From: <eg...@us...> - 2007-10-24 14:39:44
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Revision: 9193 http://cdk.svn.sourceforge.net/cdk/?rev=9193&view=rev Author: egonw Date: 2007-10-24 07:39:41 -0700 (Wed, 24 Oct 2007) Log Message: ----------- Fixed mistyping: S.2 != S.planar3 Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java trunk/cdk/src/org/openscience/cdk/config/data/cdk_atomtypes.xml trunk/cdk/src/org/openscience/cdk/test/atomtype/CDKAtomTypeMatcherTest.java Modified: trunk/cdk/src/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java 2007-10-24 14:38:51 UTC (rev 9192) +++ trunk/cdk/src/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java 2007-10-24 14:39:41 UTC (rev 9193) @@ -96,6 +96,8 @@ return factory.getAtomType("C.sp2"); } else if (atom.getHybridization() == CDKConstants.HYBRIDIZATION_SP3) { return factory.getAtomType("C.sp3"); + } else if (atom.getHybridization() == CDKConstants.HYBRIDIZATION_SP1) { + return factory.getAtomType("C.sp"); } } else if (atom.getFormalCharge() != CDKConstants.UNSET && atom.getFormalCharge() != 0) { @@ -349,7 +351,7 @@ } } } - if (bothNeighborsSP2) return factory.getAtomType("S.2"); + if (bothNeighborsSP2) return factory.getAtomType("S.planar3"); } return factory.getAtomType("S.3"); } else if (neighborcount == 1) { Modified: trunk/cdk/src/org/openscience/cdk/config/data/cdk_atomtypes.xml =================================================================== --- trunk/cdk/src/org/openscience/cdk/config/data/cdk_atomtypes.xml 2007-10-24 14:38:51 UTC (rev 9192) +++ trunk/cdk/src/org/openscience/cdk/config/data/cdk_atomtypes.xml 2007-10-24 14:39:41 UTC (rev 9193) @@ -233,6 +233,15 @@ <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp3</scalar> </atomType> + <atomType id="S.planar3"> <!-- e.g. thiophene --> + <atom elementType="S" formalCharge="0"> + <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">2</scalar> + <scalar dataType="xsd:integer" dictRef="cdk:lonePairCount">2</scalar> + <scalar dataType="xsd:integer" dictRef="cdk:piBondCount">0</scalar> + </atom> + <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar> + </atomType> + <atomType id="S.minus"> <!-- e.g. H[S-] --> <atom elementType="S" formalCharge="-1"> <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">1</scalar> Modified: trunk/cdk/src/org/openscience/cdk/test/atomtype/CDKAtomTypeMatcherTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/atomtype/CDKAtomTypeMatcherTest.java 2007-10-24 14:38:51 UTC (rev 9192) +++ trunk/cdk/src/org/openscience/cdk/test/atomtype/CDKAtomTypeMatcherTest.java 2007-10-24 14:39:41 UTC (rev 9193) @@ -892,7 +892,7 @@ "C.sp2", "N.sp2", "C.sp2", - "S.2", + "S.planar3", "C.sp2" }; Molecule molecule = MoleculeFactory.makeThiazole(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |