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OEMutex.
OEMutex.
OETryMutex class that allows for an ``Attempted lock''
through the function OETryMutex::Try()
OEFileCorrectSeparators and
OEFileDeterminePathAndName functions.
bool OEIsNaN() function which
is overloaded for float and double. As the name implies, this function
returns a boolean which is true if the number passed is a nan.
new on
zero bytes, then reset the pointer, causing small leaks on some platforms.
operator && (const OEIter<T>&,
bool).
FirstBit, LastBit,
NextBit, and PrevBit functions.
CheckHelp now also checks for ``-help defaults'', which will
list the default arguments of all parameters.
CreatePredicateCopy() to the
OEUnaryPredicate and OEBinaryPredicate base classes which
allow users to use this virtual constructor method without unnecessary
casts.
OEFizzGrid::GetFloatsSet and
OEFizzGrid::GetIntegersSet to determine if the floats and integers
are set for this grid.
SetRangeOn and SetRangeOff to
OEBitVector.
Sort(const OEBinaryPredicate &) member function to
iterators. This allows arbitrary sorting of the order in which objects
come out of any OEIter.
OEFileExtension and OEFileExtensions
which return a string containing the specified filenames file extension or list
of extensions respectively.
Sweep to ensure that atoms/bonds are reindexed
sequentially even if there have been no deletions.
SetStereo was returning 'false' even when the
stereo was set correctly.
DeleteAtom and DeleteBond
member functions of OEMCMolBase and OEMol. The behavior of
these functions was not changed.
IsDeleted(OEAtomBase*) and
IsDeleted(OEBondBase*) methods to OEMol, OEGraphMol
and OEQMol.
OEAddExplicitHydrogens() to return bool rather than void
to reflect its failures.
OESet3DHydrogenGeom() to return an appropriate boolean
value rather than always returning true.
bool OERMSD(const OEMolBase&,const OEMCMolBase&, double
*rmsdArray, const OEMatchBase &match, bool overlay = false, double *rot =
0, double *trans = 0) fixed bug that the first conformer of the
OEMCMolBase's was used repeatedly rather than using each conformer
in succession.
oemolostream::GetString() when the stream is
wrapping a gzstream.
OESubsetMolecule() in the case when a
ring bond it the only item removed from the original molecule.
OEAtomBase implementation that
caused problems for an atom after 65536 neighboring bonds had been deleted.
This occurred in codes repeatedly created temporary bonds then deleted them
without calling Sweep.
OECalcCartesianCoord when rotating around the y
axis. Prior implementation would give wildly incorrect results.
OEReadMol2File function no longer requires the
use of tell and seek on it's input stream.
OERMSD for recognizing and dealing with
degenerate roots. When the heuristic fails, inappropriate rotation matrixes
were generated.
OESet3DHydrogenGeom where memcmp was comparing
coordinates of type double, but using sizeof(float), so only a
partial comparison was being carried out.
OEMCMolBase member function
SetActive() for significant performance gains in binary i/o.
OEMCMolBase.
oemolistream and oemolostream fail
to allocate a gzstream.
OEMol and OEMCMolBase contain a separate
dimensionality (eg - the value returned by
OEMolBase::GetDimension()) for each conformer rather than a single
value for the molecule. This allows depictions and conformers to be stored
on the same molecules and still be handled correctly by the .sd writers.
OEMDLPercieveParity (and thereby the MDL mol file
writer) is improved to record chiral centers that don't have stereo
specifiled as the mdl parity value ``3" (unspecified chiral center).
OEMolBase member functions
GetAtom, GetBond and Sweep.
OERandomizeTorsions.
OEInSamePart to a template class so
that parts can be tested for bonds (and other objects) as well atoms.
OEIsRotor constructor to allow the option of hydrogen
rotors.
OEMDLStereoFromBondStereo function from
previously internal code.
OELibraryGen
class for generating combinatorial libraries; OEUniMolecularRxn
class primarily for applying normalizations; OEParseSMIRKS function
for converting Daylight's SMIRKS format to an OEQMolBase; and
OEReadRxnFile that takes an OEMolBase for reading MDL's rxn
files.
OEVectorBindings class to handle SMARTS vector bindings.
OEBinaryIOHandler.
OEDisassembleExpressions function which converts query
expressions into data directly on atoms/bonds.
OEUnaryToBinaryAnd and
OEUnaryToBinaryOr that turn a Unary functor into a binary 'or' or
'and' functor.
OEMDLStereoFromParity that sets the OEChem
stereochemistry of each atom from the MDL stereo parity flag stored in
generic data.
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