From 58a2e0e76adb9de3ae34d0ad9dc6926c2f9b6d28 Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egonw@users.sourceforge.net>
Date: Thu, 21 Oct 2010 14:52:53 +0200
Subject: [PATCH] Added missing atom type: positively charged P with three
 neighbors, of which one double bonded

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
---
 .../cdk/atomtype/CDKAtomTypeMatcher.java      | 10 ++++-
 .../cdk/dict/data/cdk-atom-types.owl          |  9 +++++
 .../cdk/atomtype/CDKAtomTypeMatcherTest.java  | 37 +++++++++++++++++++
 3 files changed, 54 insertions(+), 2 deletions(-)

diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
index 60e26ebcf97..0cd4e59a297 100644
--- a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
+++ b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -907,8 +907,14 @@ private IAtomType perceivePhosphors(IAtomContainer atomContainer, IAtom atom)
             // no idea how to deal with this yet
             return null;
         } else if (neighborcount == 3) {
-            IAtomType type = getAtomType("P.ine");
-            if (isAcceptable(atom, atomContainer, type)) return type;
+            if (atom.getFormalCharge() != null &
+                atom.getFormalCharge().intValue() == 1) {
+                IAtomType type = getAtomType("P.anium");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            } else {
+                IAtomType type = getAtomType("P.ine");
+                if (isAcceptable(atom, atomContainer, type)) return type;
+            }
         } else if (neighborcount == 2) {
             if (maxBondOrder == CDKConstants.BONDORDER_DOUBLE) {
                 IAtomType type = getAtomType("P.irane");
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
index 0c8a961a713..6097946b547 100644
--- a/src/main/org/openscience/cdk/dict/data/cdk-atom-types.owl
+++ b/src/main/org/openscience/cdk/dict/data/cdk-atom-types.owl
@@ -1084,6 +1084,15 @@
     <at:hybridization rdf:resource="&at;sp3"/>
   </at:AtomType>
 
+  <at:AtomType rdf:ID="P.anium">
+    <at:formalCharge>1</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;P"/>
+    <at:formalNeighbourCount>3</at:formalNeighbourCount>
+    <at:lonePairCount>0</at:lonePairCount>
+    <at:piBondCount>1</at:piBondCount>
+    <at:hybridization rdf:resource="&at;sp2"/>
+  </at:AtomType>
+
   <at:AtomType rdf:ID="P.irane">
     <at:formalCharge>0</at:formalCharge>
     <at:hasElement rdf:resource="&elem;P"/>
diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
index 480724e3a4f..abba0e88452 100644
--- a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
+++ b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -39,6 +39,7 @@
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomType;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IMolecule;
 import org.openscience.cdk.interfaces.IAtomType.Hybridization;
 import org.openscience.cdk.interfaces.IBond.Order;
@@ -1103,6 +1104,42 @@ public void testTetrahydropyran() throws Exception {
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
 
+    /**
+     * @cdk.inchi InChI=1S/HO3P/c1-4(2)3/h(H-,1,2,3)/p+1
+     */
+    @Test public void testPhosphorousAcid() throws Exception {
+        IMolecule mol = new Molecule();
+        IChemObjectBuilder builder = mol.getBuilder();
+        IAtom a1 = builder.newInstance(IAtom.class,"P");
+        a1.setFormalCharge(1);
+        mol.addAtom(a1);
+        IAtom a2 = builder.newInstance(IAtom.class,"O");
+        mol.addAtom(a2);
+        IAtom a3 = builder.newInstance(IAtom.class,"O");
+        mol.addAtom(a3);
+        IAtom a4 = builder.newInstance(IAtom.class,"O");
+        mol.addAtom(a4);
+        IAtom a5 = builder.newInstance(IAtom.class,"H");
+        mol.addAtom(a5);
+        IAtom a6 = builder.newInstance(IAtom.class,"H");
+        mol.addAtom(a6);
+        IBond b1 = builder.newInstance(IBond.class,a1, a2, IBond.Order.SINGLE);
+        mol.addBond(b1);
+        IBond b2 = builder.newInstance(IBond.class,a1, a3, IBond.Order.SINGLE);
+        mol.addBond(b2);
+        IBond b3 = builder.newInstance(IBond.class,a1, a4, IBond.Order.DOUBLE);
+        mol.addBond(b3);
+        IBond b4 = builder.newInstance(IBond.class,a2, a5, IBond.Order.SINGLE);
+        mol.addBond(b4);
+        IBond b5 = builder.newInstance(IBond.class,a3, a6, IBond.Order.SINGLE);
+        mol.addBond(b5);
+
+        String[] expectedTypes = {
+            "P.anium", "O.sp3", "O.sp3", "O.sp2", "H", "H"
+        };
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
     @Test public void testDiethylPhosphine() throws Exception {
     	IMolecule mol = new Molecule();
         IAtom atom = new Atom("C");