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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>
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1 parent 1b9afc9 commit 2f74024a48c7b73382a5b505e411e0ceeb3446f0 @egonw egonw committed with rajarshi May 21, 2011
@@ -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);
@@ -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"/>

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