Handle -P(=O)[O-]-

johnmay · johnmay · commit 2f724d9a9637 · 2020-01-28T09:27:06.000Z
diff --git a/base/standard/src/main/java/org/openscience/cdk/stereo/Stereocenters.java b/base/standard/src/main/java/org/openscience/cdk/stereo/Stereocenters.java
@@ -636,6 +636,9 @@ private boolean verifyTerminalHCount(int v) {
                     Integer implHCount = atom.getImplicitHydrogenCount();
                     if (implHCount != null)
                         terminalHCount += implHCount;
+                    // O, S, Se, Te, or N with -1 charge is equiv to having a H
+                    if (atom.getFormalCharge() == -1)
+                        terminalHCount++;
                 }
             }
 
diff --git a/base/test-standard/src/test/java/org/openscience/cdk/stereo/StereocentersTest.java b/base/test-standard/src/test/java/org/openscience/cdk/stereo/StereocentersTest.java
@@ -370,6 +370,7 @@ public void phosphorus_v5_neutral_reject_h() throws Exception {
     public void phosphorus_v5_neutral_reject_h_on_terminal() throws Exception {
         none("P(=N)(N)(C)CC");
         none("P(=O)(O)(C)CC");
+        none("P(=O)([O-])(C)CC");
         none("P(=S)(S)(C)CC");
         none("P(=[Se])([SeH])(C)C");
         none("P(=[Te])([TeH])(C)C");

Original file line number	Diff line number	Diff line change
`@@ -636,6 +636,9 @@ private boolean verifyTerminalHCount(int v) {`
`636`	`636`	`Integer implHCount = atom.getImplicitHydrogenCount();`
`637`	`637`	`if (implHCount != null)`
`638`	`638`	`terminalHCount += implHCount;`
	`639`	`+ // O, S, Se, Te, or N with -1 charge is equiv to having a H`
	`640`	`+ if (atom.getFormalCharge() == -1)`
	`641`	`+ terminalHCount++;`
`639`	`642`	`}`
`640`	`643`	`}`
`641`	`644`