Menu
▾
▴
[Cdk-commits] SF.net SVN: cdk: [8996] trunk/cdk/src/org/openscience/cdk
|
From: <eg...@us...> - 2007-09-30 20:22:17
|
Revision: 8996
http://cdk.svn.sourceforge.net/cdk/?rev=8996&view=rev
Author: egonw
Date: 2007-09-30 13:22:05 -0700 (Sun, 30 Sep 2007)
Log Message:
-----------
Added C- and Fe2++ atom types, as in ferrocene.
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 2007-09-30 19:27:27 UTC (rev 8995)
+++ trunk/cdk/src/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java 2007-09-30 20:22:05 UTC (rev 8996)
@@ -100,6 +100,12 @@
if (maxBondOrder == CDKConstants.BONDORDER_SINGLE) {
return factory.getAtomType("C.plus.sp2");
}
+ } else if (atom.getFormalCharge() == -1) {
+ double maxBondOrder = atomContainer.getMaximumBondOrder(atom);
+ if (maxBondOrder == CDKConstants.BONDORDER_SINGLE &&
+ atomContainer.getConnectedBondsCount(atom) <= 3) {
+ return factory.getAtomType("C.minus.sp2");
+ }
}
return null;
} else if (atomContainer.getConnectedBondsCount(atom) > 4) {
@@ -387,6 +393,11 @@
atom.getFormalCharge() == +2)) {
return factory.getAtomType("Mg.2plus");
}
+ } else if ("Fe".equals(atom.getSymbol())) {
+ if ((atom.getFormalCharge() != CDKConstants.UNSET &&
+ atom.getFormalCharge() == +2)) {
+ return factory.getAtomType("Fe.2plus");
+ }
} else if ("K".equals(atom.getSymbol())) {
if ((atom.getFormalCharge() != CDKConstants.UNSET &&
atom.getFormalCharge() == +1)) {
Modified: trunk/cdk/src/org/openscience/cdk/config/data/cdk_atomtypes.xml
===================================================================
--- trunk/cdk/src/org/openscience/cdk/config/data/cdk_atomtypes.xml 2007-09-30 19:27:27 UTC (rev 8995)
+++ trunk/cdk/src/org/openscience/cdk/config/data/cdk_atomtypes.xml 2007-09-30 20:22:05 UTC (rev 8996)
@@ -62,6 +62,15 @@
<scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar>
</atomType>
+ <atomType id="C.minus.sp2">
+ <atom elementType="C" formalCharge="-1">
+ <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">3</scalar>
+ <scalar dataType="xsd:integer" dictRef="cdk:lonePairCount">1</scalar>
+ <scalar dataType="xsd:integer" dictRef="cdk:piBondCount">0</scalar>
+ </atom>
+ <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar>
+ </atomType>
+
<atomType id="O.sp3">
<atom elementType="O" formalCharge="0">
<scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">2</scalar>
@@ -365,6 +374,12 @@
</atom>
</atomType>
+ <atomType id="Fe.2plus">
+ <atom elementType="Fe" formalCharge="2">
+ <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">0</scalar>
+ </atom>
+ </atomType>
+
<atomType id="Si.sp3">
<atom elementType="Si" formalCharge="0">
<scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">4</scalar>
Modified: trunk/cdk/src/org/openscience/cdk/test/atomtype/CDKAtomTypeMatcherTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/atomtype/CDKAtomTypeMatcherTest.java 2007-09-30 19:27:27 UTC (rev 8995)
+++ trunk/cdk/src/org/openscience/cdk/test/atomtype/CDKAtomTypeMatcherTest.java 2007-09-30 20:22:05 UTC (rev 8996)
@@ -36,6 +36,7 @@
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
@@ -659,6 +660,38 @@
assertAtomType(testedAtomTypes, "Mg.2plus", atm.findMatchingAtomType(mol, atom));
}
+ @Test public void testFerrocene() throws Exception {
+ IAtomContainer ferrocene = new Molecule();
+ ferrocene.addAtom(new Atom("C"));
+ ferrocene.addAtom(new Atom("C"));
+ ferrocene.addAtom(new Atom("C"));
+ ferrocene.addAtom(new Atom("C"));
+ ferrocene.addAtom(new Atom("C")); ferrocene.getAtom(4).setFormalCharge(-1);
+ ferrocene.addAtom(new Atom("C"));
+ ferrocene.addAtom(new Atom("C"));
+ ferrocene.addAtom(new Atom("C"));
+ ferrocene.addAtom(new Atom("C"));
+ ferrocene.addAtom(new Atom("C")); ferrocene.getAtom(9).setFormalCharge(-1);
+ ferrocene.addAtom(new Atom("Fe")); ferrocene.getAtom(10).setFormalCharge(+2);
+ ferrocene.addBond(0,1,CDKConstants.BONDORDER_DOUBLE);
+ ferrocene.addBond(1,2,CDKConstants.BONDORDER_SINGLE);
+ ferrocene.addBond(2,3,CDKConstants.BONDORDER_DOUBLE);
+ ferrocene.addBond(3,4,CDKConstants.BONDORDER_SINGLE);
+ ferrocene.addBond(4,0,CDKConstants.BONDORDER_SINGLE);
+ ferrocene.addBond(5,6,CDKConstants.BONDORDER_DOUBLE);
+ ferrocene.addBond(6,7,CDKConstants.BONDORDER_SINGLE);
+ ferrocene.addBond(7,8,CDKConstants.BONDORDER_DOUBLE);
+ ferrocene.addBond(8,9,CDKConstants.BONDORDER_SINGLE);
+ ferrocene.addBond(0,9,CDKConstants.BONDORDER_SINGLE);
+ CDKAtomTypeMatcher atm = CDKAtomTypeMatcher.getInstance(ferrocene.getBuilder());
+ assertAtomType(testedAtomTypes, "Fe.2plus", atm.findMatchingAtomType(
+ ferrocene, ferrocene.getAtom(10))
+ );
+ assertAtomType(testedAtomTypes, "C.minus.sp2", atm.findMatchingAtomType(
+ ferrocene, ferrocene.getAtom(4))
+ );
+ }
+
@Test public void testStructGenMatcher() throws Exception {
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(DefaultChemObjectBuilder.getInstance());
Assert.assertNotNull(matcher);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|