updated copyright notice, email addresses, build file, bumped release

build.xml

@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project name="MX" default="compile" basedir=".">
   <!-- properties -->
-  <property name="full-name" value="MX Tools for Cheminformatics" />
+  <property name="full-name" value="MX - Essential Cheminformatics" />
   <property name="unix-name" value="mx" />
-  <property name="version" value="1.0-beta1" />
+  <property name="version" value="1.0-beta-2" />
   <property name="source.dir" location="src" />
   <property name="resource.dir" location="resources" />
   <property name="lib.dir" location="lib" />
@@ -14,10 +14,13 @@
   <property name="doc.dir" location="${build.dir}/doc" />
   <property name="dist.dir" location="${build.dir}/dist" />
   <property name="test.dir" location="${build.dir}/test" />
+  <property name="molfile.dir" location="${resource.dir}/molfiles" />
   <property name="testenv.dir" location ="testenv" />
-  <property name="lib-licenses.file" location="${lib.dir}/LICENSES.txt" />
-  <property name="license.file" location="LICENSE.txt" />
+  <property name="lib-licenses.file" location="${lib.dir}/LICENSES" />
+  <property name="license.file" location="LICENSE" />
+  <property name="readme.file" location="README" />
   <property name="junit.lib" value="${lib.dir}/junit-4.5.jar" />
+  <property name="mockito.lib" value="${lib.dir}/mockito-all-1.7.jar" />
   <property name="test.class" value = "com.metamolecular.mx.test.MXTest" />
   <!-- filesets -->
   <fileset dir="${lib.dir}" id="libs">
@@ -70,7 +73,7 @@
       <classpath>
         <fileset refid="libs" />
       </classpath>
-      <bottom><![CDATA[<i>Copyright &copy; 2007, 2008 <a href="http://metamolecular.com">Metamolecular, LLC</a>. All Rights Reserved.</i>]]>
+      <bottom><![CDATA[<i>Copyright &copy; 2007-2009 <a href="http://metamolecular.com">Metamolecular, LLC</a> and others. All Rights Reserved.</i>]]>
       </bottom>
     </javadoc>
   </target>
@@ -83,15 +86,21 @@
     <mkdir dir="${dist.dir}/src" />
     <mkdir dir="${dist.dir}/doc" />
     <mkdir dir="${dist.dir}/resources" />
+    <mkdir dir="${dist.dir}/resources/molfiles" />
     <copy file="${junit.lib}" todir="${dist.dir}/lib" />
+    <copy file="${mockito.lib}" todir="${dist.dir}/lib" />
     <copy file="${lib-licenses.file}" todir="${dist.dir}/lib" />
     <copy file="${license.file}" todir="${dist.dir}" />
+    <copy file="${readme.file}" todir="${dist.dir}" />
     <copy todir="${dist.dir}/src">
       <fileset dir="${source.dir}" includes="com/metamolecular/mx/**/*.java" />
     </copy>
     <copy todir="${dist.dir}/doc">
       <fileset dir="${doc.dir}" />
     </copy>
+    <copy todir="${dist.dir}/resources/molfiles">
+      <fileset dir="${molfile.dir}" />
+    </copy>
     <copy file="${resource.dir}/atomic_system.pdf" todir="${dist.dir}/resources" />
     <copy file="${resource.dir}/atomic_system.xml" todir="${dist.dir}/resources" />
     <copy file="${resource.dir}/pubchem_sample_33.sdf" todir="${dist.dir}/resources" />

src/com/metamolecular/mx/calc/DefaultMeasurement.java

@@ -1,5 +1,5 @@
 /*
- * MX Cheminformatics Tools for Java
+ * MX - Essential Cheminformatics
  * 
  * Copyright (c) 2007-2009 Metamolecular, LLC
  * 
@@ -26,7 +26,7 @@
 package com.metamolecular.mx.calc;
 
 /**
- * @author Richard L. Apodaca
+ * @author Richard L. Apodaca <rapodaca at metamolecular.com>
  */
 public class DefaultMeasurement implements Measurement
 {

src/com/metamolecular/mx/calc/MassCalculator.java

@@ -1,9 +1,9 @@
 /*
- * MX Cheminformatics Tools for Java
+ * MX - Essential Cheminformatics
  * 
  * Copyright (c) 2007-2009 Metamolecular, LLC
  * 
- * http://metamolecular.com
+ * http://metamolecular.com/mx
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -23,14 +23,15 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
+
 package com.metamolecular.mx.calc;
 
 import com.metamolecular.mx.model.Atom;
 import com.metamolecular.mx.model.AtomicSystem;
 import com.metamolecular.mx.model.Molecule;
 
 /**
- * @author Richard L. Apodaca
+ * @author Richard L. Apodaca <rapodaca at metamolecular.com>
  */
 public class MassCalculator
 {

src/com/metamolecular/mx/calc/Measurement.java

@@ -1,9 +1,9 @@
 /*
- * MX Cheminformatics Tools for Java
+ * MX - Essential Cheminformatics
  * 
  * Copyright (c) 2007-2009 Metamolecular, LLC
  * 
- * http://metamolecular.com
+ * http://metamolecular.com/mx
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -23,10 +23,11 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
+
 package com.metamolecular.mx.calc;
 
 /**
- * @author Richard L. Apodaca
+ * @author Richard L. Apodaca <rapodaca at metamolecular.com>
  */
 public interface Measurement
 {

src/com/metamolecular/mx/fingerprint/BloomFilter.java

@@ -1,10 +1,10 @@
 /*
- * MX Cheminformatics Tools for Java
+ * MX - Essential Cheminformatics
  * 
  * Copyright (c) 2007-2009 Metamolecular, LLC
  * Copyright (c) Ian Clarke
  * 
- * http://metamolecular.com
+ * http://metamolecular.com/mx
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

src/com/metamolecular/mx/fingerprint/Fingerprinter.java

@@ -1,9 +1,9 @@
 /*
- * MX Cheminformatics Tools for Java
- *
- * Copyright (c) 2007-2008 Metamolecular, LLC
- *
- * http://metamolecular.com
+ * MX - Essential Cheminformatics
+ * 
+ * Copyright (c) 2007-2009 Metamolecular, LLC
+ * 
+ * http://metamolecular.com/mx
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -23,6 +23,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
+
 package com.metamolecular.mx.fingerprint;
 
 import com.metamolecular.mx.model.Molecule;

src/com/metamolecular/mx/fingerprint/PathFingerprinter.java

@@ -1,9 +1,9 @@
 /*
- * MX Cheminformatics Tools for Java
- *
- * Copyright (c) 2007-2008 Metamolecular, LLC
- *
- * http://metamolecular.com
+ * MX - Essential Cheminformatics
+ * 
+ * Copyright (c) 2007-2009 Metamolecular, LLC
+ * 
+ * http://metamolecular.com/mx
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -23,6 +23,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
+
 package com.metamolecular.mx.fingerprint;
 
 import com.metamolecular.mx.model.Atom;

src/com/metamolecular/mx/io/Molecules.java

@@ -1,9 +1,9 @@
 /*
- * MX Cheminformatics Tools for Java
+ * MX - Essential Cheminformatics
  * 
  * Copyright (c) 2007-2009 Metamolecular, LLC
  * 
- * http://metamolecular.com
+ * http://metamolecular.com/mx
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -23,12 +23,13 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
+
 package com.metamolecular.mx.io;
 
 import com.metamolecular.mx.model.*;
 
 /**
- * @author Richard L. Apodaca
+ * @author Richard L. Apodaca <rapodaca at metamolecular.com>
  * @author Duan Lian
  */
 public class Molecules

src/com/metamolecular/mx/io/daylight/SMILESBuilder.java

@@ -1,9 +1,9 @@
 /*
- * MX Cheminformatics Tools for Java
+ * MX - Essential Cheminformatics
  * 
  * Copyright (c) 2007-2009 Metamolecular, LLC
  * 
- * http://metamolecular.com
+ * http://metamolecular.com/mx
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -23,6 +23,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
+
 package com.metamolecular.mx.io.daylight;
 
 import com.metamolecular.mx.model.Atom;
@@ -33,7 +34,7 @@
 import java.util.Map;
 
 /**
- * @author Richard L. Apodaca
+ * @author Richard L. Apodaca <rapodaca at metamolecular.com>
  */
 public class SMILESBuilder
 {

src/com/metamolecular/mx/io/daylight/SMILESReader.java

@@ -1,9 +1,9 @@
 /*
- * MX Cheminformatics Tools for Java
+ * MX - Essential Cheminformatics
  * 
  * Copyright (c) 2007-2009 Metamolecular, LLC
  * 
- * http://metamolecular.com
+ * http://metamolecular.com/mx
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -23,14 +23,15 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
+
 package com.metamolecular.mx.io.daylight;
 
 import com.metamolecular.mx.model.DefaultMolecule;
 import com.metamolecular.mx.model.Molecule;
 import java.util.regex.Pattern;
 
 /**
- * @author Richard L. Apodaca
+ * @author Richard L. Apodaca <rapodaca at metamolecular.com>
  */
 public class SMILESReader
 {

src/com/metamolecular/mx/io/daylight/SMILESTokenizer.java

@@ -1,9 +1,9 @@
 /*
- * MX Cheminformatics Tools for Java
+ * MX - Essential Cheminformatics
  * 
  * Copyright (c) 2007-2009 Metamolecular, LLC
  * 
- * http://metamolecular.com
+ * http://metamolecular.com/mx
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -23,6 +23,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
+
 package com.metamolecular.mx.io.daylight;
 
 import java.util.ArrayList;
@@ -32,7 +33,7 @@
 import java.util.regex.Pattern;
 
 /**
- * @author Richard L. Apodaca
+ * @author Richard L. Apodaca <rapodaca at metamolecular.com>
  */
 public class SMILESTokenizer
 {

src/com/metamolecular/mx/io/mdl/MDLStringKit.java

@@ -1,9 +1,9 @@
 /*
- * MX Cheminformatics Tools for Java
+ * MX - Essential Cheminformatics
  * 
  * Copyright (c) 2007-2009 Metamolecular, LLC
  * 
- * http://metamolecular.com
+ * http://metamolecular.com/mx
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -27,7 +27,7 @@
 package com.metamolecular.mx.io.mdl;
 
 /**
- * @author Richard L. Apodaca
+ * @author Richard L. Apodaca <rapodaca at metamolecular.com>
  */
 public class MDLStringKit
 {

src/com/metamolecular/mx/io/mdl/MolfileReader.java

@@ -1,9 +1,9 @@
 /*
- * MX Cheminformatics Tools for Java
+ * MX - Essential Cheminformatics
  * 
  * Copyright (c) 2007-2009 Metamolecular, LLC
  * 
- * http://metamolecular.com
+ * http://metamolecular.com/mx
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -23,6 +23,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
+
 package com.metamolecular.mx.io.mdl;
 
 import java.io.LineNumberReader;
@@ -36,7 +37,7 @@
 import com.metamolecular.mx.model.Superatom;
 
 /**
- * @author Richard L. Apodaca
+ * @author Richard L. Apodaca <rapodaca at metamolecular.com>
  */
 public class MolfileReader
 {

src/com/metamolecular/mx/io/mdl/MolfileWriter.java

@@ -1,9 +1,9 @@
 /*
- * MX Cheminformatics Tools for Java
+ * MX - Essential Cheminformatics
  * 
  * Copyright (c) 2007-2009 Metamolecular, LLC
  * 
- * http://metamolecular.com
+ * http://metamolecular.com/mx
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -23,6 +23,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
+
 package com.metamolecular.mx.io.mdl;
 
 import java.text.DecimalFormat;
@@ -36,7 +37,7 @@
 import com.metamolecular.mx.model.Superatom;
 
 /**
- * @author Richard L. Apodaca
+ * @author Richard L. Apodaca <rapodaca at metamolecular.com>
  */
 public class MolfileWriter
 {