Added detection of a Te atom type, found in ChEMBL

Signed-off-by: jonalv <jonathan.alvarsson@gmail.com> Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
cdk · May 21, 2011 · 2f74024 · 2f74024
1 parent 1b9afc9
commit 2f74024
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diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -129,6 +129,8 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
             type = perceiveBeryllium(atomContainer, atom);
         } else if ("Se".equals(atom.getSymbol())) {
             type = perceiveSelenium(atomContainer, atom);
+        } else if ("Te".equals(atom.getSymbol())) {
+            type = perceiveTellurium(atomContainer, atom);
         } else if ("Ga".equals(atom.getSymbol())) {
             type = perceiveGallium(atomContainer, atom);
         } else if ("Ge".equals(atom.getSymbol())) {
@@ -174,6 +176,15 @@ private IAtomType perceiveSelenium(IAtomContainer atomContainer, IAtom atom) thr
 		return null;
 	}
 
+    private IAtomType perceiveTellurium(IAtomContainer atomContainer, IAtom atom) throws CDKException {
+        IBond.Order maxBondOrder = atomContainer.getMaximumBondOrder(atom);
+        if (!isCharged(atom) && maxBondOrder == IBond.Order.SINGLE && atomContainer.getConnectedAtomsCount(atom) <= 2) {
+            IAtomType type = getAtomType("Te.3");
+            if (isAcceptable(atom, atomContainer, type)) return type;
+        }
+        return null;
+    }
+
 	private IAtomType perceiveBorons(IAtomContainer atomContainer, IAtom atom)
 		throws CDKException {
 	    IBond.Order maxBondOrder = atomContainer.getMaximumBondOrder(atom);

diff --git a/src/main/org/openscience/cdk/dict/data/cdk-atom-types.owl b/src/main/org/openscience/cdk/dict/data/cdk-atom-types.owl
@@ -1432,6 +1432,15 @@
     <at:hybridization rdf:resource="&at;sp3"/>
   </at:AtomType>
 
+  <at:AtomType rdf:ID="Te.3">
+    <at:formalCharge>0</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;Te"/>
+    <at:formalNeighbourCount>2</at:formalNeighbourCount>
+    <at:lonePairCount>2</at:lonePairCount>
+    <at:piBondCount>0</at:piBondCount>
+    <at:hybridization rdf:resource="&at;sp3"/>
+  </at:AtomType>
+
   <at:AtomType rdf:ID="Ga.3plus">
     <at:formalCharge>3</at:formalCharge>
     <at:hasElement rdf:resource="&elem;Ga"/>