From: <raj...@us...> - 2007-07-02 15:50:50
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Revision: 8493 http://svn.sourceforge.net/cdk/?rev=8493&view=rev Author: rajarshi Date: 2007-07-02 08:50:41 -0700 (Mon, 02 Jul 2007) Log Message: ----------- Updated to take into account changes to the types in IAtomType and the new default values Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/tools/ValencyHybridChecker.java Modified: trunk/cdk/src/org/openscience/cdk/tools/ValencyHybridChecker.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/tools/ValencyHybridChecker.java 2007-07-02 15:42:03 UTC (rev 8492) +++ trunk/cdk/src/org/openscience/cdk/tools/ValencyHybridChecker.java 2007-07-02 15:50:41 UTC (rev 8493) @@ -290,21 +290,24 @@ } logger.debug("Found atomtypes: ", atomTypes.length); - for (int f = 0; f < atomTypes.length; f++) { - IAtomType type = atomTypes[f]; + for (IAtomType type : atomTypes) { if (couldMatchAtomType(atom, bondOrderSum, maxBondOrder, type)) { logger.debug("This type matches: ", type); - int formalNeighbourCount = type.getFormalNeighbourCount(); - if (type.getHybridization() == CDKConstants.HYBRIDIZATION_UNSET) { - missingHydrogens = (int) (type.getBondOrderSum() - bondOrderSum); + int formalNeighbourCount = type.getFormalNeighbourCount() == CDKConstants.UNSET ? 0 : type.getFormalNeighbourCount(); + if (type.getHybridization() == CDKConstants.UNSET) { + double typeBoSum = type.getBondOrderSum() == CDKConstants.UNSET ? 0 : type.getBondOrderSum(); + missingHydrogens = (int) (typeBoSum - bondOrderSum); } else { switch (atom.getHybridization()) { case CDKConstants.HYBRIDIZATION_SP3: - missingHydrogens = formalNeighbourCount - neighbourCount; break; + missingHydrogens = formalNeighbourCount - neighbourCount; + break; case CDKConstants.HYBRIDIZATION_SP2: - missingHydrogens = formalNeighbourCount - neighbourCount; break; + missingHydrogens = formalNeighbourCount - neighbourCount; + break; case CDKConstants.HYBRIDIZATION_SP1: - missingHydrogens = formalNeighbourCount - neighbourCount; break; + missingHydrogens = formalNeighbourCount - neighbourCount; + break; default: missingHydrogens = (int) (type.getBondOrderSum() - bondOrderSum); } @@ -312,7 +315,7 @@ break; } } - + logger.debug("missing hydrogens: ", missingHydrogens); return missingHydrogens; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |