Menu
▾
▴
[Cdk-commits] SF.net SVN: cdk: [7331] trunk/cdk/src
|
From: <mig...@us...> - 2006-11-21 19:12:16
|
Revision: 7331
http://svn.sourceforge.net/cdk/?rev=7331&view=rev
Author: miguelrojasch
Date: 2006-11-21 11:10:06 -0800 (Tue, 21 Nov 2006)
Log Message:
-----------
test for ReactionList
Modified Paths:
--------------
trunk/cdk/src/data/cml/reaction.1.cml
trunk/cdk/src/org/openscience/cdk/test/io/cml/CML2Test.java
Added Paths:
-----------
trunk/cdk/src/data/cml/reactionList.1.cml
Modified: trunk/cdk/src/data/cml/reaction.1.cml
===================================================================
--- trunk/cdk/src/data/cml/reaction.1.cml 2006-11-21 19:00:47 UTC (rev 7330)
+++ trunk/cdk/src/data/cml/reaction.1.cml 2006-11-21 19:10:06 UTC (rev 7331)
@@ -2,7 +2,7 @@
<reactionList>
<reaction>
<reactantList>
-<reactant>
+<reactant id="react">
<molecule>
<atomArray>
<atom id="a14293164" elementType="C" x2="222.99999999999997" y2="934.0" formalCharge="0" hydrogenCount="0"/>
Added: trunk/cdk/src/data/cml/reactionList.1.cml
===================================================================
--- trunk/cdk/src/data/cml/reactionList.1.cml (rev 0)
+++ trunk/cdk/src/data/cml/reactionList.1.cml 2006-11-21 19:10:06 UTC (rev 7331)
@@ -0,0 +1,113 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<reactionList>
+<reaction id="1.3.2">
+<reactantList>
+<reactant id="actey">
+<molecule>
+<atomArray>
+<atom id="a14293164" elementType="C" x2="222.99999999999997" y2="934.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a9045316" elementType="C" x2="191.82308546376018" y2="952.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a23053324" elementType="C" x2="191.8230854637602" y2="988.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a4199273" elementType="C" x2="223.00000000000003" y2="1006.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a12213211" elementType="C" x2="254.1769145362398" y2="988.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a14982605" elementType="C" x2="254.1769145362398" y2="952.0" formalCharge="0" hydrogenCount="0"/>
+</atomArray>
+<bondArray><bond id="b17477791" atomRefs2="a14293164 a9045316" order="S"/>
+<bond id="b13748088" atomRefs2="a9045316 a23053324" order="S"/>
+<bond id="b8303462" atomRefs2="a23053324 a4199273" order="S"/>
+<bond id="b3403998" atomRefs2="a4199273 a12213211" order="S"/>
+<bond id="b701508" atomRefs2="a12213211 a14982605" order="S"/>
+<bond id="b12644844" atomRefs2="a14982605 a14293164" order="S"/>
+</bondArray>
+</molecule>
+</reactant>
+<reactant id="agent">
+<molecule>
+<atomArray>
+<atom id="a14293164" elementType="C" x2="222.99999999999997" y2="934.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a9045316" elementType="C" x2="191.82308546376018" y2="952.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a23053324" elementType="C" x2="191.8230854637602" y2="988.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a4199273" elementType="C" x2="223.00000000000003" y2="1006.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a12213211" elementType="C" x2="254.1769145362398" y2="988.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a14982605" elementType="C" x2="254.1769145362398" y2="952.0" formalCharge="0" hydrogenCount="0"/>
+</atomArray>
+<bondArray><bond id="b17477791" atomRefs2="a14293164 a9045316" order="S"/>
+<bond id="b13748088" atomRefs2="a9045316 a23053324" order="S"/>
+<bond id="b8303462" atomRefs2="a23053324 a4199273" order="S"/>
+<bond id="b3403998" atomRefs2="a4199273 a12213211" order="S"/>
+<bond id="b701508" atomRefs2="a12213211 a14982605" order="S"/>
+<bond id="b12644844" atomRefs2="a14982605 a14293164" order="S"/>
+</bondArray>
+</molecule>
+</reactant>
+</reactantList>
+<productList>
+<product id="prdct">
+<molecule>
+<atomArray>
+<atom id="a14222419" elementType="C" x2="416.99999999999994" y2="930.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a27988400" elementType="C" x2="385.8230854637602" y2="948.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a1465214" elementType="C" x2="385.8230854637602" y2="984.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a30462244" elementType="C" x2="417.0" y2="1002.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a5424820" elementType="C" x2="448.1769145362398" y2="984.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a7572744" elementType="C" x2="448.1769145362398" y2="948.0" formalCharge="0" hydrogenCount="0"/>
+</atomArray>
+<bondArray>
+<bond id="b6778431" atomRefs2="a14222419 a27988400" order="S"/>
+<bond id="b7802158" atomRefs2="a27988400 a1465214" order="D"/>
+<bond id="b162178" atomRefs2="a1465214 a30462244" order="S"/>
+<bond id="b7832149" atomRefs2="a30462244 a5424820" order="D"/>
+<bond id="b895244" atomRefs2="a5424820 a7572744" order="S"/>
+<bond id="b14600371" atomRefs2="a7572744 a14222419" order="D"/>
+</bondArray>
+</molecule>
+</product>
+</productList>
+</reaction>
+
+<reaction id="1.1.4">
+<reactantList>
+<reactant id="prdct">
+<molecule>
+<atomArray>
+<atom id="a14293164" elementType="C" x2="222.99999999999997" y2="934.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a9045316" elementType="C" x2="191.82308546376018" y2="952.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a23053324" elementType="C" x2="191.8230854637602" y2="988.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a4199273" elementType="C" x2="223.00000000000003" y2="1006.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a12213211" elementType="C" x2="254.1769145362398" y2="988.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a14982605" elementType="C" x2="254.1769145362398" y2="952.0" formalCharge="0" hydrogenCount="0"/>
+</atomArray>
+<bondArray><bond id="b17477791" atomRefs2="a14293164 a9045316" order="S"/>
+<bond id="b13748088" atomRefs2="a9045316 a23053324" order="S"/>
+<bond id="b8303462" atomRefs2="a23053324 a4199273" order="S"/>
+<bond id="b3403998" atomRefs2="a4199273 a12213211" order="S"/>
+<bond id="b701508" atomRefs2="a12213211 a14982605" order="S"/>
+<bond id="b12644844" atomRefs2="a14982605 a14293164" order="S"/>
+</bondArray>
+</molecule>
+</reactant>
+</reactantList>
+<productList>
+<product id="ac34">
+<molecule>
+<atomArray>
+<atom id="a14222419" elementType="C" x2="416.99999999999994" y2="930.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a27988400" elementType="C" x2="385.8230854637602" y2="948.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a1465214" elementType="C" x2="385.8230854637602" y2="984.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a30462244" elementType="C" x2="417.0" y2="1002.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a5424820" elementType="C" x2="448.1769145362398" y2="984.0" formalCharge="0" hydrogenCount="0"/>
+<atom id="a7572744" elementType="C" x2="448.1769145362398" y2="948.0" formalCharge="0" hydrogenCount="0"/>
+</atomArray>
+<bondArray>
+<bond id="b6778431" atomRefs2="a14222419 a27988400" order="S"/>
+<bond id="b7802158" atomRefs2="a27988400 a1465214" order="D"/>
+<bond id="b162178" atomRefs2="a1465214 a30462244" order="S"/>
+<bond id="b7832149" atomRefs2="a30462244 a5424820" order="D"/>
+<bond id="b895244" atomRefs2="a5424820 a7572744" order="S"/>
+<bond id="b14600371" atomRefs2="a7572744 a14222419" order="D"/>
+</bondArray>
+</molecule>
+</product>
+</productList>
+</reaction>
+</reactionList>
\ No newline at end of file
Modified: trunk/cdk/src/org/openscience/cdk/test/io/cml/CML2Test.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/io/cml/CML2Test.java 2006-11-21 19:00:47 UTC (rev 7330)
+++ trunk/cdk/src/org/openscience/cdk/test/io/cml/CML2Test.java 2006-11-21 19:10:06 UTC (rev 7331)
@@ -601,7 +601,43 @@
fail(e.toString());
}
}
+ /**
+ * This test tests wether the CMLReader is able to ignore the CMLReaction part
+ * of a CML file, while extracting the reaction.
+ */
+ public void testCMLReactionList() {
+ String filename = "data/cml/reactionList.1.cml";
+ logger.info("Testing: " + filename);
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ try {
+ CMLReader reader = new CMLReader(ins);
+ IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());
+ // test the resulting ChemFile content
+ assertNotNull(chemFile);
+ assertEquals(chemFile.getChemSequenceCount(), 1);
+ org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
+ assertNotNull(seq);
+ assertEquals(1,seq.getChemModelCount());
+ org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
+ assertNotNull(model);
+ assertEquals(2,model.getReactionSet().getReactionCount());
+ assertEquals("1.3.2",model.getReactionSet().getReaction(0).getID());
+
+ // test the reaction
+ IReaction reaction = model.getReactionSet().getReaction(0);
+ assertNotNull(reaction);
+ assertEquals("actey",reaction.getReactants().getAtomContainer(0).getID());
+ assertEquals("a14293164",reaction.getReactants().getAtomContainer(0).getAtom(0).getID());
+ assertEquals(6, reaction.getProducts().getAtomContainer(0).getAtomCount());
+ assertEquals(6, reaction.getReactants().getAtomContainer(0).getAtomCount());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail(e.toString());
+ }
+ }
+
/**
* @cdk.bug 1560486
*/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|