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Anonymous committed 237f7e9 Draft

fixed dependencies

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  • Parent commits 25c26bc

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Files changed (78)

 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry excluding="test/java/org/xmlcml/declaratron/chem/forcefield/|test/java/org/xmlcml/declaratron/chem/|test/java/org/xmlcml/declaratron/|test/java/org/xmlcml/|test/java/org/|test/|test/java/org/|test/resources/org/|test/resources/org/|test/resources/|test/resources/|test/java/|test/java/|main/|main/java/|main/java/|main/resources/|main/resources/|test/resources/" kind="src" path="src"/>
-	<classpathentry kind="src" path="src/test/java"/>
-	<classpathentry kind="src" path="src/main/java"/>
-	<classpathentry kind="src" path="src/main/resources"/>
-	<classpathentry kind="src" path="src/test/resources"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="src" output="target/classes" path="src/main/java"/>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>
+syntax: glob
+.classpath
+.project
+.settings
+target
+doc
+output

File bin/org/xmlcml/declaratron/chem/forcefield/BondsTest.class

Binary file modified.

File bin/org/xmlcml/declaratron/chem/forcefield/BuckinghamTest.class

Binary file modified.

File bin/org/xmlcml/declaratron/chem/forcefield/ElectrostaticTest.class

Binary file modified.

File bin/org/xmlcml/declaratron/chem/forcefield/Fixtures.class

Binary file modified.

File bin/org/xmlcml/declaratron/chem/forcefield/ForcefieldLookupTest.class

Binary file modified.

File bin/org/xmlcml/declaratron/chem/forcefield/ForcefieldTest.class

Binary file modified.

File bin/org/xmlcml/declaratron/chem/forcefield/HarmonicAngleTest.class

Binary file modified.

File bin/org/xmlcml/declaratron/chem/forcefield/HarmonicBondTest.class

Binary file modified.

File bin/org/xmlcml/declaratron/chem/forcefield/MoleculeTest.class

Binary file modified.

File bin/org/xmlcml/declaratron/chem/forcefield/VDWExpressionTest.class

Binary file modified.

File bin/org/xmlcml/declaratron/chem/forcefield/kk/ComputationTest.class

Binary file modified.
 <?xml version="1.0" encoding="UTF-8"?>
-<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
-         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-    <modelVersion>4.0.0</modelVersion>
+<project
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
+	xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+	<modelVersion>4.0.0</modelVersion>
 
-    <parent>
-        <groupId>cml</groupId>
-        <artifactId>declaratron</artifactId>
-        <version>0.1-SNAPSHOT</version>
-    </parent>
+	<parent>
+		<groupId>cml</groupId>
+		<artifactId>declaratron-top</artifactId>
+		<version>0.1-SNAPSHOT</version>
+	</parent>
 
-    <artifactId>declaratron-chem</artifactId>
-    <packaging>pom</packaging>
-    <name>declaratron-chem</name>
-    
+	<artifactId>declaratron-chem</artifactId>
+	<packaging>jar</packaging>
+	<name>declaratron-chem</name>
 
-    <dependencyManagement>
-        <dependencies>
-            <dependency>
-                <groupId>${jumbo.groupId}</groupId>
-                <artifactId>cmlxom</artifactId>
-                <version>${cmlxom.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>${jumbo.groupId}</groupId>
-                <artifactId>jumbo-testutil</artifactId>
-                <version>${jumbotestutil.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>${jumbo.groupId}</groupId>
-                <artifactId>jumbo</artifactId>
-                <version>${jumbo.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>log4j</groupId>
-                <artifactId>log4j</artifactId>
-                <version>1.2.13</version>
-            </dependency>
-            <dependency>
-                <groupId>xom</groupId>
-                <artifactId>xom</artifactId>
-                <version>1.2.5</version>
-            </dependency>
+	<dependencies>
+		<dependency>
+			<groupId>${jumbo.groupId}</groupId>
+			<artifactId>cmlxom</artifactId>
+			<version>${cmlxom.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>${jumbo.groupId}</groupId>
+			<artifactId>jumbo-testutil</artifactId>
+			<version>${jumbotestutil.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>${jumbo.groupId}</groupId>
+			<artifactId>jumbo</artifactId>
+			<version>${jumbo.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+			<version>1.2.13</version>
+		</dependency>
+		<dependency>
+			<groupId>xom</groupId>
+			<artifactId>xom</artifactId>
+			<version>1.2.5</version>
+		</dependency>
+		<dependency>
+			<groupId>${scmathml.groupId}</groupId>
+			<artifactId>${scmathml.artifactId}</artifactId>
+			<version>${scmathml.version}</version>
+		</dependency>
 
-<!-- the other declaratrons, core is essential, others are optional-->
-            <dependency>
-                <groupId>cml</groupId>
-                <artifactId>declaratron-core</artifactId>
-                <version>${project.version}</version>
-            </dependency>
 
-            <dependency>
-                <groupId>junit</groupId>
-                <artifactId>junit</artifactId>
-                <version>4.8.2</version>
-            </dependency>
-            <dependency>
-                <groupId>org.mockito</groupId>
-                <artifactId>mockito-core</artifactId>
-                <version>1.8.0</version>
-            </dependency>
-        </dependencies>
-    </dependencyManagement>
+		<!-- the other declaratrons, core is essential, others are optional -->
+		<dependency>
+			<groupId>cml</groupId>
+			<artifactId>declaratron-core</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>cml</groupId>
+			<artifactId>declaratron-stmml</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.8.2</version>
+		</dependency>
+		<dependency>
+			<groupId>org.mockito</groupId>
+			<artifactId>mockito-core</artifactId>
+			<version>1.8.0</version>
+		</dependency>
+	</dependencies>
 
 
 </project>

File src/test/java/org/xmlcml/declaratron/chem/Fixtures.java

+package org.xmlcml.declaratron.chem;
+
+public class Fixtures {
+	public static final String CHEM = "org/xmlcml/declaratron/chem/";
+
+}

File src/test/java/org/xmlcml/declaratron/chem/forcefield/BondsTest.java

 package org.xmlcml.declaratron.chem.forcefield;
 
-import java.util.List;
-
-
-import junit.framework.Assert;
-
+import org.junit.Assert;
 import org.junit.Test;
 import org.xmlcml.cml.base.CMLConstants;
 import org.xmlcml.cml.base.CMLElement;
 import org.xmlcml.cml.base.CMLUtil;
-import org.xmlcml.cml.element.*;
+import org.xmlcml.cml.element.CMLCml;
+import org.xmlcml.cml.element.CMLMolecule;
+
 
 public class BondsTest {
 

File src/test/java/org/xmlcml/declaratron/chem/forcefield/BuckinghamTest.java

-package org.xmlcml.cml.forcefield;
+package org.xmlcml.declaratron.chem.forcefield;
 
 import org.junit.Test;
 import org.xmlcml.mathml.BVar;

File src/test/java/org/xmlcml/declaratron/chem/forcefield/ElectrostaticTest.java

-package org.xmlcml.cml.forcefield;
+package org.xmlcml.declaratron.chem.forcefield;
 
 import java.io.File;
 import java.io.IOException;

File src/test/java/org/xmlcml/declaratron/chem/forcefield/Fixtures.java

-package org.xmlcml.cml.forcefield;
+package org.xmlcml.declaratron.chem.forcefield;
 
 import org.junit.Test;
 
 
+
 public class Fixtures {
 
 	public static final String TEST_TOP = "src/test/resources/";
 	public static final String MAIN_TOP = "src/main/resources/";
 	
-	public static final String MATHML_DIR = "org/xmlcml/mathml/";
-	public static final String CHEMISTRY_DIR = "org/xmlcml/cml/chemistry/";
-	public static final String FORCEFIELD_DIR = "org/xmlcml/cml/forcefield/";
+	public static final String MATHML_DIR = "org/xmlcml/declaratron/math/";
+	public static final String CHEMISTRY_DIR = "org/xmlcml/declaratron/chem/chemistry/";
+	public static final String FORCEFIELD_DIR = "org/xmlcml/declaratron/chem/forcefield/";
 	public static final String AMBER_DIR = FORCEFIELD_DIR+"amber/";
 	public static final String TEST_AMBER_DIR = TEST_TOP+AMBER_DIR;
 	public static final String MAIN_AMBER_DIR = MAIN_TOP+AMBER_DIR;

File src/test/java/org/xmlcml/declaratron/chem/forcefield/ForcefieldLookupTest.java

-package org.xmlcml.cml.forcefield;
+package org.xmlcml.declaratron.chem.forcefield;
 
 import java.util.List;
 

File src/test/java/org/xmlcml/declaratron/chem/forcefield/ForcefieldTest.java

-package org.xmlcml.cml.forcefield;
+package org.xmlcml.declaratron.chem.forcefield;
 
-import java.util.List;
-
-import junit.framework.Assert;
 import nu.xom.Nodes;
 
+import org.junit.Assert;
 import org.junit.Ignore;
 import org.junit.Test;
 import org.xmlcml.cml.base.CMLConstants;
 import org.xmlcml.cml.base.CMLElement;
 import org.xmlcml.cml.base.CMLUtil;
 import org.xmlcml.cml.element.CMLAtom;
-import org.xmlcml.cml.element.CMLBond;
 import org.xmlcml.cml.element.CMLList;
 import org.xmlcml.cml.element.CMLMolecule;
 

File src/test/java/org/xmlcml/declaratron/chem/forcefield/HarmonicAngleTest.java

-package org.xmlcml.cml.forcefield;
+package org.xmlcml.declaratron.chem.forcefield;
 
 
 public class HarmonicAngleTest {

File src/test/java/org/xmlcml/declaratron/chem/forcefield/HarmonicBondTest.java

-package org.xmlcml.cml.forcefield;
+package org.xmlcml.declaratron.chem.forcefield;
 
-import java.util.List;
 
-import nu.xom.*;
-
-import org.junit.*;
-import org.xmlcml.cml.base.CMLUtil;
-import org.xmlcml.cml.element.*;
-import org.xmlcml.euclid.Util;
 
 public class HarmonicBondTest {
 

File src/test/java/org/xmlcml/declaratron/chem/forcefield/MoleculeTest.java

-package org.xmlcml.cml.forcefield;
+package org.xmlcml.declaratron.chem.forcefield;
 
 
 public class MoleculeTest {

File src/test/java/org/xmlcml/declaratron/chem/forcefield/VDWExpressionTest.java

-package org.xmlcml.cml.forcefield;
+package org.xmlcml.declaratron.chem.forcefield;
 
-import nu.xom.Element;
-
-import org.junit.*;
-import org.xmlcml.cml.base.CMLUtil;
 
 public class VDWExpressionTest {
 

File src/test/java/org/xmlcml/declaratron/chem/forcefield/kk/ComputationTest.java

 package org.xmlcml.declaratron.chem.forcefield.kk;
 
-import java.util.ArrayList;
 import java.util.List;
 
-import junit.framework.Assert;
-
 import nu.xom.Element;
 
+import org.junit.Assert;
 import org.junit.Ignore;
 import org.junit.Test;
 import org.xmlcml.cml.testutil.JumboTestUtils;
+import org.xmlcml.declaratron.chem.Fixtures;
+import org.xmlcml.declaratron.core.NodeUtils;
+import org.xmlcml.declaratron.core.visitors.ExecutableVisitor;
+import org.xmlcml.declaratron.stmml.stmml.ArrayToolVisitable;
+import org.xmlcml.declaratron.stmml.stmml.TableToolVisitable;
 import org.xmlcml.mathml.Context;
 import org.xmlcml.mathml.MathMLElement;
 import org.xmlcml.mathml.MathMLParser;
-import org.xmlcml.semantic.NodeUtils;
-import org.xmlcml.semantic.visitors.ExecutableVisitor;
-import org.xmlcml.stmml.ArrayToolVisitable;
-import org.xmlcml.stmml.TableToolVisitable;
 
 import scala.actors.threadpool.Arrays;
 
 	 * 
 	 */
 	private static final String TEST_TOP = "src/test/resources/";
-	private static final String KK_DIR = "org/xmlcml/cml/forcefield/kk/";
+	private static final String KK_DIR = Fixtures.CHEM+"forcefield/kk/";
 	private static final String COMPUTATION = "Comp";
 	private static List<Double> N_LIST = (List<Double>)Arrays.asList(
 			new Double[] {

File src/test/resources/org/xmlcml/declaratron/chem/chemistry/testmol.cml

+<cml:cml xmlns:cml='http://www.xml-cml.org/schema'>
+  <cml:molecule>
+    <cml:atomArray>
+      <cml:atom id='c1' elementType='C' x3='0.0' y3='0.0' z3='0.0'>
+        <cml:atomType dictRef="amber:parm94Type">CA</cml:atomType>
+      </cml:atom>
+      <cml:atom id='h1' elementType='H' x3='1.0' y3='0.0' z3='0.0'>
+        <cml:atomType dictRef="amber:parm94Type">HA</cml:atomType>
+      </cml:atom>
+    </cml:atomArray>
+    <cml:bondArray>
+      <cml:bond id='c1_h1' atomRefs2='c1 h1'/>
+    </cml:bondArray>
+  </cml:molecule>
+</cml:cml>

File src/test/resources/org/xmlcml/declaratron/chem/cml/chemistry/testmol.cml

-<cml:cml xmlns:cml='http://www.xml-cml.org/schema'>
-  <cml:molecule>
-    <cml:atomArray>
-      <cml:atom id='c1' elementType='C' x3='0.0' y3='0.0' z3='0.0'>
-        <cml:atomType dictRef="amber:parm94Type">CA</cml:atomType>
-      </cml:atom>
-      <cml:atom id='h1' elementType='H' x3='1.0' y3='0.0' z3='0.0'>
-        <cml:atomType dictRef="amber:parm94Type">HA</cml:atomType>
-      </cml:atom>
-    </cml:atomArray>
-    <cml:bondArray>
-      <cml:bond id='c1_h1' atomRefs2='c1 h1'/>
-    </cml:bondArray>
-  </cml:molecule>
-</cml:cml>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/amber/acetic.xml

-<molecule 
-    xmlns="http://www.xml-cml.org/schema" 
-    xmlns:cml="http://www.xml-cml.org/schema" 
-    xmlns:amber='http://www.xml-cml.org/dict/amber:gaffType'>
-	<atomArray>
-		<atom elementType="C" id="C" x3="-3.9150" y3="-0.4930" z3="0.0000">
-			<atomType dictRef="amber:gaffType">c3</atomType>
-			<atomType dictRef="amber:parm94Type">CT</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>-0.2001</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="C" id="C1" x3="-2.7230" y3="0.4150" z3="0.0490">
-			<atomType dictRef="amber:gaffType">c</atomType>
-			<atomType dictRef="amber:parm94Type">C</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>0.6230999983536656</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="H" id="H" x3="-4.8240" y3="0.1060" z3="-0.0980">
-			<atomType dictRef="amber:gaffType">hc</atomType>
-			<atomType dictRef="amber:parm94Type">HC</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>0.0867</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="H" id="H1" x3="-3.9740" y3="-1.0750" z3="0.9240">
-			<atomType dictRef="amber:gaffType">hc</atomType>
-			<atomType dictRef="amber:parm94Type">HC</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>0.0687</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="H" id="H2" x3="-3.8440" y3="-1.1540" z3="-0.8680">
-			<atomType dictRef="amber:gaffType">hc</atomType>
-			<atomType dictRef="amber:parm94Type">HC</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>0.0687</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="O" id="O" x3="-2.7880" y3="1.6330" z3="0.0830">
-			<atomType dictRef="amber:gaffType">o</atomType>
-			<atomType dictRef="amber:parm94Type">O</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>-0.485</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="O" id="O1" x3="-1.5520" y3="-0.2590" z3="0.0650">
-			<atomType dictRef="amber:gaffType">oh</atomType>
-			<atomType dictRef="amber:parm94Type">OH</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>-0.5840999983536654</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="H" id="H3" x3="-1.6580" y3="-1.2280" z3="0.0390">
-			<atomType dictRef="amber:gaffType">ho</atomType>
-			<atomType dictRef="amber:parm94Type">HO</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>0.422</cml:scalar>
-			</cml:property>
-		</atom>
-	</atomArray>
-	<bondArray>
-		<bond id="b1" atomRefs2="C C1" order="S" />
-		<bond id="b2" atomRefs2="C H" order="S" />
-		<bond id="b3" atomRefs2="C H1" order="S" />
-		<bond id="b4" atomRefs2="C H2" order="S" />
-		<bond id="b5" atomRefs2="O C1" order="D" />
-		<bond id="b6" atomRefs2="C1 O1" order="S" />
-		<bond id="b7" atomRefs2="O1 H3" order="S" />
-	</bondArray>
-</molecule>    

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/amber/aceticDistorted.cml

-<molecule 
-    xmlns="http://www.xml-cml.org/schema" 
-    xmlns:cml="http://www.xml-cml.org/schema" 
-    xmlns:amber='http://www.xml-cml.org/dict/amber:gaffType'>
-	<atomArray>
-		<atom elementType="C" id="C" x3="-3.9150" y3="-0.4930" z3="1.0000">
-			<atomType dictRef="amber:parm94Type">CT</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>-0.2001</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="C" id="C1" x3="-1.7230" y3="1.4150" z3="1.0490">
-			<atomType dictRef="amber:parm94Type">C</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>0.623</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="H" id="H" x3="-3.8240" y3="0.1060" z3="-0.0980">
-			<atomType dictRef="amber:parm94Type">HC</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>0.0867</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="H" id="H1" x3="-3.9740" y3="-0.0750" z3="0.9240">
-			<atomType dictRef="amber:parm94Type">HC</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>0.0687</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="H" id="H2" x3="-3.8440" y3="-0.1540" z3="-0.8680">
-			<atomType dictRef="amber:parm94Type">HC</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>0.0687</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="O" id="O" x3="-0.7880" y3="1.6330" z3="0.0830">
-			<atomType dictRef="amber:parm94Type">O</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>-0.485</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="O" id="O1" x3="-1.5520" y3="-1.2590" z3="0.0650">
-			<atomType dictRef="amber:parm94Type">OH</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>-0.5840999983536654</cml:scalar>
-			</cml:property>
-		</atom>
-		<atom elementType="H" id="H3" x3="-1.6580" y3="-0.2280" z3="0.0390">
-			<atomType dictRef="amber:parm94Type">HO</atomType>
-			<cml:property dictRef='compchem:computedcharge'>
-				<cml:scalar dataType='xsd:double'>0.422</cml:scalar>
-			</cml:property>
-		</atom>
-	</atomArray>
-        <bondArray>
-            <bond atomRefs2="C C1" id="C_C1" order="S" />
-            <bond atomRefs2="C H" id="C_H" order="S" />
-            <bond atomRefs2="C H1" id="C_H1" order="S"/>
-            <bond atomRefs2="C H2" id="C_H2" order="S"/>
-            <bond atomRefs2="C1 O" id="C1_O" order="D"/>
-            <bond atomRefs2="C1 O1" id="C1_O1" order="S"/>
-            <bond atomRefs2="O1 H3" id="O1_H3" order="S"/>
-        </bondArray>
-
-</molecule>    

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/amber/aceticStart.cml

-<molecule 
-    xmlns="http://www.xml-cml.org/schema" 
-    xmlns:cml="http://www.xml-cml.org/schema" 
-    xmlns:cmlx="http://www.xml-cml.org/schema/cmlx"
-    xmlns:amber='http://www.xml-cml.org/dict/amber:gaffType'>
-    <atomArray>
-        <atom elementType="C" id="C" x3="-3.9150" y3="-0.4930" z3="0.0000">
-            <atomType dictRef="amber:parm94Type">CT</atomType>
-            <cml:property dictRef='compchem:computedcharge'>
-                <cml:scalar dataType='xsd:double'>-0.2001</cml:scalar>
-            </cml:property>
-        </atom>
-        <atom elementType="C" id="C1" x3="-2.7230" y3="0.4150" z3="0.0490">
-            <atomType dictRef="amber:parm94Type">C</atomType>
-            <cml:property dictRef='compchem:computedcharge'>
-                <cml:scalar dataType='xsd:double'>0.623</cml:scalar>
-            </cml:property>
-        </atom>
-        <atom elementType="H" id="H" x3="-4.8240" y3="0.1060" z3="-0.0980">
-            <atomType dictRef="amber:parm94Type">HC</atomType>
-            <cml:property dictRef='compchem:computedcharge'>
-                <cml:scalar dataType='xsd:double'>0.0867</cml:scalar>
-            </cml:property>
-        </atom>
-        <atom elementType="H" id="H1" x3="-3.9740" y3="-1.0750" z3="0.9240">
-            <atomType dictRef="amber:parm94Type">HC</atomType>
-            <cml:property dictRef='compchem:computedcharge'>
-                <cml:scalar dataType='xsd:double'>0.0687</cml:scalar>
-            </cml:property>
-        </atom>
-        <atom elementType="H" id="H2" x3="-3.8440" y3="-1.1540" z3="-0.8680">
-            <atomType dictRef="amber:parm94Type">HC</atomType>
-            <cml:property dictRef='compchem:computedcharge'>
-                <cml:scalar dataType='xsd:double'>0.0687</cml:scalar>
-            </cml:property>
-        </atom>
-        <atom elementType="O" id="O" x3="-2.7880" y3="1.6330" z3="0.0830">
-            <atomType dictRef="amber:parm94Type">O</atomType>
-            <cml:property dictRef='compchem:computedcharge'>
-                <cml:scalar dataType='xsd:double'>-0.485</cml:scalar>
-            </cml:property>
-        </atom>
-        <atom elementType="O" id="O1" x3="-1.5520" y3="-0.2590" z3="0.0650">
-            <atomType dictRef="amber:parm94Type">OH</atomType>
-            <cml:property dictRef='compchem:computedcharge'>
-                <cml:scalar dataType='xsd:double'>-0.5840999983536654</cml:scalar>
-            </cml:property>
-        </atom>
-        <atom elementType="H" id="H3" x3="-1.6580" y3="-1.2280" z3="0.0390">
-            <atomType dictRef="amber:parm94Type">HO</atomType>
-            <cml:property dictRef='compchem:computedcharge'>
-                <cml:scalar dataType='xsd:double'>0.422</cml:scalar>
-            </cml:property>
-        </atom>
-    </atomArray>
-    <bondArray>
-        <bond atomRefs2="C C1" id="C_C1" order="S" />
-        <bond atomRefs2="C H" id="C_H" order="S" />
-        <bond atomRefs2="C H1" id="C_H1" order="S"/>
-        <bond atomRefs2="C H2" id="C_H2" order="S"/>
-        <bond atomRefs2="C1 O" id="C1_O" order="D"/>
-        <bond atomRefs2="C1 O1" id="C1_O1" order="S"/>
-        <bond atomRefs2="O1 H3" id="O1_H3" order="S"/>
-    </bondArray>
-</molecule>    

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/amber/sumcomputedcharge.xml

-<m:math xmlns:m='http://www.w3.org/1998/Math/MathML'>
-	<m:apply>
-		<m:sum />
-		<m:bvar> <m:ci>i</m:ci> </m:bvar>
-		<m:condition>
-			<m:apply>
-				<m:in />
-				<m:ci>i</m:ci>
-				<m:ci type="set">atoms</m:ci>
-			</m:apply>
-		</m:condition>
-		<m:apply>
-			<m:csymbol xpath="./*[local-name()='property' and @dictRef='compchem:computedcharge']/*[local-name()='scalar']/text()">x3i</m:csymbol>
-			<m:ci>i</m:ci>
-		</m:apply>
-	</m:apply>
-</m:math>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/atheta.xml

-<math display='block'>
-	<apply id="denominator.powerbracket">
-		<power />
-		<apply id="largebracket">
-			<times />
-			<apply id="3overroot32pi">
-				<divide />
-				<cn>3</cn>
-				<apply>
-					<times />
-					<apply>
-						<root />
-						<cn>32</cn>
-					</apply>
-					<ci>pi</ci>
-				</apply>
-			</apply>
-			<apply id="summationbracket">
-				<plus />
-				<cn>1</cn>
-				<apply id="summation">
-					<sum />
-					<bvar>
-						<ci>i</ci>
-					</bvar>
-					<lowlimit>
-						<cn>1</cn>
-					</lowlimit>
-					<uplimit>
-						<ci>theta</ci>
-					</uplimit>
-					<apply>
-						<selector />
-						<ci type="vector">n</ci>
-						<ci>i</ci>
-					</apply>
-				</apply>
-			</apply>
-		</apply>
-		<apply>
-			<divide />
-			<cn>1</cn>
-			<cn>3</cn>
-		</apply>
-	</apply>
-</math>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/exponentialComp.xml

-<computation xmlns:m="http://www.w3.org/1998/Math/MathML"
-	xmlns="http://www.xml-cml.org/semanticcomputation">
-	<arrayTool method="applyFunction"
-		functionRef="src/test/resources/org/xmlcml/cml/forcefield/kk/exponentialFunction.xml"
-		xpath="./*[local-name()='array']" param-U0="1" param-s="8.675" param-r0="1"
-		functionVar="r">
-		<array xmlns="http://www.xml-cml.org/schema" dataType="xsd:double"
-			size="27">0.7 0.75 0.8 0.85 0.90 0.95 1.00 1.05 1.10 1.15 1.20 1.25 1.30
-			1.35 1.4 1.45 1.5 1.55 1.6 1.65 1.7 1.75 1.8 1.85 1.9 1.95 2.0
-		</array>
-	</arrayTool>
-
-</computation>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/exponentialCompOut.xml

-<array xmlns="http://www.xml-cml.org/schema" dataType="xsd:double" size="27">2.709664891514448 1.3989607540428048 0.3443245022553208 -0.35819473229222737 -0.7618081477587043 -0.9506718923680936 -0.9999999999999999 -0.9663450628163506 -0.888527070130921 -0.7915117188096352 -0.6904070078445951 -0.5937108900850459 -0.5056915415434479 -0.4280301315218866 -0.36090738070956374 -0.30369701847808467 -0.2553929940441401 -0.21486211301201216 -0.18098541711437371 -0.15273066015571513 -0.1291834888371152 -0.10955491013125024 -0.09317597807005644 -0.07948631631077055 -0.06802034505002277 -0.05839336668803822 -0.05028861954944946</array>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/exponentialFunction.xml

-<math display='block'>
-	<apply>
-		<times />
-		<apply>
-			<divide />
-			<cn>1.0</cn>
-			<apply>
-				<minus />
-				<cn>8.675</cn>
-				<cn>6</cn>
-			</apply>
-		</apply>
-		<apply>
-			<minus />
-			<apply>
-				<times />
-				<cn>6</cn>
-				<apply>
-					<exp />
-					<apply>
-						<minus />
-						<cn>8.675</cn>
-						<apply>
-							<divide />
-							<apply>
-								<times />
-								<cn>8.675</cn>
-								<ci>r</ci>
-							</apply>
-							<cn>1.0</cn>
-						</apply>
-					</apply>
-				</apply>
-			</apply>
-			<apply>
-				<times />
-				<cn>8.675</cn>
-				<apply>
-					<power />
-					<apply>
-						<divide />
-						<cn>1.0</cn>
-						<ci>r</ci>
-					</apply>
-					<cn>6</cn>
-				</apply>
-			</apply>
-		</apply>
-	</apply>
-</math>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/lennardJonesComp.xml

-<computation  
-    xmlns:m="http://www.w3.org/1998/Math/MathML"
-    xmlns="http://www.xml-cml.org/semanticcomputation"
-    >
-    <arrayTool method="applyFunction" functionRef="src/test/resources/org/xmlcml/cml/forcefield/kk/lennardJonesFunction.xml"
-         xpath="./*[local-name()='array']" param-U0="1" param-s="7" param-r0="1" functionVar="r">
-      <array xmlns="http://www.xml-cml.org/schema" dataType="xsd:double" size="27">0.7 0.75 0.8 0.85 0.90 0.95 1.00 1.05 1.10 1.15 1.20 1.25 1.30 1.35 1.4 1.45 1.5 1.55 1.6 1.65 1.7 1.75 1.8 1.85 1.9 1.95 2.0</array>
-    </arrayTool>
-    
-       
-</computation>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/lennardJonesCompHuman.xml

-<computation  
-    xmlns:m="http://www.w3.org/1998/Math/MathML"
-    xmlns="http://www.xml-cml.org/semanticcomputation"
-    >
-    <arrayTool method="applyFunction" functionRef="src/test/resources/org/xmlcml/cml/forcefield/kk/lennardJonesFunction.xml"
-         xpath="./*[@id='values']" param-U0="1" param-s="7" param-r0="1" functionVar="r">
-      <array dataType="xsd:double" size="27">0.7 0.75 0.8 0.85 0.90 0.95 1.00 1.05 1.10 1.15 1.20 1.25 1.30 1.35 1.4 1.45 1.5 1.55 1.6 1.65 1.7 1.75 1.8 1.85 1.9 1.95 2.0</array>
-    </arrayTool>
-    
-       
-</computation>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/lennardJonesCompHuman0.xml

-<computation id="computeMe" xmlns="http://www.xml-cml.org/semanticcomputation"
-    functionRef="${lennardJonesFunction}">
-	<parameter id="r" dictRef="ff:interatomic">
-		<scalar dataType="xsd:double" units="units:dimensionless">2.0</scalar>
-	</parameter>
-	<parameter id="U0" dictRef="ff:uzero">
-		<scalar dataType="xsd:double" units="units:dimensionless">1</scalar>
-	</parameter>
-	<parameter id="r0" dictRef="ff:rzero">
-		<scalar dataType="xsd:double" units="units:dimensionless">1</scalar>
-	</parameter>
-	<parameter id="s" dictRef="ff:ljexponent">
-		<scalar dataType="xsd:double" units="units:dimensionless">7</scalar>
-	</parameter>
-</computation>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/lennardJonesCompHuman2.xml

-<computation id="computeMe" xmlns="http://www.xml-cml.org/semanticcomputation"
-    functionRef="${lennardJonesFunction}">
-	<parameter id="r" dictRef="ff:interatomic">
-		<array dataType="xsd:double" units="units:dimensionless"
-			size="27">0.7 0.75 0.8 0.85
-			0.90 0.95 1.00 1.05 1.10 1.15 1.20 1.25 1.30
-			1.35 1.4 1.45 1.5 1.55
-			1.6 1.65 1.7 1.75 1.8 1.85 1.9 1.95 2.0
-		</array>
-	</parameter>
-	<parameter id="U0" dictRef="ff:uzero">
-		<scalar dataType="xsd:double" units="units:dimensionless">1</scalar>
-	</parameter>
-	<parameter id="r0" dictRef="ff:rzero">
-		<scalar dataType="xsd:double" units="units:dimensionless">1</scalar>
-	</parameter>
-	<parameter id="s" dictRef="ff:ljexponent">
-		<array dataType="xsd:double" units="units:dimensionless">7 8 9 10 11 12</array>
-	</parameter>
-</computation>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/lennardJonesCompHumanUnbound.xml

-<computation id="computeMe" xmlns="http://www.xml-cml.org/semanticcomputation"
-    functionRef="${lennardJonesFunction}">
-	<parameter id="r" dictRef="ff:interatomic">
-		<scalar dataType="xsd:double"/>
-	</parameter>
-	<parameter id="U0" dictRef="ff:uzero">
-		<scalar dataType="xsd:double"/>
-	</parameter>
-	<parameter id="r0" dictRef="ff:rzero">
-		<scalar dataType="xsd:double"/>
-	</parameter>
-	<parameter id="s" dictRef="ff:ljexponent">
-		<scalar dataType="xsd:double"/>
-	</parameter>
-</computation>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/lennardJonesCompOut.xml

-<array xmlns="http://www.xml-cml.org/schema" dataType="xsd:double"
-	size="27">13.356922467922153 5.61865569272976 1.9073486328125
-	0.1559687258626994 -0.6272254743863073 -0.930782307684078 -1.0
-	-0.9594197956756645 -0.8723688009922013 -0.7706709318423401
-	-0.6697959533607682 -0.5767168000000003 -0.4940355801556231
-	-0.42216547704464724 -0.3604851234240348 -0.30794423709742796
-	-0.2633744855967078 -0.22564195372179985 -0.19371509552001953
-	-0.16668839834983729 -0.1437836691546741 -0.12434080551956603
-	-0.10780437841014653 -0.09370930259323386 -0.08166719766939626
-	-0.07135413662675144 -0.0625</array>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/lennardJonesFunction.xml

-<math xmlns="http://www.w3.org/1998/Math/MathML">
-	<apply>
-		<times />
-		<apply>
-			<divide />
-			<ci>U0</ci>
-			<apply>
-				<minus />
-				<ci>s</ci>
-				<cn>6</cn>
-			</apply>
-		</apply>
-		<apply>
-			<minus />
-			<apply>
-				<times />
-				<cn>6</cn>
-				<apply>
-					<power />
-					<apply>
-						<divide />
-						<ci>r0</ci>
-						<ci>r</ci>
-					</apply>
-					<ci>s</ci>
-				</apply>
-			</apply>
-			<apply>
-				<times />
-				<ci>s</ci>
-				<apply>
-					<power />
-					<apply>
-						<divide />
-						<ci>r0</ci>
-						<ci>r</ci>
-					</apply>
-					<cn>6</cn>
-				</apply>
-			</apply>
-		</apply>
-	</apply>
-</math>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/lennardJonesRSSweep.xml

-<computation xmlns:m="http://www.w3.org/1998/Math/MathML"
-	xmlns="http://www.xml-cml.org/semanticcomputation">
-	<arrayTool method="parameterSweep" param-U0="1" param-r0="1"
-		functionRef="src/test/resources/org/xmlcml/cml/forcefield/kk/lennardJonesFunction.xml"
-		xpath-1="./*[local-name()='array' and @id='var1']" var-1="r"
-		xpath-2="./*[local-name()='array' and @id='var2']" var-2="s">
-		<array id="var1" xmlns="http://www.xml-cml.org/schema" dataType="xsd:double"
-			size="27">0.7 0.75 0.8 0.85 0.90 0.95 1.00 1.05 1.10 1.15 1.20 1.25 1.30
-			1.35 1.4 1.45 1.5 1.55 1.6 1.65 1.7 1.75 1.8 1.85 1.9 1.95 2.0
-		</array>
-		<array id="var2" xmlns="http://www.xml-cml.org/schema" dataType="xsd:double"
-			size="6">7 8 9 10 11 12</array>
-	</arrayTool>
-</computation>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/lennardJonesRSSweep1.xml

-<computation xmlns:m="http://www.w3.org/1998/Math/MathML"
-	xmlns="http://www.xml-cml.org/semanticcomputation">
-	<arrayTool method="parameterSweep" param-U0="1" param-r0="1"
-		functionRef="src/test/resources/org/xmlcml/cml/forcefield/kk/lennardJonesFunction.xml"
-		xpath-1="./*[local-name()='array' and @id='var1']" var-1="r"
-		xpath-2="./*[local-name()='array' and @id='var2']" var-2="s">
-		<array id="var1" xmlns="http://www.xml-cml.org/schema" dataType="xsd:double"
-			size="27">0.7 0.75 0.8 0.85 0.90 0.95 1.00 1.05 1.10 1.15 1.20 1.25 1.30
-			1.35 1.4 1.45 1.5 1.55 1.6 1.65 1.7 1.75 1.8 1.85 1.9 1.95 2.0
-		</array>
-		<array id="var2" xmlns="http://www.xml-cml.org/schema" dataType="xsd:double"
-			size="6">7 8 9 10 11 12</array>
-	</arrayTool>
-</computation>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/lennardJonesRSSweepOut.xml

-<list xmlns="http://www.xml-cml.org/schema">
-	<array dataType="xsd:double" size="27">13.356922467922153
-		5.61865569272976 1.9073486328125 0.1559687258626994
-		-0.6272254743863073 -0.930782307684078 -1.0 -0.9594197956756645
-		-0.8723688009922013 -0.7706709318423401 -0.6697959533607682
-		-0.5767168000000003 -0.4940355801556231 -0.42216547704464724
-		-0.3604851234240348 -0.30794423709742796 -0.2633744855967078
-		-0.22564195372179985 -0.19371509552001953 -0.16668839834983729
-		-0.1437836691546741 -0.12434080551956603 -0.10780437841014653
-		-0.09370930259323386 -0.08166719766939626 -0.07135413662675144 -0.0625
-	</array>
-	<array dataType="xsd:double" size="27">18.04051865797277
-		7.491540923639679 2.6226043701171875 0.4036837610563957
-		-0.5575337550100512 -0.9194772594126119 -1.0 -0.9543435004604488
-		-0.8583735795859093 -0.7486050621077235 -0.6418877886374029
-		-0.5452595200000002 -0.46093642217993636 -0.38885451347751726
-		-0.3279601498820167 -0.27685555840416876 -0.23411065386374025
-		-0.198402835264529 -0.1685693860054016 -0.14361686737430696
-		-0.1227106887302104 -0.1051567955251187 -0.09038144856608245
-		-0.0779119148140517 -0.06735924595082143 -0.058403486389316916
-		-0.05078125</array>
-	<array dataType="xsd:double" size="27">24.06228518803785
-		9.780622872529584 3.4570693969726562 0.6805417415669954
-		-0.48267968605036826 -0.9077755427807427 -1.0 -0.9494283574742879
-		-0.8452265534163624 -0.7284579636543782 -0.6170805311055226
-		-0.5179965440000002 -0.43292944235435504 -0.36130100040347146
-		-0.301630409395621 -0.2521990201302045 -0.21134989584920993
-		-0.17760737923801043 -0.14971010386943817 -0.12660452635194624
-		-0.10742244803010928 -0.0914539312433706 -0.07812086830544476
-		-0.06695336653479922 -0.057569594774954436 -0.0496590302460919
-		-0.04296875</array>
-	<array dataType="xsd:double" size="27">31.852348238836324
-		12.589950718894467 4.433095455169678 0.9903998219217396
-		-0.40223307170863976 -0.8956614998268768 -1.0 -0.94466861128043
-		-0.832869890990146 -0.7100419305960926 -0.5949865673661917
-		-0.49429872640000017 -0.40913330215289967 -0.33838543355996575
-		-0.28016835202435736 -0.23247748614345803 -0.19346644312350758
-		-0.16154073999535035 -0.13536919141188264 -0.11386116006931862
-		-0.09613248331596466 -0.08147041583809699 -0.069301854433758
-		-0.059166219819689836 -0.050693058422675394 -0.043583889585730604
-		-0.03759765625</array>
-	<array dataType="xsd:double" size="27">41.98830582447649
-		16.051320090094652 5.577504634857178 1.337659696110533
-		-0.31572547655970384 -0.8831188133068256 -1.0 -0.9400587256968557
-		-0.8212499667406393 -0.6931888437478252 -0.5752699658069995
-		-0.47363758489600016 -0.38882937170054044 -0.3192205021611317
-		-0.262549867814133 -0.21656552307567806 -0.1792680655049196
-		-0.1489748667829668 -0.12430900824256241 -0.10416074234994946
-		-0.08764281302202187 -0.07404849710263588 -0.0628154577812491
-		-0.053495932839063925 -0.045732732078951954 -0.0392401743838733
-		-0.0337890625</array>
-	<array dataType="xsd:double" size="27">55.24789630438073
-		20.331980407985064 6.922520697116852 1.7273476769186964
-		-0.2226466848456905 -0.870130477777904 -1.0 -0.9355933750956955
-		-0.8103170423971979 -0.6777480416364471 -0.5576392985761532
-		-0.4555685232640001 -0.3714304396480149 -0.30310092364047037
-		-0.2479820391814439 -0.20361327029731205 -0.1678756437685462
-		-0.13902455901407262 -0.11565657587198075 -0.09665622248158585
-		-0.08114200759789526 -0.06841873723504421 -0.057937958008513125
-		-0.04926619244136725 -0.04205988094964684 -0.0360458040759511
-		-0.031005859375</array>
-</list>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/potentialEnergySum.xml

-<math display='block'>
-	<apply>
-		<plus />
-		<apply id="term1">
-			<sum />
-			<bvar>
-				<ci>i</ci>
-			</bvar>
-			<lowlimit>
-				<cn>1</cn>
-			</lowlimit>
-			<uplimit>
-				<ci>theta</ci>
-			</uplimit>
-			<apply id="summand">
-				<times />
-				<apply id="nsubi">
-					<selector />
-					<ci type="vector">n</ci>
-					<ci>i</ci>
-				</apply>
-				<apply id="apower-s/2">
-					<power />
-					<apply id="asubi">
-						<selector />
-						<ci type="vector">a</ci>
-						<ci>i</ci>
-					</apply>
-					<apply is="minuss/2">
-						<minus />
-						<apply>
-							<divide />
-							<ci>s</ci>
-							<cn>2</cn>
-						</apply>
-					</apply>
-				</apply>
-			</apply>
-		</apply>
-		<apply id="term2">
-			<divide />
-			<apply id="term2.numerator">
-				<times />
-				<ci>pi</ci>
-				<apply>
-					<root />
-					<cn>32</cn>
-				</apply>
-			</apply>
-			<apply id="term2.denominator">
-				<times />
-				<apply id="term2.sminus3">
-					<minus />
-					<ci>s</ci>
-					<cn>3</cn>
-				</apply>
-				<apply>
-					<power />
-					<apply id="denominator.powerbracket">
-						<power />
-						<apply id="largebracket">
-							<times />
-							<apply id="3overroot32pi">
-								<divide />
-								<cn>3</cn>
-								<apply>
-									<times />
-									<apply>
-										<root />
-										<cn>32</cn>
-									</apply>
-									<ci>pi</ci>
-								</apply>
-							</apply>
-							<apply id="summationbracket">
-								<plus />
-								<cn>1</cn>
-								<apply id="summation">
-									<sum />
-									<bvar>
-										<ci>i</ci>
-									</bvar>
-									<lowlimit>
-										<cn>1</cn>
-									</lowlimit>
-									<uplimit>
-										<ci>theta</ci>
-									</uplimit>
-									<apply>
-										<selector />
-										<ci type="vector">n</ci>
-										<ci>i</ci>
-									</apply>
-								</apply>
-							</apply>
-						</apply>
-						<apply>
-							<divide />
-							<cn>1</cn>
-							<cn>3</cn>
-						</apply>
-					</apply>
-					<apply id="denominator.exponent">
-						<minus />
-						<ci>s</ci>
-						<cn>3</cn>
-					</apply>
-				</apply>
-			</apply>
-		</apply>
-	</apply>
-</math>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/potentialEnergySum0.xml

-<math display='block'>
-	<apply>
-		<plus />
-		<apply id="term1">
-			<sum />
-			<bvar>
-				<ci>i</ci>
-			</bvar>
-			<lowlimit>
-				<cn>1</cn>
-			</lowlimit>
-			<uplimit>
-				<ci>theta</ci>
-			</uplimit>
-			<apply id="summand">
-				<times />
-				<apply id="nsubi">
-					<selector />
-					<ci type="vector">n</ci>
-					<ci>i</ci>
-				</apply>
-				<apply id="apower-s/2">
-					<power />
-					<apply id="asubi">
-						<selector />
-						<ci type="vector">a</ci>
-						<ci>i</ci>
-					</apply>
-					<apply is="minuss/2">
-						<minus />
-						<cn>0</cn>
-						<apply>
-							<divide />
-							<ci>s</ci>
-							<cn>2</cn>
-						</apply>
-					</apply>
-				</apply>
-			</apply>
-		</apply>
-		<apply id="term2" >
-			<divide/>
-			<apply id="term2.numerator">
-				<times />
-				<ci>pi</ci>
-				<apply>
-					<root />
-					<cn>32</cn>
-				</apply>
-			</apply>
-			<apply id="term2.denominator">
-				<times />
-				<apply id="term2.sminus3">
-					<minus />
-					<ci>s</ci>
-					<cn>3</cn>
-				</apply>
-				<apply id="denominator.powerbracket">
-					<power />
-					<apply id="largebracket">
-						<times />
-						<apply id="3overroot32pi">
-							<divide />
-							<cn>3</cn>
-							<apply>
-								<times />
-								<apply>
-									<root />
-									<cn>32</cn>
-								</apply>
-								<ci>pi</ci>
-							</apply>
-						</apply>
-						<apply id="summationbracket">
-							<plus />
-							<cn>1</cn>
-							<apply id="summation">
-								<sum />
-								<bvar>
-									<ci>i</ci>
-								</bvar>
-								<lowlimit>
-									<cn>1</cn>
-								</lowlimit>
-								<uplimit>
-									<ci>theta</ci>
-								</uplimit>
-								<apply>
-									<selector />
-									<ci type="vector">n</ci>
-									<ci>i</ci>
-								</apply>
-							</apply>
-						</apply>
-					</apply>
-					<apply id="denominator.exponent">
-						<divide />
-						<apply>
-							<minus />
-							<ci>s</ci>
-							<cn>3</cn>
-						</apply>
-						<cn>3</cn>
-					</apply>
-				</apply>
-			</apply>
-		</apply>
-	</apply>
-</math>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/selector1.xml

-<computation xmlns:m="http://www.w3.org/1998/Math/MathML"
-	xmlns="http://www.xml-cml.org/semanticcomputation">
-	
-	<tableTool method="applyFunction"
-		functionRef="src/test/resources/org/xmlcml/cml/forcefield/kk/selectorSum.xml"
-		xpath=".//*[local-name()='table' ]" 
-		xpath-1=".//*[local-name()='array' and @id='a1']" var-1="a" 
-		xpath-2=".//*[local-name()='array' and @id='a2']" var-2="b"
-		param-s="7" 
-		param-pi="3.14159265358979323846"
-		param-n="6">
-		<table xmlns="http://www.xml-cml.org/schema" >
-			<array xmlns="http://www.xml-cml.org/schema" dataType="xsd:double"
-				id="a1" size="5">
-				1 2 3 4 5
-			</array>
-			<array xmlns="http://www.xml-cml.org/schema" dataType="xsd:double"
-				id="a2" size="5">
-				10 9 8 7 6
-			</array>
-		</table>
-	
-	</tableTool>
-
-</computation>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/table1Cubic7Out.xml

-<scalar xmlns="http://www.xml-cml.org/schema" dataType="xsd:double">12.311193766582377</scalar>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/table1cubic.xml

-<computation xmlns:m="http://www.w3.org/1998/Math/MathML"
-	xmlns="http://www.xml-cml.org/semanticcomputation">
-	
-	<tableTool method="applyFunction"
-		functionRef="src/test/resources/org/xmlcml/cml/forcefield/kk/potentialEnergySum.xml"
-		xpath=".//*[local-name()='table' ]" 
-		xpath-1=".//*[local-name()='array' and @id='a1']" var-1="a" 
-		xpath-2=".//*[local-name()='array' and @id='a2']" var-2="b"
-		param-s="7" 
-		param-pi="3.14159265358979323846"
-		param-n="6">
-		<table xmlns="http://www.xml-cml.org/schema" >
-			<array xmlns="http://www.xml-cml.org/schema" dataType="xsd:double"
-				id="a1" size="60">
-				1 2 3 4 5
-				6 7 8 9 10
-				11 12 13 15 16
-				17 18 19 20 21
-				22 23 24 25 26
-				27 28 29 31 32
-				33 34 35 36 37
-				38 39 40 41 42
-				43 44 45 47 48
-				49 50 51 52 53
-				54 55 57 58 59 
-				60 61 63 64 65
-			</array>
-			<array xmlns="http://www.xml-cml.org/schema" dataType="xsd:double"
-				id="a2" size="60">
-				12 6 24 12 24
-				8 48 6 36 24
-				24 24 72 48 12
-				48 30 72 24 48
-				24 48 8 84 24
-				96 48 24 96 6
-				96 48 48 36 120
-				24 48 24 48 48
-				120 24 120 96 24 
-				108 30 48 72 72
-				32 144 96 72 72
-				48 120 144 12 72
-			</array>
-		</table>
-	
-	</tableTool>
-
-</computation>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/table1hexagonal.xml

-<computation xmlns:m="http://www.w3.org/1998/Math/MathML"
-	xmlns="http://www.xml-cml.org/semanticcomputation">
-	
-	<tableTool method="applyFunction"
-		functionRef="src/test/resources/org/xmlcml/cml/chemistry/potentialEnergySum.xml"
-		xpath=".//*[local-name()='table' ]" 
-		xpath-1=".//*[local-name()='array' and @id='a1']" var-1="a" 
-		xpath-2=".//*[local-name()='array' and @id='a2']" var-2="b"
-		param-s="10" 
-		param-pi="3.14159265358979323846"
-		param-n="20">
-		<table xmlns="http://www.xml-cml.org/schema" >
-			<array xmlns="http://www.xml-cml.org/schema" dataType="xsd:double"
-				id="a1" size="130">
-				1 2 2.7 3 3.7
-				4 5 5.7 6 6.3
-				6.7 7 7.3 8.3 9
-				9.7 10 10.3 10.7 11
-				11.3 11.7 12 12.3 13
-				13.7 14.3 14.7 15 15.3 
-				15.7 16 16.3 17 17.7
-				
-				18 18.3 18.7 19 19.7
-				20.3 21 21.7 22 22.3
-				22.7 23 23.3 23.7 24 
-				25 26 26.3 26.7 27
-				27.3 27.7 28 28.3 29
-				29.7 30.3 30.7 31 31.3
-				31.7 32.3 33 33.7 34
-
-				35 35.7 36 36.3 37
-				37.7 38 38.3 38.7 39
-				39.3 39.7 40 40.3 41
-				41.7 42 42.3 42.7 43
-				43.3 43.7 45 45.7 46.3
-				46.7 47 47.3 47.7 48 
-				48.3 49 49.7 50 50.3
-
-				50.7 51 51.7 52 52.3
-				53 53.3 54 54.3 54.7 
-				55 55.3 55.7 56.3 57
-				58 58.3 58.7 59 59.3
-				59.7 60 60.3 61 61.7
-			</array>
-			<array xmlns="http://www.xml-cml.org/schema" dataType="xsd:double"
-				id="a2" size="130">
-				12 6 2 18 12
-				6 12 126 6
-				12 24 6 12 12
-				24 12 12 2 12
-				6 24 6 12 24
-				12 6 24 12 12
-				24 6 12 24 24
-
-				18 12 12 24 12
-				12 36 24 12 18
-				12 24 12 48 2
-				36 24 12 12 42
-				6 12 24 12 12
-				36 12 24 72 12
-				24 12 48 24 24
-				
-				24 12 18 24 72
-				12 24 12 36 36
-				6 24 12 12 24
-				48 36 12 2 72
-				12 12 60 36 6
-				24 48 12 24 6
-				12 60 48 30 24
-				
-				12 36 48 36 12
-				36 24 18 6 36
-				48 18 24 24 48
-				36 24 24 36 6
-				60 12 24 72 24				
-			</array>
-		</table>
-	
-	</tableTool>
-
-</computation>

File src/test/resources/org/xmlcml/declaratron/chem/cml/forcefield/kk/term2.xml

-<math display='block'>
-
-	<apply id="term2">
-		<divide />
-		<apply id="term2.numerator">
-			<times />
-			<ci>pi</ci>
-			<apply>
-				<root />
-				<cn>32</cn>
-			</apply>
-		</apply>
-		<apply id="term2.denominator">
-			<times />
-			<apply id="term2.sminus3">
-				<minus />
-				<ci>s</ci>
-				<cn>3</cn>
-			</apply>
-			<apply id="denominator.powerbracket">
-				<power />
-				<apply id="largebracket">
-					<times />
-					<apply id="3overroot32pi">
-						<divide />
-						<cn>3</cn>
-						<apply>
-							<times />
-							<apply>
-								<root />
-								<cn>32</cn>
-							</apply>
-							<ci>pi</ci>
-						</apply>
-					</apply>
-					<apply id="summationbracket">
-						<plus />
-						<cn>1</cn>
-						<apply id="summation">
-							<sum />
-							<bvar>
-								<ci>i</ci>
-							</bvar>
-							<lowlimit>
-								<cn>1</cn>
-							</lowlimit>
-							<uplimit>
-								<ci>theta</ci>
-							</uplimit>
-							<apply>
-								<selector />
-								<ci type="vector">n</ci>
-								<ci>i</ci>
-							</apply>
-						</apply>
-					</apply>
-				</apply>
-				<apply id="denominator.exponent">
-					<divide />
-					<apply>
-						<minus />
-						<ci>s</ci>
-						<cn>3</cn>
-					</apply>
-					<cn>3</cn>
-				</apply>
-			</apply>
-		</apply>
-	</apply>
-</math>

File src/test/resources/org/xmlcml/declaratron/chem/forcefield/amber/acetic.xml

+<molecule 
+    xmlns="http://www.xml-cml.org/schema" 
+    xmlns:cml="http://www.xml-cml.org/schema" 
+    xmlns:amber='http://www.xml-cml.org/dict/amber:gaffType'>
+	<atomArray>
+		<atom elementType="C" id="C" x3="-3.9150" y3="-0.4930" z3="0.0000">
+			<atomType dictRef="amber:gaffType">c3</atomType>
+			<atomType dictRef="amber:parm94Type">CT</atomType>
+			<cml:property dictRef='compchem:computedcharge'>
+				<cml:scalar dataType='xsd:double'>-0.2001</cml:scalar>
+			</cml:property>
+		</atom>
+		<atom elementType="C" id="C1" x3="-2.7230" y3="0.4150" z3="0.0490">
+			<atomType dictRef="amber:gaffType">c</atomType>
+			<atomType dictRef="amber:parm94Type">C</atomType>
+			<cml:property dictRef='compchem:computedcharge'>
+				<cml:scalar dataType='xsd:double'>0.6230999983536656</cml:scalar>
+			</cml:property>
+		</atom>
+		<atom elementType="H" id="H" x3="-4.8240" y3="0.1060" z3="-0.0980">
+			<atomType dictRef="amber:gaffType">hc</atomType>
+			<atomType dictRef="amber:parm94Type">HC</atomType>
+			<cml:property dictRef='compchem:computedcharge'>
+				<cml:scalar dataType='xsd:double'>0.0867</cml:scalar>
+			</cml:property>
+		</atom>
+		<atom elementType="H" id="H1" x3="-3.9740" y3="-1.0750" z3="0.9240">
+			<atomType dictRef="amber:gaffType">hc</atomType>
+			<atomType dictRef="amber:parm94Type">HC</atomType>
+			<cml:property dictRef='compchem:computedcharge'>
+				<cml:scalar dataType='xsd:double'>0.0687</cml:scalar>
+			</cml:property>
+		</atom>
+		<atom elementType="H" id="H2" x3="-3.8440" y3="-1.1540" z3="-0.8680">
+			<atomType dictRef="amber:gaffType">hc</atomType>
+			<atomType dictRef="amber:parm94Type">HC</atomType>
+			<cml:property dictRef='compchem:computedcharge'>
+				<cml:scalar dataType='xsd:double'>0.0687</cml:scalar>
+			</cml:property>
+		</atom>
+		<atom elementType="O" id="O" x3="-2.7880" y3="1.6330" z3="0.0830">
+			<atomType dictRef="amber:gaffType">o</atomType>
+			<atomType dictRef="amber:parm94Type">O</atomType>
+			<cml:property dictRef='compchem:computedcharge'>
+				<cml:scalar dataType='xsd:double'>-0.485</cml:scalar>
+			</cml:property>
+		</atom>
+		<atom elementType="O" id="O1" x3="-1.5520" y3="-0.2590" z3="0.0650">
+			<atomType dictRef="amber:gaffType">oh</atomType>
+			<atomType dictRef="amber:parm94Type">OH</atomType>
+			<cml:property dictRef='compchem:computedcharge'>
+				<cml:scalar dataType='xsd:double'>-0.5840999983536654</cml:scalar>
+			</cml:property>
+		</atom>
+		<atom elementType="H" id="H3" x3="-1.6580" y3="-1.2280" z3="0.0390">
+			<atomType dictRef="amber:gaffType">ho</atomType>
+			<atomType dictRef="amber:parm94Type">HO</atomType>
+			<cml:property dictRef='compchem:computedcharge'>
+				<cml:scalar dataType='xsd:double'>0.422</cml:scalar>
+			</cml:property>
+		</atom>
+	</atomArray>
+	<bondArray>
+		<bond id="b1" atomRefs2="C C1" order="S" />
+		<bond id="b2" atomRefs2="C H" order="S" />
+		<bond id="b3" atomRefs2="C H1" order="S" />
+		<bond id="b4" atomRefs2="C H2" order="S" />
+		<bond id="b5" atomRefs2="O C1" order="D" />
+		<bond id="b6" atomRefs2="C1 O1" order="S" />
+		<bond id="b7" atomRefs2="O1 H3" order="S" />
+	</bondArray>
+</molecule>    

File src/test/resources/org/xmlcml/declaratron/chem/forcefield/amber/aceticDistorted.cml

+<molecule 
+    xmlns="http://www.xml-cml.org/schema" 
+    xmlns:cml="http://www.xml-cml.org/schema" 
+    xmlns:amber='http://www.xml-cml.org/dict/amber:gaffType'>
+	<atomArray>
+		<atom elementType="C" id="C" x3="-3.9150" y3="-0.4930" z3="1.0000">
+			<atomType dictRef="amber:parm94Type">CT</atomType>
+			<cml:property dictRef='compchem:computedcharge'>
+				<cml:scalar dataType='xsd:double'>-0.2001</cml:scalar>
+			</cml:property>
+		</atom>
+		<atom elementType="C" id="C1" x3="-1.7230" y3="1.4150" z3="1.0490">
+			<atomType dictRef="amber:parm94Type">C</atomType>
+			<cml:property dictRef='compchem:computedcharge'>
+				<cml:scalar dataType='xsd:double'>0.623</cml:scalar>
+			</cml:property>
+		</atom>
+		<atom elementType="H" id="H" x3="-3.8240" y3="0.1060" z3="-0.0980">
+			<atomType dictRef="amber:parm94Type">HC</atomType>
+			<cml:property dictRef='compchem:computedcharge'>
+				<cml:scalar dataType='xsd:double'>0.0867</cml:scalar>
+			</cml:property>
+		</atom>
+		<atom elementType="H" id="H1" x3="-3.9740" y3="-0.0750" z3="0.9240">
+			<atomType dictRef="amber:parm94Type">HC</atomType>
+			<cml:property dictRef='compchem:computedcharge'>
+				<cml:scalar dataType='xsd:double'>0.0687</cml:scalar>
+			</cml:property>
+		</atom>
+		<atom elementType="H" id="H2" x3="-3.8440" y3="-0.1540" z3="-0.8680">
+			<atomType dictRef="amber:parm94Type">HC</atomType>
+			<cml:property dictRef='compchem:computedcharge'>
+				<cml:scalar dataType='xsd:double'>0.0687</cml:scalar>
+			</cml:property>