for dubious calls to that function. For example,
when the first and four atom pointers refer to the same atom. Previously,
we'd do nothing, but not indicate a failure with the return value.
OESubSearch that prevent
excessive run-times for pathological substructure search patterns. Previously,
substructure searching of ``*.*.*.*'' wouldn't honor the match limit setting,
and spew multiple ``match limit reached'' warnings.
OEWritePDBFile to allow it to honor the
OEPDBOFlag::RADIUS flag to write an atom's radius in the PDB
occupancy field, even when writing a molecule without residue information.
OEWriteMDLFile,
OEWritePDBFile and OEWriteMacroModelFile. Previously, a
Cartesian co-ordinate larger than these file format's fixed width fields
would corrupt the following fields on the same line.
OEReadMDLFile. We were overly aggressive
when marking double bonds in rings as cis vs. trans due to a missing
call to OEFindRingAtomsAndBonds. We also no longer attempt
to attribute E/Z stereochemistry to connection tables without co-ordinates,
or when any of the relevant bond lengths are zero.
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