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File 00changelog.i

Binary file removed.

File declaratron-chem/declaratron-chem-all/pom.xml

-<?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>
-
-    <parent>
-        <groupId>cml</groupId>
-        <artifactId>declaratron</artifactId>
-        <version>0.1-SNAPSHOT</version>
-        <relativePath>../../pom.xml</relativePath>
-    </parent>
-
-    <artifactId>declaratron-chem-all</artifactId>
-    <name>declaratron-chem-all</name>
-    <packaging>pom</packaging>
-	
-    <dependencies>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-chem-common</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-chem-dummy</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-chem-amber</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-    </dependencies>
-
-</project>
-
-

File declaratron-chem/declaratron-chem-amber/pom.xml

-<?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>
-
-    <parent>
-        <groupId>cml</groupId>
-        <artifactId>declaratron</artifactId>
-        <version>0.1-SNAPSHOT</version>
-        <relativePath>../../pom.xml</relativePath>
-    </parent>
-
-    <artifactId>declaratron-chem-amber</artifactId>
-    <name>declaratron-chem-amber</name>
-
-    <dependencies>
-        <dependency>
-            <groupId>${jumbo.groupId}</groupId>
-            <artifactId>jumbo</artifactId>
-            <version>${jumbo.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-core</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-chem-common</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>xom</groupId>
-            <artifactId>xom</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-testutils</artifactId>
-            <scope>test</scope>
-        </dependency>
-
-    </dependencies>
-
-</project>
-
-

File declaratron-chem/declaratron-chem-amber/src/main/resources/META-INF/declaratron

-org.xmlcml.cml.declaratron.chem.amber.AmberConverters

File declaratron-chem/declaratron-chem-amber/src/main/resources/log4j.properties

-log4j.rootLogger=DEBUG, A1
-log4j.appender.A1=org.apache.log4j.ConsoleAppender
-log4j.appender.A1.layout=org.apache.log4j.PatternLayout
-log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
-log4j.logger.uk.ac.cam=DEBUG
-
-log4j.logger.org.xmlcml.cml.converters.marker = INFO

File declaratron-chem/declaratron-chem-common/pom.xml

-<?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>
-
-    <parent>
-        <groupId>cml</groupId>
-        <artifactId>declaratron</artifactId>
-        <version>0.1-SNAPSHOT</version>
-        <relativePath>../../pom.xml</relativePath>
-    </parent>
-
-    <artifactId>declaratron-chem-common</artifactId>
-    <name>declaratron-chem-common</name>
-
-    <dependencies>
-        <dependency>
-            <groupId>${jumbo.groupId}</groupId>
-            <artifactId>jumbo</artifactId>
-            <version>${jumbo.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-core</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-testutils</artifactId>
-            <scope>test</scope>
-        </dependency>
-
-    </dependencies>
-
-</project>
-
-

File declaratron-chem/declaratron-chem-common/src/main/java/org/xmlcml/declaratron/compchem/package-info.java

-/** 
-Common (often base) class for all chem modules
-*/
-package org.xmlcml.declaratron.chem;

File declaratron-chem/declaratron-chem-common/src/main/resources/log4j.properties

-log4j.rootLogger=DEBUG, A1
-log4j.appender.A1=org.apache.log4j.ConsoleAppender
-log4j.appender.A1.layout=org.apache.log4j.PatternLayout
-log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
-log4j.logger.uk.ac.cam=DEBUG
-
-log4j.logger.org.xmlcml.cml.converters.marker = INFO

File declaratron-chem/declaratron-chem-common/src/main/resources/org/xmlcml/cml/declaratron/chem/cmlxDict.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<cml xmlns="http://www.xml-cml.org/schema">
-  <!-- first try at CompChem dictionary -->
-  <dictionary 
-    xmlns:h="http://www.w3.org/1999/xhtml" 
-    namespace="http://www.xml-cml.org/dictionary/cmlx/"
-    xmlns:convention="http://www.xml-cml.org/convention/" 
-    convention="convention:dictionary"
-    dictionaryPrefix="cmlx" 
-    title="extended CML dictionary" 
-    xmlns="http://www.xml-cml.org/schema"
-    xmlns:cmlx="http://www.xml-cml.org/dictionary/cmlx/"
-    >
-      <definition>
-        <h:p>extended CML dictionary</h:p>
-      </definition>
-      <description>
-        <h:p>Collection of ad hoc and loosely regulated identifiers and terms</h:p>
-      </description>
-    
-    <entry id="junk" term="junk">
-      <definition>
-        <h:p>junk</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="x" term="x">
-      <definition>
-        <h:p>an x coordinate</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="y" term="y">
-      <definition>
-        <h:p>a y coordinate</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="z" term="z">
-      <definition>
-        <h:p>a z coordinate</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="unparsed" term="unparsed information">
-      <definition>
-        <h:p>unparsed information</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="name" term="name">
-      <definition>
-        <h:p>the name of a name-value pair</h:p>
-      </definition>
-      <description>
-        <h:p>Should be accompanied by x:value elements</h:p>
-      </description>
-    </entry>
-
-    <entry id="value" term="value">
-      <definition>
-        <h:p>the value of a name-value pair</h:p>
-      </definition>
-      <description>
-        <h:p>Should be accompanied by x:name elements</h:p>
-      </description>
-    </entry>
-
-  </dictionary>
-</cml>

File declaratron-chem/declaratron-chem-common/src/main/resources/org/xmlcml/cml/declaratron/chem/compchem.dtd

-<!ENTITY % output      'output          (VERBOSE|NORMAL|NONE)  "NONE"'>
-<!ENTITY % formatType  'formatType      (FORTRAN|WHITESPACE|REGEX)'>
-<!ENTITY % id          'id              CDATA'>
-<!ENTITY % linesToRead 'linesToRead     CDATA'>
-<!ENTITY % makeArray   'makeArray       CDATA'>
-<!ENTITY % name        'name            CDATA'>
-<!ENTITY % names       'names           CDATA'>
-<!ENTITY % pattern     'pattern         CDATA'>
-<!ENTITY % reading     'reading         (WHILE|UNTIL|ALL|ONCE)'>
-
-
-<!ELEMENT include (template*)>
-<!-- parameter entities don't seem to work -->
-<!ELEMENT templateList (include | template*)>
-<!ATTLIST templateList
-    %id;         #REQUIRED
-    >
-<!ELEMENT template (
-    comment|
-    readLines|
-    record|
-    comment|
-    templateList)*>
-<!ATTLIST template
-    id        CDATA #REQUIRED
-    output    CDATA #IMPLIED
-    name      CDATA #IMPLIED
-    pattern   CDATA #IMPLIED
-    >
-
-<!ELEMENT record   (#PCDATA)>
-<!ATTLIST record
-    id          CDATA   #REQUIRED
-    output      CDATA   #IMPLIED
-    formatType  CDATA   #IMPLIED
-    reading     CDATA   #IMPLIED
-    linesToRead CDATA   #IMPLIED
-    makeArray   CDATA   #IMPLIED
-    names       CDATA   #IMPLIED
-    >
-    
-<!ELEMENT readLines (#PCDATA)>
-<!ATTLIST readLines
-    id          CDATA   #REQUIRED
-    output      CDATA   #IMPLIED
-    formatType  CDATA   #IMPLIED
-    reading     CDATA   #IMPLIED
-    linesToRead CDATA   #IMPLIED
-    >
-
-<!ELEMENT comment (#PCDATA)>
-<!ATTLIST comment
-    role CDATA     #IMPLIED
-    >
-    

File declaratron-chem/declaratron-chem-common/src/main/resources/org/xmlcml/cml/declaratron/chem/compchemDict.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<cml xmlns="http://www.xml-cml.org/schema">
-  <dictionary 
-    xmlns:h="http://www.w3.org/1999/xhtml"
-    namespace="http://www.xml-cml.org/dictionary/compchem/"
-    xmlns:convention="http://www.xml-cml.org/convention/" 
-    convention="convention:dictionary"
-    dictionaryPrefix="compchem" 
-    title="CompChem dictionary" 
-    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:si="http://www.xml-cml.org/unit/si/" 
-    xmlns:nonSi="http://www.xml-cml.org/unit/nonSi/" 
-    xmlns:unitType="http://www.xml-cml.org/unit/unitType/" 
-    
-    >
-    <!--
-      <definition>
-        <h:p>Compchem dictionary</h:p>
-      </definition>
-      -->
-      <description>
-        <h:p>terms common more than one code dictionary</h:p>
-      </description>
-
-    <entry id="environment" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="environment">
-      <definition>
-        <h:p>compchem environment module</h:p>
-      </definition>
-      <description>
-        <h:p>an optional toplevel modules defined by compchem convention
-        </h:p>
-      </description>
-    </entry>
-    
-    <entry id="misc" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="miscellaneous markup">
-      <definition>
-        <h:p>miscellaneous</h:p>
-      </definition>
-      <description>
-        <h:p>TODO MOVE</h:p>
-      </description>
-    </entry>
-    
-    <entry id="parameter" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="parameter">
-      <definition>
-        <h:p>parameter</h:p>
-      </definition>
-      <description>
-        <h:p>TODO MOVE</h:p>
-      </description>
-    </entry>
-    <entry id="property" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="property">
-      <definition>
-        <h:p>property</h:p>
-      </definition>
-      <description>
-        <h:p>TODO MOVE</h:p>
-      </description>
-    </entry>
-
-    <entry id="startid" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="startid">
-      <definition>
-        <h:p>???</h:p>
-      </definition>
-      <description>
-        <h:p>???</h:p>
-      </description>
-    </entry>
-    
-    <entry id="data" units="si:unknown" unitType="unitType:unknown"  term="data" dataType="xsd:string">
-      <definition>
-        <h:p>data</h:p>
-      </definition>
-      <description>
-        <h:p>TODO MOVE</h:p>
-      </description>
-    </entry>
-    
-    <entry id="title" units="si:unknown" unitType="unitType:unknown"  term="title" dataType="xsd:string">
-      <definition>
-        <h:p>an arbitrary title</h:p>
-      </definition>
-      <description>
-        <h:p>title is not used for reference, though could be used for
-          lexical indexing (e.g. by Solr) TODO MOVE</h:p>
-      </description>
-    </entry>
-    
-    <entry id="iter" units="si:unknown" unitType="unitType:unknown"  term="serial number of iteration" dataType="xsd:integer">
-      <definition>
-        <h:p>serial number of iteration</h:p>
-      </definition>
-      <description>
-        <h:p>serial number of iteration TODO MOVE</h:p>
-      </description>
-    </entry>
-    <!-- unitType should be added to entry attributes <entry id="energy" 
-     dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="energy" dataType="xsd:double" unitType="unitType:energy"> <definition><h:p>energy</h:p></definition> 
-      <description><h:p>energy of unspecified typeTODO MOVE</h:p></description> 
-      </entry> 
-      -->
-    <entry id="energy" units="si:unknown" term="energy" dataType="xsd:double" unitType="unitType:energy">
-      <definition>
-        <h:p>energy</h:p>
-      </definition>
-      <description>
-        <h:p>energy of unspecified typeTODO MOVE</h:p>
-      </description>
-    </entry>
-    
-    <entry id="deltae" units="si:unknown" term="deltae" dataType="xsd:double"
-      unitType="unitType:energy">
-      <definition>
-        <h:p>change in energy between cycles</h:p>
-      </definition>
-      <description>
-        <h:p>change in energy between cycles</h:p>
-      </description>
-    </entry>
-    
-    <entry id="rmsdens" units="si:unknown" unitType="unitType:unknown"  term="RMS electron density" dataType="xsd:double">
-      <definition>
-        <h:p>rms density</h:p>
-      </definition>
-      <description>
-        <h:p>RMS electron density</h:p>
-      </description>
-    </entry>
-    
-    <entry id="diiserr" units="si:unknown" unitType="unitType:unknown"  term="diiserr" dataType="xsd:double">
-      <definition>
-        <h:p>error in DIIS</h:p>
-      </definition>
-      <description>
-        <h:p>error in DIIS</h:p>
-      </description>
-    </entry>
-    
-    <entry id="time" units="si:unknown" unitType="unitType:unknown"  term="cumulative time" dataType="xsd:double">
-      <definition>
-        <h:p>cumulative time</h:p>
-      </definition>
-      <description>
-        <h:p>TODO MOVE</h:p>
-      </description>
-    </entry>
-
-
-    <entry id="sumatomener" units="si:unknown" unitType="unitType:unknown"  term="Sum of atom energies" dataType="xsd:double">
-      <definition>
-        <h:p>Sum of atom energies</h:p>
-      </definition>
-      <description>
-        <h:p>Sum of atom energies</h:p>
-      </description>
-    </entry>
-    
-    <entry id="totener" units="si:unknown" unitType="unitType:unknown"  term="Total energy" dataType="xsd:double">
-      <definition>
-        <h:p>Total energy</h:p>
-      </definition>
-      <description>
-        <h:p>TODO MOVE</h:p>
-      </description>
-    </entry>
-    
-    <entry id="ener1e" units="si:unknown" unitType="unitType:unknown"  term="1-electron energy" dataType="xsd:double">
-      <definition>
-        <h:p>1-electron energy</h:p>
-      </definition>
-      <description>
-        <h:p>1-electron energy</h:p>
-      </description>
-    </entry>
-    
-    <entry id="ener2e" units="si:unknown" unitType="unitType:unknown"  term="TODO ener2e" dataType="xsd:double">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-    
-    <entry id="homo" units="si:unknown" unitType="unitType:unknown"  term="HOMO" dataType="xsd:double">
-      <definition>
-        <h:p>Highest Occupied Molecular Orbital</h:p>
-      </definition>
-      <description>
-        <h:p>TODO MOVE</h:p>
-      </description>
-    </entry>
-    
-    <entry id="lumo" units="si:unknown" unitType="unitType:unknown"  term="LUMO" dataType="xsd:double">
-      <definition>
-        <h:p>Lowest Occupied Moecular Orbital</h:p>
-      </definition>
-      <description>
-        <h:p>TODO MOVE</h:p>
-      </description>
-    </entry>
-    
-    <entry id="totaldft" units="si:unknown" unitType="unitType:unknown"  term="Total DFT energy" dataType="xsd:double">
-      <definition>
-        <h:p>Total DFT energy</h:p>
-      </definition>
-      <description>
-        <h:p>TODO MOVE</h:p>
-      </description>
-    </entry>
-
-    <entry id="oneelecener" units="si:unknown" unitType="unitType:unknown"  term="1-electron energy" dataType="xsd:double">
-      <definition>
-        <h:p>1-electron energy</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-    <entry id="coulomb" units="si:unknown" unitType="unitType:unknown"  term="Coulomb energy" dataType="xsd:double">
-      <definition>
-        <h:p>Coulomb energy</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-    <entry id="nucrepener" units="si:unknown" unitType="unitType:unknown"  term="Nuclear repulsion energy"
-      dataType="xsd:double">
-      <definition>
-        <h:p>Nuclear repulsion energy</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="atomsym" units="si:unknown" unitType="unitType:unknown"  term="Atom symbol" dataType="cml:elementType">
-      <definition>
-        <h:p>Symbol of the atom</h:p>
-      </definition>
-      <description>
-        <h:p>This may not always be a CML elementType TODO</h:p>
-      </description>
-    </entry>
-    
-    <entry id="atommass" units="si:unknown" unitType="unitType:unknown"  term="Mass of the atom" dataType="xsd:double">
-      <definition>
-        <h:p>Mass of the atom</h:p>
-      </definition>
-      <description>
-        <h:p>May not always be that from a table of atomic masses TODO
-        </h:p>
-      </description>
-    </entry>
-    
-    <entry id="echangecorr" units="si:unknown" unitType="unitType:unknown"  term="Exchange correlation energy"
-      dataType="xsd:double">
-      <definition>
-        <h:p>Exchange correlation energy</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-    
-    <entry id="basis" units="si:unknown" unitType="unitType:unknown"  term="basis set?" dataType="xsd:string">
-      <definition>
-        <h:p>The basis set</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-    
-    <entry id="elsym" units="si:unknown" unitType="unitType:unknown"  term="TODO elsym" dataType="cml:elementType">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-    <entry id="elemname" units="si:unknown" unitType="unitType:unknown"  term="TODO elemname" dataType="cml:elementType">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="atnum" units="si:unknown" unitType="unitType:unknown"  term="TODO atnum" dataType="xsd:integer">
-      <definition>
-        <h:p>serial number of atom</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="bfn" units="si:unknown" unitType="unitType:unknown"  term="TODO bfn" dataType="xsd:integer">
-      <definition>
-        <h:p>basis function</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="irrep" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="Irreducible representation">
-      <definition>
-        <h:p>Irreducible representation</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="serial" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="Serial">
-      <definition>
-        <h:p>A serial number</h:p>
-      </definition>
-      <description>
-        <h:p>a serial number from 1...n</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="elementType" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="element type">
-      <definition>
-        <h:p>the type of the element</h:p>
-      </definition>
-      <description>
-        <h:p>the atomic symbol as in CML:@elementTypeS</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="atomType" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="atom type">
-      <definition>
-        <h:p>an atom type</h:p>
-      </definition>
-      <description>
-        <h:p>An atom type (not the element type). Cf cml:atomType</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="natoms" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="atom count">
-      <definition>
-        <h:p>number of atoms</h:p>
-      </definition>
-      <description>
-        <h:p>normally the count of atoms in a molecule or other collection of atoms</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="hostname" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="host name">
-      <definition>
-        <h:p>host name</h:p>
-      </definition>
-      <description>
-        <h:p>uncontrolled vocabulary</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="finalization" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="finalization module">
-      <definition>
-        <h:p>finalization module</h:p>
-      </definition>
-      <description>
-        <h:p>the finalization module in the Compchem convention</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="initialization" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="initialization module">
-      <definition>
-        <h:p>initialization module</h:p>
-      </definition>
-      <description>
-        <h:p>the initialization module in the Compchem convention</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="calculation" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="calculation module">
-      <definition>
-        <h:p>calculation module</h:p>
-      </definition>
-      <description>
-        <h:p>the calculation module in the Compchem convention</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="version" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="program version">
-      <definition>
-        <h:p>program version</h:p>
-      </definition>
-      <description>
-        <h:p>no controlled syntax</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="executable" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="executable program">
-      <definition>
-        <h:p>executable program</h:p>
-      </definition>
-      <description>
-        <h:p>no controlled syntax</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="input" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="program input">
-      <definition>
-        <h:p>program input</h:p>
-      </definition>
-      <description>
-        <h:p>no controlled syntax</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="date" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="date">
-      <definition>
-        <h:p>An unspecified date</h:p>
-      </definition>
-      <description>
-        <h:p>no controlled syntax</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="nuclearDipole" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="nuclear dipole">
-      <definition>
-        <h:p>nuclear dipole</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="nproc" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="number of processors">
-      <definition>
-        <h:p>number of processors</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="centerofmass" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="center of mass">
-      <definition>
-        <h:p>center of mass</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-        <h:p class="example">TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="calculationType" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="Type of calculation">
-      <definition>
-        <h:p>calculationType</h:p>
-      </definition>
-      <description>
-        <h:p>Type of calculation</h:p>
-        <h:p class="example">TODO MOVE</h:p>
-      </description>
-    </entry>
-    
-    <entry id="metadata" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="metadata">
-      <definition>
-        <h:p>metadata</h:p>
-      </definition>
-      <description>
-        <h:p>Metadata TODO MOVE</h:p>
-      </description>
-    </entry>
-
-    <entry id="x3" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="CML cartesian x">
-      <definition>
-        <h:p>CML x3 coordinate</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="y3" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="CML cartesian y">
-      <definition>
-        <h:p>CML y3 coordinate</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="z3" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="CML cartesian z">
-      <definition>
-        <h:p>CML z3 coordinate</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="program" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="program">
-      <definition>
-        <h:p>the program being run</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="atomtype" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="atom type">
-      <definition>
-        <h:p>CML atomType element</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="atomtypeRef" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="reference to atom type">
-      <definition>
-        <h:p>Reference to CML atomType element</h:p>
-      </definition>
-      <description>
-        <h:p>This should be the normal usage for atomtype symbols/refs</h:p>
-      </description>
-    </entry>
-
-    <entry id="totalener" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="total energy">
-      <definition>
-        <h:p>The total energy</h:p>
-      </definition>
-      <description>
-        <h:p>This may be a code-specific term so may be overridden by code-specific dictionaries</h:p>
-      </description>
-    </entry>
-
-    <entry id="id" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="CML id">
-      <definition>
-        <h:p>A CML id</h:p>
-      </definition>
-      <description>
-        <h:p>usable throughout cml documents. Need not be unique</h:p>
-      </description>
-    </entry>
-
-    <entry id="atomicmass" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="atomic mass">
-      <definition>
-        <h:p>Atomic mass</h:p>
-      </definition>
-      <description>
-        <h:p>normally the mass of an isolated atom, but the isotopic variation may not be clear</h:p>
-      </description>
-    </entry>
-
-    <entry id="grouporder" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="twoeener" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-   <entry id="groupnumber" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-  <entry id="groupname" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-  <entry id="mass" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="oneeener" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="nuclearEnergy" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-    
-    <entry id="cputime" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-    
-    <entry id="walltime" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="cell.a" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="cell.b" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="cell.c" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="cell.alpha" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="cell.beta" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="cell.gamma" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="cell.omega" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="lattice.recip.units" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="citation" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="charge" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="pointgroup" dataType="xsd:string" units="si:unknown" unitType="unitType:unknown"  term="TODO">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-    <entry id="compx" term="TODO" dataType="xsd:string" units="units:none"
-      unitType="unitType:none">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-
-    <entry id="molmass" term="TODO" dataType="xsd:string" units="units:none"
-      unitType="unitType:none">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-
-    <entry id="basis.coefficient" term="TODO" dataType="xsd:string" units="units:none"
-      unitType="unitType:none">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-
-    <entry id="tensorname" term="TODO" dataType="xsd:string" units="units:none"
-      unitType="unitType:none">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-
-    <entry id="basis.shellnum" term="TODO" dataType="xsd:string" units="units:none"
-      unitType="unitType:none">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-
-    <entry id="atomicNumber" term="TODO" dataType="xsd:string" units="units:none"
-      unitType="unitType:none">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-
-    <entry id="compz" term="TODO" dataType="xsd:string" units="units:none"
-      unitType="unitType:none">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-
-    <entry id="compy" term="TODO" dataType="xsd:string" units="units:none"
-      unitType="unitType:none">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-
-    <entry id="shellsym" term="TODO" dataType="xsd:string" units="units:none"
-      unitType="unitType:none">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-
-    <entry id="row.z" term="TODO" dataType="xsd:string" units="units:none"
-      unitType="unitType:none">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-
-    <entry id="row.x" term="TODO" dataType="xsd:string" units="units:none"
-      unitType="unitType:none">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-
-    <entry id="row.y" term="TODO" dataType="xsd:string" units="units:none"
-      unitType="unitType:none">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-
-    <entry id="basis.exponent" term="TODO" dataType="xsd:string" units="units:none"
-      unitType="unitType:none">
-      <definition>
-        <h:p>TODO</h:p>
-      </definition>
-      <description>
-        <h:p>TODO</h:p>
-      </description>
-    </entry>
-
-
-
-  </dictionary>
-</cml>

File declaratron-chem/declaratron-chem-common/src/main/resources/org/xmlcml/cml/declaratron/chem/doc.css

-.comment {
-    background-color : yellow;
-    }
-    

File declaratron-chem/declaratron-chem-common/src/main/resources/org/xmlcml/cml/declaratron/chem/makecompchem.xml

-<transformList>
-
-  <!-- structuring for the compchem convention -->
-  <transform process="createWrapperParameter" 
-      xpath=".//cml:scalar[@dictRef='cc:hostname' or 
-                           @dictRef='cc:jobname' or
-                           @dictRef='cc:method' or
-                           @dictRef='cc:basis'
-                           ]"/>
-  <transform process="createWrapperMetadata" 
-      xpath=".//cml:scalar[@dictRef='cc:version' or
-                           @dictRef='cc:date' or
-                           @dictRef='cc:title']"/>
-  <transform process="createWrapperProperty" 
-      xpath=".//*[@dictRef='cc:electronicstate' or
-                           @dictRef='cc:hfenergy' or
-                           @dictRef='cc:dipole' or
-                           @dictRef='cc:dipolederiv' or
-                           @dictRef='cc:polarizability' or
-                           @dictRef='cc:pointgroup' or
-                           @dictRef='cc:rmsd' or
-                           @dictRef='cc:rmsf']"/>
-  
-
-  <!--  wrap scalars and arrays -->
-  <transform process="addChild" xpath="." elementName="cml:parameterList"/>
-  <transform process="move" xpath=".//cml:parameter" to="./cml:parameterList"/>
-  <transform process="addChild" xpath="." elementName="cml:propertyList"/>
-  <transform process="move" xpath=".//cml:property" to="./cml:propertyList"/>
-  <transform process="addChild" xpath="." elementName="cml:metadataList"/>
-  <transform process="move" xpath=".//cml:metadata" to="./cml:metadataList"/>
-
-  <!-- manage conventions -->  
-  <transform process="addAttribute" xpath="./cml:molecule" name="convention" value="convention:molecular"/>
-  <transform process="addAttribute" xpath="." name="convention" value="convention:compchem"/>
-  <transform process="addNamespace" xpath="." name="convention" value="http://www.xml-cml.org/convention/"/>
-  
-  <!--  finalization -->  
-  <transform process="addDictRef" xpath="." value="compchem:finalization"/>
-  <transform process="addNamespace" xpath="." name="compchem" value="http://www.xml-cml.org/dictionary/compchem/"/>
-
-  <!--  create other parts of cmlcomp -->
-  <!--  job -->
-  <transform process="createWrapper" elementName="cml:module" xpath="." id="job"/>
-  <transform process="createWrapper" elementName="cml:module" xpath="/*" id="jobList"/>
-  <!--  initialization -->
-  <transform process="addChild" elementName="cml:module" xpath="//cml:module[@id='job']" id="initialization"/>
-  <transform process="move" xpath=".//cml:parameterList" to="//cml:module[@id='initialization']"/>
-  <transform process="addDictRef" xpath="//cml:module[@id='initialization']" value="compchem:initialization"/>
-  <!--  environment -->
-  <transform process="addChild" elementName="cml:module" xpath="//cml:module[@id='job']" id="environment"/>
-  <transform process="move" xpath=".//cml:metadataList" to="//cml:module[@id='environment']"/>
-  <transform process="addDictRef" xpath="//cml:module[@id='environment']" value="compchem:environment"/>
-  <!--  calculation -->
-  <transform process="addChild" elementName="cml:module" xpath="//cml:module[@id='job']" id="calculation"/>
-  <transform process="addDictRef" xpath="//cml:module[@id='calculation']" value="compchem:calculation"/>
-  <transform process="move" xpath="//cml:module[@dictRef='compchem:finalization']" to="//cml:module[@id='job']"/>
-  <!--  add namespaces -->  
-  <transform process="addNamespace" xpath="/*" name="cc" value="http://www.xml-cml.org/dictionary/compchem/"/>
-  <transform process="addNamespace" xpath="/*" name="g" value="http://www.xml-cml.org/dictionary/gaussian/"/>
-  <transform process="addNamespace" xpath="/*" name="x" value="http://www.xml-cml.org/dictionary/cmlx/"/>
-  <transform process="addNamespace" xpath="/*" name="si" value="http://www.xml-cml.org/unit/si/"/>
-  <transform process="addNamespace" xpath="/*" name="nonsi" value="http://www.xml-cml.org/unit/nonsi/"/>
-
-  
-</transformList>    
- 

File declaratron-chem/declaratron-chem-common/src/test/java/org/xmlcml/declaratron/chem/common/CompchemTest.java

-package org.xmlcml.declaratron.chem.common;
-
-import org.junit.Test;
-
-public class CompchemTest {
-	@Test
-	public void dummy() {
-		
-	}
-}

File declaratron-chem/declaratron-chem-dummy/pom.xml

-<?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>
-
-    <parent>
-        <groupId>cml</groupId>
-        <artifactId>declaratron</artifactId>
-        <version>0.1-SNAPSHOT</version>
-        <relativePath>../../pom.xml</relativePath>
-    </parent>
-
-    <artifactId>declaratron-chem-dummy</artifactId>
-    <name>declaratron-chem-dummy</name>
-
-    <dependencies>
-        <dependency>
-            <groupId>${jumbo.groupId}</groupId>
-            <artifactId>jumbo</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-core</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-chem-common</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-testutils</artifactId>
-            <scope>test</scope>
-        </dependency>
-    </dependencies>
-
-</project>
-
-

File declaratron-chem/declaratron-chem-dummy/src/main/java/org/xmlcml/declaratron/chem/dummy/DummyModule.java

-package org.xmlcml.declaratron.chem.dummy;
-
-
-/**
- * @author pm286
- */
-public class DummyModule /*extends AbstractConverterModule */ {
-
-
-    public DummyModule() {
-    	super();
-    }
-
-}

File declaratron-chem/declaratron-chem-dummy/src/main/java/org/xmlcml/declaratron/chem/dummy/package-info.java

-/** 
-Converters for Dummy files to XML, CML
-Serves as a cloneable stub for other codes
-*/
-package org.xmlcml.declaratron.chem.dummy;

File declaratron-chem/declaratron-chem-dummy/src/main/resources/META-INF/declaratron

-org.xmlcml.cml.converters.compchem.dummy.DummyConverters

File declaratron-chem/declaratron-chem-dummy/src/main/resources/log4j.properties

-log4j.rootLogger=DEBUG, A1
-log4j.appender.A1=org.apache.log4j.ConsoleAppender
-log4j.appender.A1.layout=org.apache.log4j.PatternLayout
-log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
-log4j.logger.uk.ac.cam=DEBUG
-
-log4j.logger.org.xmlcml.cml.converters.marker = INFO

File declaratron-chem/declaratron-chem-dummy/src/test/java/org/xmlcml/declaratron/chem/dummy/RegressionTest.java

- package org.xmlcml.declaratron.chem.dummy;
-
-import org.junit.Test;
-
-
-/**
- *
- * @author ojd20
- */
-public class RegressionTest {
-
-    @Test
-    public void dummyLog2XML() {
-    }
-}

File declaratron-chem/declaratron-chem-testutils/pom.xml

-<?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>
-
-    <parent>
-        <groupId>cml</groupId>
-        <artifactId>declaratron</artifactId>
-        <version>0.1-SNAPSHOT</version>
-        <relativePath>../../pom.xml</relativePath>
-    </parent>
-
-    <artifactId>declaratron-chem-testutils</artifactId>
-
-    <name>declaratron-chem-testutils</name>
-
-    <dependencies>
-        <dependency>
-            <groupId>${jumbo.groupId}</groupId>
-            <artifactId>jumbo</artifactId>
-            <version>${jumbo.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-core</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-chem-common</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>cml</groupId>
-            <artifactId>declaratron-testutils</artifactId>
-        </dependency>
-
-    </dependencies>
-
-</project>
-
-

File declaratron-chem/pom.xml

-<?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>
-
-    <parent>
-        <groupId>cml</groupId>
-        <artifactId>declaratron</artifactId>
-        <version>0.1-SNAPSHOT</version>
-    </parent>
-
-    <artifactId>declaratron-chem</artifactId>
-    <packaging>pom</packaging>
-    <name>declaratron-chem</name>
-
-    <modules>
-        <module>declaratron-chem-all</module>
-        <module>declaratron-chem-amber</module>
-        <module>declaratron-chem-common</module>
-        <module>declaratron-chem-dummy</module>
-    </modules>
-
-
-</project>
-
-

File declaratron-core/pom.xml

-<?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>
-
-    <parent>
-        <groupId>cml</groupId>
-        <artifactId>declaratron</artifactId>
-        <version>0.1-SNAPSHOT</version>
-    </parent>
-
-    <artifactId>declaratron-core</artifactId>
-    <name>declaratron-core</name>
-
-    <dependencies>
-        <dependency>
-            <groupId>org.xml-cml</groupId>
-            <artifactId>jumbo</artifactId>
-            <version>6.1-SNAPSHOT</version>
-        </dependency>
-        <dependency>
-            <groupId>commons-io</groupId>
-            <artifactId>commons-io</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>jtidy</groupId>
-            <artifactId>jtidy</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>log4j</groupId>
-            <artifactId>log4j</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>xom</groupId>
-            <artifactId>xom</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <scope>test</scope>
-        </dependency>