[Cdk-commits] SF.net SVN: cdk: [6734] trunk/cdk/src/org/openscience/cdk/test/tools

[<mig...@us...>]

Revision: 6734
Author:   miguelrojasch
Date:     2006-08-03 05:12:40 -0700 (Thu, 03 Aug 2006)
ViewCVS:  http://svn.sourceforge.net/cdk/?rev=6734&view=rev

Log Message:
-----------
check for halogens which are added to double bonds and contains charge.

Modified Paths:
--------------
    trunk/cdk/src/org/openscience/cdk/config/data/hybridization_atomtypes.xml
    trunk/cdk/src/org/openscience/cdk/test/tools/ValencyHybridCheckerTest.java
Modified: trunk/cdk/src/org/openscience/cdk/config/data/hybridization_atomtypes.xml
===================================================================
--- trunk/cdk/src/org/openscience/cdk/config/data/hybridization_atomtypes.xml	2006-08-03 11:41:59 UTC (rev 6733)
+++ trunk/cdk/src/org/openscience/cdk/config/data/hybridization_atomtypes.xml	2006-08-03 12:12:40 UTC (rev 6734)
@@ -227,6 +227,12 @@
       <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">0.0</scalar>
     </atom>
   </atomType>
+  <atomType id="F+">
+    <atom elementType="F" formalCharge="1">
+      <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
+      <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">2.0</scalar>
+    </atom>
+  </atomType>
   <atomType id="Cl">
     <atom elementType="Cl" formalCharge="0">
       <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
@@ -239,6 +245,12 @@
       <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">0.0</scalar>
     </atom>
   </atomType>
+  <atomType id="Cl+">
+    <atom elementType="F" formalCharge="1">
+      <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
+      <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">2.0</scalar>
+    </atom>
+  </atomType>
   <atomType id="Br">
     <atom elementType="Br" formalCharge="0">
       <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
@@ -251,6 +263,12 @@
       <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">0.0</scalar>
     </atom>
   </atomType>
+  <atomType id="Br+">
+    <atom elementType="F" formalCharge="1">
+      <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
+      <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">2.0</scalar>
+    </atom>
+  </atomType>
   <atomType id="I">
     <atom elementType="I" formalCharge="0">
       <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
@@ -263,5 +281,11 @@
       <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">0.0</scalar>
     </atom>
   </atomType>
+  <atomType id="I+">
+    <atom elementType="F" formalCharge="1">
+      <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
+      <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">2.0</scalar>
+    </atom>
+  </atomType>
 
 </atomTypeList>

Modified: trunk/cdk/src/org/openscience/cdk/test/tools/ValencyHybridCheckerTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/tools/ValencyHybridCheckerTest.java	2006-08-03 11:41:59 UTC (rev 6733)
+++ trunk/cdk/src/org/openscience/cdk/test/tools/ValencyHybridCheckerTest.java	2006-08-03 12:12:40 UTC (rev 6734)
@@ -34,6 +34,7 @@
 import org.openscience.cdk.smiles.SmilesParser;
 import org.openscience.cdk.test.CDKTestCase;
 import org.openscience.cdk.tools.IValencyChecker;
+import org.openscience.cdk.tools.ValencyChecker;
 import org.openscience.cdk.tools.ValencyHybridChecker;
 
 /**
@@ -105,5 +106,17 @@
 		Molecule mol = p.parseSmiles("c2ccc1[nH]ccc1c2");
 		new ValencyHybridChecker().saturate(mol);
 	}
+	
+	/**
+     * 
+     * @throws CDKException
+     */
+    public void test1() throws CDKException {
+    	SmilesParser sp = new SmilesParser();
+		Molecule mol = sp.parseSmiles("[F+]=C=C");
+		
+		assertTrue(satcheck.isSaturated(mol.getAtom(0),mol));
+    }
+    
 }
 


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