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[Cdk-commits] SF.net SVN: cdk:[12216] cdk/trunk
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From: <eg...@us...> - 2008-09-07 08:25:44
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Revision: 12216
http://cdk.svn.sourceforge.net/cdk/?rev=12216&view=rev
Author: egonw
Date: 2008-09-07 08:25:34 +0000 (Sun, 07 Sep 2008)
Log Message:
-----------
Merge branch 'cdk-1.2.x'
Modified Paths:
--------------
cdk/trunk/build.props
cdk/trunk/pmd/custom-test.xml
cdk/trunk/pmd/customJunit.xml
cdk/trunk/pmd/migrating.xml
cdk/trunk/pmd-migrating.xml
cdk/trunk/pmd.xml
cdk/trunk/src/main/org/openscience/cdk/RingSet.java
cdk/trunk/src/main/org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java
cdk/trunk/src/main/org/openscience/cdk/charges/MMFF94PartialCharges.java
cdk/trunk/src/main/org/openscience/cdk/debug/DebugRingSet.java
cdk/trunk/src/main/org/openscience/cdk/geometry/CrystalGeometryTools.java
cdk/trunk/src/main/org/openscience/cdk/graph/SpanningTree.java
cdk/trunk/src/main/org/openscience/cdk/interfaces/IRingSet.java
cdk/trunk/src/main/org/openscience/cdk/io/CMLReader.java
cdk/trunk/src/main/org/openscience/cdk/io/INChIReader.java
cdk/trunk/src/main/org/openscience/cdk/layout/RingPlacer.java
cdk/trunk/src/main/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
cdk/trunk/src/main/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java
cdk/trunk/src/main/org/openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java
cdk/trunk/src/main/org/openscience/cdk/modeling/builder3d/MMFF94ParametersCall.java
cdk/trunk/src/main/org/openscience/cdk/modeling/forcefield/AngleBending.java
cdk/trunk/src/main/org/openscience/cdk/modeling/forcefield/BondStretching.java
cdk/trunk/src/main/org/openscience/cdk/modeling/forcefield/StretchBendInteractions.java
cdk/trunk/src/main/org/openscience/cdk/modeling/forcefield/Torsions.java
cdk/trunk/src/main/org/openscience/cdk/modeling/forcefield/VanDerWaalsInteractions.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/StabilizationPlusChargeDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/ringsearch/FiguerasSSSRFinder.java
cdk/trunk/src/main/org/openscience/cdk/ringsearch/RingPartitioner.java
cdk/trunk/src/main/org/openscience/cdk/ringsearch/SSSRFinder.java
cdk/trunk/src/main/org/openscience/cdk/smiles/SmilesParser.java
cdk/trunk/src/main/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java
cdk/trunk/src/main/org/openscience/cdk/tools/CDKValencyChecker.java
cdk/trunk/src/main/org/openscience/cdk/tools/IValencyChecker.java
cdk/trunk/src/main/org/openscience/cdk/tools/IonizationPotentialTool.java
cdk/trunk/src/main/org/openscience/cdk/tools/manipulator/RingSetManipulator.java
cdk/trunk/src/test/org/openscience/cdk/RingSetTest.java
cdk/trunk/src/test/org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java
cdk/trunk/src/test/org/openscience/cdk/smiles/SmilesGeneratorTest.java
cdk/trunk/src/test/org/openscience/cdk/smiles/SmilesParserTest.java
cdk/trunk/src/test/org/openscience/cdk/smiles/smarts/parser/ParserTest.java
Added Paths:
-----------
cdk/trunk/pmd/custom-qm.xml
cdk/trunk/pmd/migrating-qm.xml
cdk/trunk/src/test/data/cml/test1.cml
Modified: cdk/trunk/build.props
===================================================================
--- cdk/trunk/build.props 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/build.props 2008-09-07 08:25:34 UTC (rev 12216)
@@ -1,2 +1 @@
-version=svn-20080221
-jcp.version=2.3.2
+version=cdk-1.2.x-alpha
Added: cdk/trunk/pmd/custom-qm.xml
===================================================================
--- cdk/trunk/pmd/custom-qm.xml (rev 0)
+++ cdk/trunk/pmd/custom-qm.xml 2008-09-07 08:25:34 UTC (rev 12216)
@@ -0,0 +1,31 @@
+<?xml version="1.0"?>
+<ruleset name="custom-data">
+
+ <description>
+ This ruleset checks the CDK sources for bad code.
+ </description>
+
+ <!-- In the below paths, rulesets/ refers to the classpath, and the
+ pmd/ refers to this directory, and needs to be excluded because
+ the are called from ../pmd.xml -->
+
+ <!-- The rule sets that come with PMD -->
+
+ <rule ref="rulesets/basic.xml"/>
+ <rule ref="pmd/customNaming.xml"/>
+ <rule ref="rulesets/unusedcode.xml"/>
+ <rule ref="rulesets/imports.xml"/>
+ <rule ref="rulesets/strings.xml"/>
+ <rule ref="rulesets/codesize.xml">
+ <exclude name="TooManyMethods"/>
+ <exclude name="ExcessivePublicCount"/>
+ </rule>
+ <rule ref="rulesets/strictexception.xml"/>
+ <rule ref="pmd/migrating-qm.xml"/>
+
+ <!-- Rules specific for CDK -->
+
+ <rule ref="pmd/customCDK.xml"/>
+ <rule ref="pmd/customOptimization.xml"/>
+
+</ruleset>
Modified: cdk/trunk/pmd/custom-test.xml
===================================================================
--- cdk/trunk/pmd/custom-test.xml 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/pmd/custom-test.xml 2008-09-07 08:25:34 UTC (rev 12216)
@@ -14,6 +14,7 @@
<rule ref="rulesets/basic.xml"/>
<rule ref="rulesets/unusedcode.xml"/>
<rule ref="rulesets/imports.xml"/>
+ <rule ref="rulesets/migrating_to_junit4.xml"/>
<!-- Rules specific for CDK -->
Modified: cdk/trunk/pmd/customJunit.xml
===================================================================
--- cdk/trunk/pmd/customJunit.xml 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/pmd/customJunit.xml 2008-09-07 08:25:34 UTC (rev 12216)
@@ -8,5 +8,7 @@
<rule ref="rulesets/junit.xml">
<exclude name="JUnitAssertionsShouldIncludeMessage"/>
</rule>
+
+ <!-- to JUnit4 migration tested in migration*.xml -->
</ruleset>
Copied: cdk/trunk/pmd/migrating-qm.xml (from rev 12187, cdk/trunk/pmd/migrating.xml)
===================================================================
--- cdk/trunk/pmd/migrating-qm.xml (rev 0)
+++ cdk/trunk/pmd/migrating-qm.xml 2008-09-07 08:25:34 UTC (rev 12216)
@@ -0,0 +1,17 @@
+<?xml version="1.0"?>
+<ruleset name="custom">
+
+ <description>
+ This ruleset checks for migration clean up in the CDK sources.
+ </description>
+
+ <!-- The rule sets that come with PMD -->
+
+ <rule ref="rulesets/migrating_to_13.xml">
+ <exclude name="ReplaceVectorWithList"/>
+ </rule>
+ <rule ref="rulesets/migrating_to_14.xml"/>
+ <rule ref="rulesets/migrating_to_15.xml"/>
+ <rule ref="rulesets/migrating_to_junit4.xml"/>
+
+</ruleset>
Modified: cdk/trunk/pmd/migrating.xml
===================================================================
--- cdk/trunk/pmd/migrating.xml 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/pmd/migrating.xml 2008-09-07 08:25:34 UTC (rev 12216)
@@ -10,5 +10,6 @@
<rule ref="rulesets/migrating_to_13.xml"/>
<rule ref="rulesets/migrating_to_14.xml"/>
<rule ref="rulesets/migrating_to_15.xml"/>
+ <rule ref="rulesets/migrating_to_junit4.xml"/>
</ruleset>
Modified: cdk/trunk/pmd-migrating.xml
===================================================================
--- cdk/trunk/pmd-migrating.xml 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/pmd-migrating.xml 2008-09-07 08:25:34 UTC (rev 12216)
@@ -27,57 +27,57 @@
<target name="pmd" id="pmd">
<!-- the data classes modules -->
- <antcall target="test-module"><param name="module" value="data"/></antcall>
- <antcall target="test-module"><param name="module" value="datadebug"/></antcall>
- <antcall target="test-module"><param name="module" value="nonotify"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="data"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="datadebug"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="nonotify"/></antcall>
<!-- the other modules -->
- <antcall target="test-module"><param name="module" value="interfaces"/></antcall>
- <antcall target="test-module"><param name="module" value="core"/></antcall>
- <antcall target="test-module"><param name="module" value="standard"/></antcall>
- <antcall target="test-module"><param name="module" value="atomtype"/></antcall>
- <antcall target="test-module"><param name="module" value="io"/></antcall>
- <antcall target="test-module"><param name="module" value="extra"/></antcall>
- <antcall target="test-module"><param name="module" value="formula"/></antcall>
- <antcall target="test-module"><param name="module" value="render"/></antcall>
- <antcall target="test-module"><param name="module" value="reaction"/></antcall>
- <antcall target="test-module"><param name="module" value="libiocml"/></antcall>
- <antcall target="test-module"><param name="module" value="builder3d"/></antcall>
- <antcall target="test-module"><param name="module" value="smiles"/></antcall>
- <antcall target="test-module"><param name="module" value="smarts"/></antcall>
- <antcall target="test-module"><param name="module" value="pcore"/></antcall>
- <antcall target="test-module"><param name="module" value="forcefield"/></antcall>
- <antcall target="test-module"><param name="module" value="qsar"/></antcall>
- <antcall target="test-module"><param name="module" value="qsaratomic"/></antcall>
- <antcall target="test-module"><param name="module" value="qsarbond"/></antcall>
- <antcall target="test-module"><param name="module" value="qsarmolecular"/></antcall>
- <antcall target="test-module"><param name="module" value="qsarprotein"/></antcall>
- <antcall target="test-module"><param name="module" value="structgen"/></antcall>
- <antcall target="test-module"><param name="module" value="valencycheck"/></antcall>
- <antcall target="test-module"><param name="module" value="charges"/></antcall>
- <antcall target="test-module"><param name="module" value="diff"/></antcall>
- <antcall target="test-module"><param name="module" value="qm"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="interfaces"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="core"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="standard"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="atomtype"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="io"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="extra"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="formula"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="render"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="reaction"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="libiocml"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="builder3d"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="smiles"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="smarts"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="pcore"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="forcefield"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="qsar"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="qsaratomic"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="qsarbond"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="qsarmolecular"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="qsarprotein"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="structgen"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="valencycheck"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="charges"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="diff"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration-qm"/><param name="module" value="qm"/></antcall>
<!-- the test modules -->
- <antcall target="test-module"><param name="module" value="test-core"/></antcall>
- <antcall target="test-module"><param name="module" value="test-data"/></antcall>
- <antcall target="test-module"><param name="module" value="test-datadebug"/></antcall>
- <antcall target="test-module"><param name="module" value="test-nonotify"/></antcall>
- <antcall target="test-module"><param name="module" value="test-atomtype"/></antcall>
- <antcall target="test-module"><param name="module" value="test-extra"/></antcall>
- <antcall target="test-module"><param name="module" value="test-forcefield"/></antcall>
- <antcall target="test-module"><param name="module" value="test-io"/></antcall>
- <antcall target="test-module"><param name="module" value="test-reaction"/></antcall>
- <antcall target="test-module"><param name="module" value="test-smiles"/></antcall>
- <antcall target="test-module"><param name="module" value="test-standard"/></antcall>
- <antcall target="test-module"><param name="module" value="test-valencycheck"/></antcall>
- <antcall target="test-module"><param name="module" value="test-charges"/></antcall>
- <antcall target="test-module"><param name="module" value="test-pcore"/></antcall>
- <antcall target="test-module"><param name="module" value="test-qsar"/></antcall>
- <antcall target="test-module"><param name="module" value="test-qsaratomic"/></antcall>
- <antcall target="test-module"><param name="module" value="test-qsarbond"/></antcall>
- <antcall target="test-module"><param name="module" value="test-qsarmolecular"/></antcall>
- <antcall target="test-module"><param name="module" value="test-qsarprotein"/></antcall>
- <antcall target="test-module"><param name="module" value="test-diff"/></antcall>
- <antcall target="test-module"><param name="module" value="test-qm"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-core"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-data"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-datadebug"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-nonotify"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-atomtype"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-extra"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-forcefield"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-io"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-reaction"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-smiles"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-standard"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-valencycheck"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-charges"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-pcore"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-qsar"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-qsaratomic"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-qsarbond"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-qsarmolecular"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-qsarprotein"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-diff"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="migration"/><param name="module" value="test-qm"/></antcall>
</target>
<target id="test-module" name="test-module"
@@ -86,7 +86,8 @@
<echo message="Checking for migrating code updates in CDK's ${module} module." />
<mkdir dir="${reports.tests}/pmd-migrating"/>
- <pmd shortFilenames="true" rulesetfiles="pmd/migrating.xml">
+
+ <pmd shortFilenames="true" rulesetfiles="pmd/${pmd.test}.xml">
<formatter type="xml" toFile="${reports.tests}/pmd-migrating/${module}.xml"/>
<fileset dir="${src}/main">
<includesfile name="${build}/${module}.javafiles"/>
Modified: cdk/trunk/pmd.xml
===================================================================
--- cdk/trunk/pmd.xml 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/pmd.xml 2008-09-07 08:25:34 UTC (rev 12216)
@@ -55,7 +55,7 @@
<antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="valencycheck"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="charges"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="diff"/></antcall>
- <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="qm"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="custom-qm"/><param name="module" value="qm"/></antcall>
<!-- the test modules -->
<antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-core"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-data"/></antcall>
Modified: cdk/trunk/src/main/org/openscience/cdk/RingSet.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/RingSet.java 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/src/main/org/openscience/cdk/RingSet.java 2008-09-07 08:25:34 UTC (rev 12216)
@@ -25,8 +25,6 @@
package org.openscience.cdk;
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
@@ -68,16 +66,16 @@
* @return A vector of all rings that this bond is part of
*/
- public List<IRing> getRings(IBond bond)
+ public IRingSet getRings(IBond bond)
{
- List<IRing> rings = new ArrayList<IRing>();
+ IRingSet rings = bond.getBuilder().newRingSet();
Ring ring;
for (int i = 0; i < getAtomContainerCount(); i++)
{
ring = (Ring)getAtomContainer(i);
if (ring.contains(bond))
{
- rings.add(ring);
+ rings.addAtomContainer(ring);
}
}
return rings;
@@ -113,9 +111,9 @@
* @return All the rings that share one or more atoms with a given ring.
*/
- public List<IRing> getConnectedRings(IRing ring)
+ public IRingSet getConnectedRings(IRing ring)
{
- List<IRing> connectedRings = new ArrayList<IRing>();
+ IRingSet connectedRings = ring.getBuilder().newRingSet();
IRing tempRing;
IAtom atom;
for (int i = 0; i < ring.getAtomCount(); i++)
@@ -126,7 +124,7 @@
tempRing = (IRing)getAtomContainer(j);
if (tempRing != ring && !connectedRings.contains(tempRing) && tempRing.contains(atom))
{
- connectedRings.add(tempRing);
+ connectedRings.addAtomContainer(tempRing);
}
}
}
Modified: cdk/trunk/src/main/org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/src/main/org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java 2008-09-07 08:25:34 UTC (rev 12216)
@@ -74,6 +74,7 @@
for (IAtom atom : atomContainer.atoms()) {
IAtomType type = cdkMatcher.findMatchingAtomType(atomContainer, atom);
atom.setAtomTypeName(type == null ? null : type.getAtomTypeName());
+ atom.setHybridization(type == null ? null : type.getHybridization());
}
CDKHueckelAromaticityDetector.detectAromaticity(atomContainer);
IAtomType[] types = new IAtomType[atomContainer.getAtomCount()];
Modified: cdk/trunk/src/main/org/openscience/cdk/charges/MMFF94PartialCharges.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/charges/MMFF94PartialCharges.java 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/src/main/org/openscience/cdk/charges/MMFF94PartialCharges.java 2008-09-07 08:25:34 UTC (rev 12216)
@@ -21,9 +21,8 @@
*/
package org.openscience.cdk.charges;
-import java.util.Hashtable;
import java.util.Map;
-import java.util.Vector;
+import java.util.List;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
@@ -75,7 +74,7 @@
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.setForceFieldConfigurator("mmff94");
ffc.assignAtomTyps((IMolecule)ac);
- Map parameterSet = ffc.getParameterSet();
+ Map<String,List> parameterSet = ffc.getParameterSet();
// for this calculation,
// we need some values stored in the vector "data" in the
// hashtable of these atomTypes:
@@ -86,30 +85,30 @@
double sumOfFormalCharges = 0;
double sumOfBondIncrements = 0;
org.openscience.cdk.interfaces.IAtom thisAtom = null;
- java.util.List<IAtom> neighboors;
- Vector data = null;
- Vector bondData = null;
- Vector dataNeigh = null;
+ List<IAtom> neighboors;
+ List data = null;
+ List bondData = null;
+ List dataNeigh = null;
java.util.Iterator<IAtom> atoms = ac.atoms().iterator();
while(atoms.hasNext()) {
//logger.debug("ATOM "+i+ " " +atoms[i].getSymbol());
thisAtom = atoms.next();
- data = (Vector) parameterSet.get("data"+thisAtom.getAtomTypeName());
+ data = parameterSet.get("data"+thisAtom.getAtomTypeName());
neighboors = ac.getConnectedAtomsList(thisAtom);
formalCharge = thisAtom.getCharge();
- theta = (Double) data.get(5);
+ theta = (Double)data.get(5);
charge = formalCharge * (1 - (neighboors.size() * theta));
sumOfFormalCharges = 0;
sumOfBondIncrements = 0;
for (IAtom neighboor : neighboors) {
IAtom neighbour = (IAtom) neighboor;
- dataNeigh = (Vector) parameterSet.get("data" + neighbour.getAtomTypeName());
+ dataNeigh = parameterSet.get("data" + neighbour.getAtomTypeName());
if (parameterSet.containsKey("bond" + thisAtom.getAtomTypeName() + ";" + neighbour.getAtomTypeName())) {
- bondData = (Vector) parameterSet.get("bond" + thisAtom.getAtomTypeName() + ";" + neighbour.getAtomTypeName());
+ bondData = parameterSet.get("bond" + thisAtom.getAtomTypeName() + ";" + neighbour.getAtomTypeName());
sumOfBondIncrements -= (Double) bondData.get(4);
} else
if (parameterSet.containsKey("bond" + neighbour.getAtomTypeName() + ";" + thisAtom.getAtomTypeName())) {
- bondData = (Vector) parameterSet.get("bond" + neighbour.getAtomTypeName() + ";" + thisAtom.getAtomTypeName());
+ bondData = parameterSet.get("bond" + neighbour.getAtomTypeName() + ";" + thisAtom.getAtomTypeName());
sumOfBondIncrements += (Double) bondData.get(4);
} else {
// Maybe not all bonds have pbci in mmff94.prm, i.e. C-N
@@ -117,7 +116,7 @@
}
- dataNeigh = (Vector) parameterSet.get("data" + neighbour.getID());
+ dataNeigh = parameterSet.get("data" + neighbour.getID());
formalChargeNeigh = neighbour.getCharge();
sumOfFormalCharges += formalChargeNeigh;
}
Modified: cdk/trunk/src/main/org/openscience/cdk/debug/DebugRingSet.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/debug/DebugRingSet.java 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/src/main/org/openscience/cdk/debug/DebugRingSet.java 2008-09-07 08:25:34 UTC (rev 12216)
@@ -20,8 +20,6 @@
*/
package org.openscience.cdk.debug;
-import java.util.List;
-
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IRing;
@@ -46,7 +44,7 @@
super();
}
- public List getRings(IBond bond) {
+ public IRingSet getRings(IBond bond) {
logger.debug("Getting rings for bond: ", bond);
return super.getRings(bond);
}
@@ -56,7 +54,7 @@
return super.getRings(atom);
}
- public List getConnectedRings(IRing ring) {
+ public IRingSet getConnectedRings(IRing ring) {
logger.debug("Getting connected rings for ring: ", ring);
return super.getConnectedRings(ring);
}
Modified: cdk/trunk/src/main/org/openscience/cdk/geometry/CrystalGeometryTools.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/geometry/CrystalGeometryTools.java 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/src/main/org/openscience/cdk/geometry/CrystalGeometryTools.java 2008-09-07 08:25:34 UTC (rev 12216)
@@ -96,31 +96,6 @@
}
/**
- * Method that transforms fractional coordinates into cartesian coordinates.
- *
- * @param aAxis the a axis vector of the unit cell in cartesian coordinates
- * @param bAxis the b axis vector of the unit cell in cartesian coordinates
- * @param cAxis the c axis vector of the unit cell in cartesian coordinates
- * @param frac a fractional coordinate to convert
- * @return an array of length 3 with the cartesian coordinates of the
- * point defined by frac
- *
- * @cdk.keyword cartesian coordinates
- * @cdk.keyword fractional coordinates
- *
- * @see #cartesianToFractional(javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Point3d)
- * @deprecated
- */
- public static double[] fractionalToCartesian(double[] aAxis, double[] bAxis, double[] cAxis,
- double[] frac) {
- double[] cart = new double[3];
- cart[0] = frac[0]*aAxis[0] + frac[1]*bAxis[0] + frac[2]*cAxis[0];
- cart[1] = frac[0]*aAxis[1] + frac[1]*bAxis[1] + frac[2]*cAxis[1];
- cart[2] = frac[0]*aAxis[2] + frac[1]*bAxis[2] + frac[2]*cAxis[2];
- return cart;
- }
-
- /**
* @cdk.dictref blue-obelisk:convertFractionIntoCartesianCoordinates
*/
@TestMethod("testFractionalToCartesian_Vector3d_Vector3d_Vector3d_Point3d")
@@ -134,19 +109,6 @@
}
/**
- * @deprecated
- */
- public static Point3d fractionalToCartesian(double[] aAxis, double[] bAxis, double[] cAxis,
- Point3d fracPoint) {
- double[] frac = new double[3];
- frac[0] = fracPoint.x;
- frac[1] = fracPoint.y;
- frac[2] = fracPoint.z;
- double[] cart = fractionalToCartesian(aAxis,bAxis,cAxis, frac);
- return new Point3d(cart[0], cart[1], cart[2]);
- }
-
- /**
* Calculates cartesian vectors for unit cell axes from axes lengths and angles
* between axes.
*
Modified: cdk/trunk/src/main/org/openscience/cdk/graph/SpanningTree.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/graph/SpanningTree.java 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/src/main/org/openscience/cdk/graph/SpanningTree.java 2008-09-07 08:25:34 UTC (rev 12216)
@@ -28,10 +28,12 @@
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.NoSuchAtomException;
-import org.openscience.cdk.interfaces.*;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IRing;
+import org.openscience.cdk.interfaces.IRingSet;
-import java.util.Iterator;
-
/**
* Spanning tree of a molecule.
* Used to discover the number of cyclic bonds in order to prevent the
@@ -154,8 +156,7 @@
cb[i][a] = 0;
// remove ATOM_NUMBER props again
- Iterator atoms = atomContainer.atoms().iterator();
- while (atoms.hasNext()) ((IAtom)atoms.next()).removeProperty(ATOM_NUMBER);
+ for (IAtom atom : atomContainer.atoms()) atom.removeProperty(ATOM_NUMBER);
}
@TestMethod("testGetSpanningTree")
@@ -172,7 +173,8 @@
IAtomContainer path = spt.getBuilder().newAtomContainer();
PathTools.resetFlags(spt);
path.addAtom(a1);
- PathTools.depthFirstTargetSearch(spt,a1,a2,path);
+ PathTools.depthFirstTargetSearch(spt,a1,a2,path);
+ if (path.getAtomCount() == 1) path.removeAtom(a1); // no path found: remove initial atom
return path;
}
Modified: cdk/trunk/src/main/org/openscience/cdk/interfaces/IRingSet.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/interfaces/IRingSet.java 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/src/main/org/openscience/cdk/interfaces/IRingSet.java 2008-09-07 08:25:34 UTC (rev 12216)
@@ -23,7 +23,6 @@
*/
package org.openscience.cdk.interfaces;
-import java.util.List;
/**
* Maintains a set of Ring objects.
@@ -41,7 +40,7 @@
* @param bond The bond to be checked
* @return A vector of all rings that this bond is part of
*/
- public List<IRing> getRings(IBond bond);
+ public IRingSet getRings(IBond bond);
/**
* Returns a vector of all rings that this atom is part of.
@@ -58,7 +57,7 @@
* @param ring A ring with which all return rings must share one or more atoms
* @return All the rings that share one or more atoms with a given ring.
*/
- public List<IRing> getConnectedRings(IRing ring);
+ public IRingSet getConnectedRings(IRing ring);
/**
* Adds all rings of another RingSet if they are not allready part of this ring set.
Modified: cdk/trunk/src/main/org/openscience/cdk/io/CMLReader.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/io/CMLReader.java 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/src/main/org/openscience/cdk/io/CMLReader.java 2008-09-07 08:25:34 UTC (rev 12216)
@@ -25,13 +25,11 @@
*/
package org.openscience.cdk.io;
+import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
-import java.io.InputStreamReader;
import java.io.Reader;
-import java.io.StringReader;
import java.util.HashMap;
-import java.util.Iterator;
import java.util.Map;
import org.openscience.cdk.exception.CDKException;
@@ -64,39 +62,25 @@
public class CMLReader extends DefaultChemObjectReader {
private XMLReader parser;
- private Reader input;
+ private InputStream input;
private String url;
- private Map userConventions = new HashMap();
+ private Map<String,ICMLModule> userConventions = new HashMap<String,ICMLModule>();
private LoggingTool logger;
/**
- * Define this CMLReader to take the input from a java.io.Reader
- * class. Possible readers are (among others) StringReader and FileReader.
- * FIXME: this can not be used in combination with Aelfred2 yet.
- *
- * @param input Reader type input
- *
- * @deprecated XML reading should not be done with a Reader, but with an
- * InputStream instead.
- */
- public CMLReader(Reader input) {
- this.init();
- this.input = input;
- }
-
- /**
* Reads CML from an java.io.InputStream, for example the FileInputStream.
*
* @param input InputStream type input
*/
public CMLReader(InputStream input) {
- this(new InputStreamReader(input));
+ this.input = input;
+ init();
}
public CMLReader() {
- this(new StringReader(""));
+ this(new ByteArrayInputStream(new byte[0]));
}
public void registerConvention(String convention, ICMLModule conv) {
@@ -118,12 +102,16 @@
return CMLFormat.getInstance();
}
+ /**
+ * This method must not be used; XML reading requires the use of an InputStream.
+ * Use setReader(InputStream) instead.
+ */
public void setReader(Reader reader) throws CDKException {
- this.input = reader;
+ throw new CDKException("Invalid method call; use SetReader(InputStream) instead.");
}
public void setReader(InputStream input) throws CDKException {
- setReader(new InputStreamReader(input));
+ this.input = input;
}
private void init() {
@@ -214,10 +202,8 @@
}
CMLHandler handler = new CMLHandler(file);
// copy the manually added conventions
- Iterator conventions = userConventions.keySet().iterator();
- while (conventions.hasNext()) {
- String conv = (String)conventions.next();
- handler.registerConvention(conv, (ICMLModule)userConventions.get(conv));
+ for (String conv : userConventions.keySet()) {
+ handler.registerConvention(conv, userConventions.get(conv));
}
parser.setContentHandler(handler);
parser.setEntityResolver(new CMLResolver());
Modified: cdk/trunk/src/main/org/openscience/cdk/io/INChIReader.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/io/INChIReader.java 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/src/main/org/openscience/cdk/io/INChIReader.java 2008-09-07 08:25:34 UTC (rev 12216)
@@ -28,15 +28,14 @@
*/
package org.openscience.cdk.io;
+import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
-import java.io.InputStreamReader;
import java.io.Reader;
-import java.io.StringReader;
+import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemObject;
-import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.io.formats.INChIFormat;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.inchi.INChIHandler;
@@ -68,46 +67,38 @@
public class INChIReader extends DefaultChemObjectReader {
private XMLReader parser;
- private Reader input;
+ private InputStream input;
private LoggingTool logger;
/**
- * Construct a INChI reader from a Reader object.
- *
- * @param input the Reader with the content
- *
- * @deprecated XML parsing should use InputStream instead of a Reader.
- */
- public INChIReader(Reader input) {
- this.init();
- this.input = input;
- }
-
- /**
* Construct a INChI reader from a InputStream object.
*
* @param input the InputStream with the content
*/
public INChIReader(InputStream input) {
- this(new InputStreamReader(input));
+ this.input = input;
+ init();
}
public INChIReader() {
- this(new StringReader(""));
+ this(new ByteArrayInputStream(new byte[0]));
}
public IResourceFormat getFormat() {
return INChIFormat.getInstance();
}
-
- public void setReader(Reader input) throws CDKException {
- this.input = input;
+ /**
+ * This method must not be used; XML reading requires the use of an InputStream.
+ * Use setReader(InputStream) instead.
+ */
+ public void setReader(Reader reader) throws CDKException {
+ throw new CDKException("Invalid method call; use SetReader(InputStream) instead.");
}
public void setReader(InputStream input) throws CDKException {
- setReader(new InputStreamReader(input));
+ this.input = input;
}
/**
Modified: cdk/trunk/src/main/org/openscience/cdk/layout/RingPlacer.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/layout/RingPlacer.java 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/src/main/org/openscience/cdk/layout/RingPlacer.java 2008-09-07 08:25:34 UTC (rev 12216)
@@ -28,8 +28,6 @@
*/
package org.openscience.cdk.layout;
-import java.util.Iterator;
-import java.util.List;
import java.util.Vector;
import javax.vecmath.Point2d;
@@ -629,7 +627,7 @@
*/
void placeConnectedRings(IRingSet rs, IRing ring, int handleType, double bondLength)
{
- List connectedRings = rs.getConnectedRings(ring);
+ IRingSet connectedRings = rs.getConnectedRings(ring);
IRing connectedRing;
IAtomContainer sharedAtoms;
int sac;
@@ -637,9 +635,8 @@
Vector2d tempVector, oldRingCenterVector, newRingCenterVector;
// logger.debug(rs.reportRingList(molecule));
- Iterator iter = connectedRings.iterator();
- while (iter.hasNext()) {
- connectedRing = (IRing)iter.next();
+ for (IAtomContainer container : connectedRings.atomContainers()) {
+ connectedRing = (IRing)container;
if (!connectedRing.getFlag(CDKConstants.ISPLACED))
{
// logger.debug(ring.toString(molecule));
Modified: cdk/trunk/src/main/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/src/main/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java 2008-09-07 08:25:34 UTC (rev 12216)
@@ -24,27 +24,33 @@
*/
package org.openscience.cdk.modeling.builder3d;
+import java.io.InputStream;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.exception.NoSuchAtomTypeException;
-import org.openscience.cdk.interfaces.*;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IPseudoAtom;
+import org.openscience.cdk.interfaces.IRing;
+import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.ringsearch.SSSRFinder;
import org.openscience.cdk.tools.HOSECodeGenerator;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.RingSetManipulator;
-import java.io.InputStream;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
/**
* Reads in a force field configuration file, set the atom types into a vector, and the data into a hashtable
- * Therfore it uses the class MM2BasedParamterSetReader
+ * Therefore, it uses the class {@link MM2BasedParameterSetReader}.
* private Hashtable parameterSet;
* key=nameofdatafield+atomid1+;atomid2;atomxid
*
@@ -260,7 +266,7 @@
ringSetA = ringSetMolecule.getRings(atom);
RingSetManipulator.sort(ringSetA);
IRing sring = (IRing) ringSetA.getAtomContainer(ringSetA.getAtomContainerCount()-1);
- atom.setProperty("RING_SIZE", new Integer(sring.getRingSize()));
+ atom.setProperty("RING_SIZE", Integer.valueOf(sring.getRingSize()));
isInHeteroRing = false;
Iterator containers = RingSetManipulator.getAllAtomContainers(ringSetA).iterator();
while (!isInHeteroRing && containers.hasNext()) {
@@ -429,9 +435,9 @@
if (j == 0) {
//csp3
if (atom.getFlag(CDKConstants.ISINRING)) {
- if (atom.getProperty("RING_SIZE").equals(new Integer(3))) {
+ if (atom.getProperty("RING_SIZE").equals(Integer.valueOf(3))) {
ID=ids[21];
- }else if (atom.getProperty("RING_SIZE").equals(new Integer(6)) & atom.getFlag(CDKConstants.ISAROMATIC)) {
+ }else if (atom.getProperty("RING_SIZE").equals(Integer.valueOf(6)) & atom.getFlag(CDKConstants.ISAROMATIC)) {
ID=ids[1];
}else if (atom.getFlag(CDKConstants.ISAROMATIC)){
ID=ids[1];
@@ -440,8 +446,8 @@
} else if (j == 1) {
//csp2
if (atom.getFlag(CDKConstants.ISINRING)) {
- if (atom.getProperty("RING_SIZE").equals(new Integer(6)) & atom.getFlag(CDKConstants.ISAROMATIC)) {
- }else if (atom.getProperty("RING_SIZE").equals(new Integer(3))) {
+ if (atom.getProperty("RING_SIZE").equals(Integer.valueOf(6)) & atom.getFlag(CDKConstants.ISAROMATIC)) {
+ }else if (atom.getProperty("RING_SIZE").equals(Integer.valueOf(3))) {
ID=ids[37];
}else{
ID=ids[1];
@@ -457,10 +463,10 @@
} else if (j == 5) {
//OH/Ether
if (atom.getFlag(CDKConstants.ISINRING)) {
- if (atom.getProperty("RING_SIZE").equals(new Integer(3))) {
+ if (atom.getProperty("RING_SIZE").equals(Integer.valueOf(3))) {
ID=ids[48];
//EPOXY
- }else if (atom.getProperty("RING_SIZE").equals(new Integer(5)) & atom.getFlag(CDKConstants.ISAROMATIC)){
+ }else if (atom.getProperty("RING_SIZE").equals(Integer.valueOf(5)) & atom.getFlag(CDKConstants.ISAROMATIC)){
ID=ids[40];
}else{
ID=ids[5];
@@ -469,7 +475,7 @@
} else if (j == 7) {
//n sp3
if (atom.getFlag(CDKConstants.ISINRING) & atom.getFlag(CDKConstants.ISAROMATIC)) {
- if (atom.getProperty("RING_SIZE").equals(new Integer(5))) {
+ if (atom.getProperty("RING_SIZE").equals(Integer.valueOf(5))) {
ID=ids[39];
}
}
@@ -482,7 +488,7 @@
} else if (j == 8) {
//nsp2
if (atom.getFlag(CDKConstants.ISINRING)) {
- if (atom.getProperty("RING_SIZE").equals(new Integer(6))) {
+ if (atom.getProperty("RING_SIZE").equals(Integer.valueOf(6))) {
ID=ids[36];
}
}
@@ -555,7 +561,7 @@
*/
public org.openscience.cdk.interfaces.IAtom configureMMFF94BasedAtom(org.openscience.cdk.interfaces.IAtom atom, String hoseCode, boolean isInHetRing) throws Exception {
//logger.debug("****** Configure MMFF94 AtomType ******");
- Vector atomTypePattern = null;
+ List atomTypePattern = null;
MMFF94BasedAtomTypePattern atp = new MMFF94BasedAtomTypePattern();
atomTypePattern = atp.getAtomTypePatterns();
Pattern p = null;
@@ -582,31 +588,31 @@
}
for (int j = 0; j < atomTypePattern.size(); j++) {
- p = (Pattern) atomTypePattern.elementAt(j);
+ p = (Pattern) atomTypePattern.get(j);
mat = p.matcher(hoseCode);
if (mat.matches()) {
ID = ids[j];
if (j == 0) {//csp3
if (atom.getFlag(CDKConstants.ISINRING)) {
- p = (Pattern) atomTypePattern.elementAt(13);//c beta heteroaromatic ring
+ p = (Pattern) atomTypePattern.get(13);//c beta heteroaromatic ring
mat = p.matcher(hoseCode);
- p2 = (Pattern) atomTypePattern.elementAt(12);//c alpha heteroaromatic ring
+ p2 = (Pattern) atomTypePattern.get(12);//c alpha heteroaromatic ring
mat2 = p2.matcher(hoseCode);
- if (mat.matches() && isInHetRing && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
+ if (mat.matches() && isInHetRing && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(Integer.valueOf(5))){
ID = ids[13];
- }else if (mat2.matches() && isInHetRing && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
+ }else if (mat2.matches() && isInHetRing && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(Integer.valueOf(5))){
ID = ids[12];
- }else if (atom.getProperty("RING_SIZE").equals(new Integer(3))& !atom.getFlag(CDKConstants.ISAROMATIC)) {
+ }else if (atom.getProperty("RING_SIZE").equals(Integer.valueOf(3))& !atom.getFlag(CDKConstants.ISAROMATIC)) {
ID = ids[9];//sp3 3mem rings
- }else if (atom.getProperty("RING_SIZE").equals(new Integer(4)) & !atom.getFlag(CDKConstants.ISAROMATIC)) {
+ }else if (atom.getProperty("RING_SIZE").equals(Integer.valueOf(4)) & !atom.getFlag(CDKConstants.ISAROMATIC)) {
ID = ids[8];//sp3 4mem rings
- }else if (atom.getFlag(CDKConstants.ISAROMATIC) && isInHetRing && atom.getProperty("RING_SIZE").equals(new Integer(5))) {
+ }else if (atom.getFlag(CDKConstants.ISAROMATIC) && isInHetRing && atom.getProperty("RING_SIZE").equals(Integer.valueOf(5))) {
ID = ids[14];//C in het 5 ring
}else if (atom.getFlag(CDKConstants.ISAROMATIC)) {
ID = ids[11];//C in benzene, pyroll
}
}else{
- p = (Pattern) atomTypePattern.elementAt(66);//S=C
+ p = (Pattern) atomTypePattern.get(66);//S=C
mat = p.matcher(hoseCode);
if (mat.matches()){
ID = ids[66];
@@ -614,7 +620,7 @@
}
} else if (j == 1) {//csp2
if (atom.getFlag(CDKConstants.ISINRING)) {
- if (atom.getProperty("RING_SIZE").equals(new Integer(4)) & !atom.getFlag(CDKConstants.ISAROMATIC) && !isInHetRing) {
+ if (atom.getProperty("RING_SIZE").equals(Integer.valueOf(4)) & !atom.getFlag(CDKConstants.ISAROMATIC) && !isInHetRing) {
ID = ids[29];//C= in 4 ring
}
}
@@ -626,68 +632,68 @@
} else if (j == 36) {//n sp3
//Amid
- p = (Pattern) atomTypePattern.elementAt(48);
+ p = (Pattern) atomTypePattern.get(48);
mat = p.matcher(hoseCode);
if (mat.matches() & !atom.getFlag(CDKConstants.ISINRING)) {
ID = ids[48];
}
- p = (Pattern) atomTypePattern.elementAt(44);//sp3 n-oxide
+ p = (Pattern) atomTypePattern.get(44);//sp3 n-oxide
mat = p.matcher(hoseCode);
if (mat.matches()){
ID = ids[44];
}
- p = (Pattern) atomTypePattern.elementAt(56);//npyd
+ p = (Pattern) atomTypePattern.get(56);//npyd
mat = p.matcher(hoseCode);
- if (atom.getFlag(CDKConstants.ISAROMATIC)){//id in pyridin, pyrol etc... if (mat.matches() && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
- if(atom.getProperty("RING_SIZE").equals(new Integer(6)) && mat.matches()){
+ if (atom.getFlag(CDKConstants.ISAROMATIC)){//id in pyridin, pyrol etc... if (mat.matches() && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(Integer.valueOf(5))){
+ if(atom.getProperty("RING_SIZE").equals(Integer.valueOf(6)) && mat.matches()){
ID = ids[56];
- }else if(atom.getProperty("RING_SIZE").equals(new Integer(5)) && mat.matches()){
+ }else if(atom.getProperty("RING_SIZE").equals(Integer.valueOf(5)) && mat.matches()){
ID = ids[57];
}else{
ID=ids[64];
}
}
- p = (Pattern) atomTypePattern.elementAt(61);//npyd
+ p = (Pattern) atomTypePattern.get(61);//npyd
mat = p.matcher(hoseCode);
- if (atom.getFlag(CDKConstants.ISAROMATIC)){//id in pyridin, pyrol etc... if (mat.matches() && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
- if(atom.getProperty("RING_SIZE").equals(new Integer(6)) && mat.matches()){
+ if (atom.getFlag(CDKConstants.ISAROMATIC)){//id in pyridin, pyrol etc... if (mat.matches() && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(Integer.valueOf(5))){
+ if(atom.getProperty("RING_SIZE").equals(Integer.valueOf(6)) && mat.matches()){
ID = ids[61];
- }else if(atom.getProperty("RING_SIZE").equals(new Integer(5)) && mat.matches()){
+ }else if(atom.getProperty("RING_SIZE").equals(Integer.valueOf(5)) && mat.matches()){
ID = ids[62];
}else{
ID=ids[43];
}
}
- p = (Pattern) atomTypePattern.elementAt(45);//NC#N
+ p = (Pattern) atomTypePattern.get(45);//NC#N
mat = p.matcher(hoseCode);
if (mat.matches()){
ID = ids[45];
}
}else if (j == 37) {//N=C n in imine
- p = (Pattern) atomTypePattern.elementAt(59);//n beta heteroaromatic ring
+ p = (Pattern) atomTypePattern.get(59);//n beta heteroaromatic ring
mat = p.matcher(hoseCode);
if (atom.getFlag(CDKConstants.ISINRING)) {
- if (mat.matches() && isInHetRing && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
+ if (mat.matches() && isInHetRing && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(Integer.valueOf(5))){
ID = ids[59];
- }else if( atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(6))){
+ }else if( atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(Integer.valueOf(6))){
ID = ids[56];
- }else if( atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
+ }else if( atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(Integer.valueOf(5))){
ID = ids[57];
}
}
- p = (Pattern) atomTypePattern.elementAt(43);//N2OX
+ p = (Pattern) atomTypePattern.get(43);//N2OX
mat = p.matcher(hoseCode);
if (mat.matches()){
- if (atom.getFlag(CDKConstants.ISAROMATIC)&& atom.getProperty("RING_SIZE").equals(new Integer(6))){
+ if (atom.getFlag(CDKConstants.ISAROMATIC)&& atom.getProperty("RING_SIZE").equals(Integer.valueOf(6))){
ID = ids[61];//npox
- }else if (mat.matches() && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(new Integer(5))){
+ }else if (mat.matches() && atom.getFlag(CDKConstants.ISAROMATIC) && atom.getProperty("RING_SIZE").equals(Integer.valueOf(5))){
ID = ids[62];//n5ox
}else{
ID = ids[43];
@@ -696,44 +702,44 @@
}else if (j==43){//sp2 n oxide
if (atom.getFlag(CDKConstants.ISINRING) && atom.getFlag(CDKConstants.ISAROMATIC)
- && atom.getProperty("RING_SIZE").equals(new Integer(5))){
+ && atom.getProperty("RING_SIZE").equals(Integer.valueOf(5))){
ID = ids[62];
}else if (atom.getFlag(CDKConstants.ISINRING) && atom.getFlag(CDKConstants.ISAROMATIC)
- && atom.getProperty("RING_SIZE").equals(new Integer(6))){
+ && atom.getProperty("RING_SIZE").equals(Integer.valueOf(6))){
ID = ids[61];
}
}else if (j==40 || j==41){//n in c=n=n or terminal n in azido
if (atom.getFlag(CDKConstants.ISINRING) && atom.getFlag(CDKConstants.ISAROMATIC)
- && atom.getProperty("RING_SIZE").equals(new Integer(5))){
+ && atom.getProperty("RING_SIZE").equals(Integer.valueOf(5))){
ID = ids[59];//aromatic N 5R alpha
}
}else if (j==50){//n+=
if (atom.getFlag(CDKConstants.ISINRING) && atom.getFlag(CDKConstants.ISAROMATIC)
- && atom.getProperty("RING_SIZE").equals(new Integer(5))){
+ && atom.getProperty("RING_SIZE").equals(Integer.valueOf(5))){
ID = ids[63];//n5+
}else if (atom.getFlag(CDKConstants.ISINRING) && atom.getFlag(CDKConstants.ISAROMATIC)
- && atom.getProperty("RING_SIZE").equals(new Integer(6))){
+ && atom.getProperty("RING_SIZE").equals(Integer.valueOf(6))){
ID = ids[58];//npd+
}
}else if (j==28){//O ->furan
if (atom.getFlag(CDKConstants.ISINRING) && atom.getFlag(CDKConstants.ISAROMATIC)
- && atom.getProperty("RING_SIZE").equals(new Integer(5))){
+ && atom.getProperty("RING_SIZE").equals(Integer.valueOf(5))){
ID = ids[35];
}
}else if (j==16){//H-Object-> enol
- p = (Pattern) atomTypePattern.elementAt(21);//enol
+ p = (Pattern) atomTypePattern.get(21);//enol
mat = p.matcher(hoseCode);
if (mat.matches()){
ID = ids[21];
}
- p = (Pattern) atomTypePattern.elementAt(18);//enol
+ p = (Pattern) atomTypePattern.get(18);//enol
mat = p.matcher(hoseCode);
if (mat.matches()){
ID = ids[18];
}
}else if (j==74){//P
- p = (Pattern) atomTypePattern.elementAt(75);//-P=C
+ p = (Pattern) atomTypePattern.get(75);//-P=C
mat = p.matcher(hoseCode);
if (mat.matches()){
ID = ids[75];
Modified: cdk/trunk/src/main/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java 2008-09-07 08:13:38 UTC (rev 12215)
+++ cdk/trunk/src/main/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java 2008-09-07 08:25:34 UTC (rev 12216)
@@ -34,11 +34,13 @@
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
import org.openscience.cdk.AtomType;
-import org.openscience.cdk.tools.LoggingTool;
+import org.openscience.cdk.interfaces.IAtomType;
/**
* AtomType list configurator that uses the ParameterSet originally
@@ -57,28 +59,28 @@
private String configFile = "org/openscience/cdk/modeling/forcefield/data/mm2.prm";
private InputStream ins = null;
- private Hashtable parameterSet;
- private Vector atomTypes;
+ private Map parameterSet;
+ private List<IAtomType> atomTypes;
private StringTokenizer st;
private String key = "";
/**
- *Constructor for the MM2BasedParameterSetReader object
+ * Constructor for the MM2BasedParameterSetReader object.
*/
public MM2BasedParameterSetReader() {
parameterSet = new Hashtable();
- atomTypes = new Vector();
+ atomTypes = new Vector<IAtomType>();
}
- public Hashtable getParamterSet(){
+ public Map getParamterSet(){
return parameterSet;
}
- public Vector getAtomTypes(){
+ public List<IAtomType> getAtomTypes(){
return atomTypes;
}
/**
- * Sets the file containing the config data
+ * Sets the file containing the config data.
*
* @param ins The new inputStream type InputStream
*/
@@ -288,7 +290,7 @@
"Malformed Number");
}
- AtomType atomType = new AtomType(name, rootType);
+ IAtomType atomType = new AtomType(name, rootType);
atomType.setAtomicNumber(an);
atomType.setExactMass(mass);
atomType.setFormalNeighbourCount(maxbond);
@@ -296,7 +298,7 @@
Color co = new Color(rl, gl, bl);
atomType.setProperty("org.openscience.cdk.renderer.color", co);
atomType.setAtomTypeName(sid);
- atomTypes.addElement(atomType);
+ atomTypes.add(atomType);
}
/**
@@ -305,7 +307,7 @@
* @exception Exception Description of the Exception
*/
private void setvdWaals() throws Exception {
- Vector data = new Vector();
+ List data = new Vector();
st.nextToken();
String sid = st.nextToken();
String sradius = st.nextToken();
@@ -331,7 +333,7 @@
* @exception Exception Description of the Exception
*/
private void setvdWaalpr() throws Exception {
- Vector data = new Vector();
+ List data = new Vector();
st.nextToken();
String sid1 = st.nextToken();
String sid2 = st.nextToken();
@@ -356,7 +358,7 @@
* @exception Exception Description of the Exception
*/
private void setBond() throws Exception {
- Vector data = new Vector();
+ List data = new Vector();
st.nextToken();
String sid1 = st.nextToken();
String sid2 = st.nextToken();
@@ -382,7 +384,7 @@
* @exception Exception Description of the Exception
*/
private void setBond3() throws Exception {
- Vector data = new Vector();
+ List data = new Vector();
st.nextToken();
String sid1 = st.nextToken();
String sid2 = st.nextToken();
@@ -408,7 +410,7 @@
* @exception Exception Description of the Exception
*/
private void setBond4() throws Exception {
- Vector data = new Vector();
+ List data = new Vector();
st.nextToken();
String sid1 = st.nextToken();
String sid2 = st.nextToken();
@@ -434,7 +436,7 @@
* @exception Exception Description of the Exception
*/
private void setAngle() throws Exception {
- Vector data = new Vector();
+ List data = new Vector();
st.nextToken();
String sid1 = st.nextToken();
String sid2 = st.nextToken();
@@ -476,7 +478,7 @@
* @exception Exception Description of the Exception
*/
private void setAngle3() throws Exception {
- Vector data = new Vector();
+ List data = new Vector();
st.nextToken();
String sid1 = st.nextToken();
String sid2 = st.nextToken();
@@ -509,7 +511,7 @@
* @exception Exception Description of the Exception
*/
private void setAngle4() throws Exception {
- Vector data = new Vector();
+ List data = new Vector();
st.nextToken();
String sid1 = st.nextToken();
String sid2 = st.nextToken();
@@ -542,7 +544,7 @@
* @exception Exception Description of the Exception
*/
private void setStrBnd() throws Exception {
- Vector data = new Vector();
+ List data = new Vector();
st.nextToken();
String sid1 = st.nextToken();
String value1 = st.nextToken();
@@ -563,7 +565,7 @@
* @exception Exception Description of the Exception
*/
private void setOpBend() throws Exception {
- Vector data = new Vector();
+ List data = new Vector();
st.nextToken();
String sid1 = st.nextToken();
String sid2 = st.nextToken();
@@ -592,7 +594,7 @@
* @exception Exception Description of the Exception
*/
private void setTorsion() throws Exception {
- Vector data = new Vector();
+ List data = new Vector();
st.nextToken();
String sid1 = st.nextToken();
String sid2 = st.nextToken();
@@ -636,7 +638,7 @@
* @exception Exception Description of the Exception
*/
private void setTorsion4() throws Exception {
- Vector data = new Vector();
+ List data = new Vector();
st.nextToken();
String sid1 = st.nextToken();
String sid...
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