From 882eb89984515f94711e351fd22469ed5ce37224 Mon Sep 17 00:00:00 2001
From: Jerry James <loganjerry@gmail.com>
Date: Feb 23 2021 00:31:56 +0000
Subject: Version 14.31.31.


---

diff --git a/jmol-build.patch b/jmol-build.patch
index d4e8a23..57e2506 100644
--- a/jmol-build.patch
+++ b/jmol-build.patch
@@ -1,5 +1,5 @@
---- build.xml.orig	2020-09-26 11:17:37.000000000 -0600
-+++ build.xml	2020-09-29 17:19:38.952711528 -0600
+--- build.xml.orig	2021-02-05 17:54:49.000000000 -0700
++++ build.xml	2021-02-22 17:21:35.360733827 -0700
 @@ -60,10 +60,10 @@ when the Jmol code is modified, is as fo
    <property file="${user.home}/.jmol.build.properties" />
    <!-- compile options -->
@@ -22,7 +22,16 @@
    <if><available file="${Private.propertyFile}" /><then>
    	<property file="${Private.propertyFile}" />
  	<echo>using ${Private.keystore} ${Private.storetype}</echo>
-@@ -149,7 +149,6 @@ when the Jmol code is modified, is as fo
+@@ -112,7 +112,7 @@ when the Jmol code is modified, is as fo
+   <property name="docbook-xml" value="docbook-xml-4.4" />
+   <property name="naga.jar" value="naga-3_0.jar" />
+   <property name="commons-cli.jar" value="commons-cli-1.2.jar" />
+-  <property name="inchi.jar" value="jni-inchi-0.7-jar-with-dependencies.jar" />
++  <property name="inchi.jar" value="jni-inchi.jar" />
+   <property name="saxon.jar" value="saxon.jar" />
+   <property name="saxon.main" value="com.icl.saxon.StyleSheet" />
+   <property name="selfsign.store" value="ca-cert/selfSignedCertificate/selfSignedCertificate.store" />
+@@ -150,7 +150,6 @@ when the Jmol code is modified, is as fo
    <path id="apisio-project.class.path">
      <fileset dir="${lib.dir}">
        <!-- include name="${vecmath.jar}" / -->
@@ -30,16 +39,7 @@
        <include name="gnujaxp.jar" />
      </fileset>
    </path>
-@@ -321,7 +320,7 @@ Release Note: When releasing stable vers
- 	
- 	
- 	
--  <target name="main" id="main" depends="init,jar,applet-jar,signed-applet,smiles-applet-jar"/>
-+  <target name="main" id="main" depends="init,jar,applet-jar,smiles-applet-jar"/>
-   
-   <target name="all" id="all" depends="doc,main"/>
- 
-@@ -446,7 +445,7 @@ Release Note: When releasing stable vers
+@@ -447,7 +446,7 @@ Release Note: When releasing stable vers
      <mkdir dir="${classes.dir}"/>
      <javac srcdir="src" destdir="${classes.dir}" encoding="UTF8"
             debug="${debug}" deprecation="${deprecation}"
@@ -48,7 +48,7 @@
        <classpath refid="project.class.path" />
        <exclude name="astex/**/*.java"/>
        <exclude name="java_cup/**/*.java"/>
-@@ -485,7 +484,7 @@ Release Note: When releasing stable vers
+@@ -486,7 +485,7 @@ Release Note: When releasing stable vers
        </fileset>
      </copy>
  
@@ -57,7 +57,7 @@
    	
      <!-- 
  
-@@ -530,7 +529,7 @@ all support for previous versions remove
+@@ -531,7 +530,7 @@ all support for previous versions remove
      <javac srcdir="src" destdir="${applet.classes.dir}"
             debug="${debug}" deprecation="${deprecation}"
             optimize="${optimization}"
@@ -66,7 +66,7 @@
             includesfile="applet.classes"
             classpathref="applet-project.class.path" />
  
-@@ -557,7 +556,7 @@ all support for previous versions remove
+@@ -558,7 +557,7 @@ all support for previous versions remove
      <mkdir dir="${apisio.classes.dir}"/>
      <javac srcdir="src" destdir="${apisio.classes.dir}"
             debug="${debug}" deprecation="${deprecation}"
@@ -75,7 +75,7 @@
             includesfile="apisio.classes"
             classpathref="apisio-project.class.path" />
      <copy todir="${apisio.classes.dir}" >
-@@ -628,8 +627,8 @@ all support for previous versions remove
+@@ -630,14 +629,13 @@ all support for previous versions remove
      <!-- unjar dest="${appjars.dir}" src="${lib.dir}/${vecmath.jar}"/ -->
      <!-- unjar dest="${appjars.dir}" src="${lib.dir}/Acme.jar"/ -->
      <!-- unjar dest="${appjars.dir}" src="${lib.dir}/${itext.jar}"/ -->
@@ -86,18 +86,15 @@
    	<delete dir="${appjars.dir}/javajs" />
    	<delete dir="${appjars.dir}/org/jmol" />
    	<delete dir="${appjars.dir}/org/apache/tools" />
-@@ -639,7 +638,7 @@ all support for previous versions remove
- 
-   <target name="jar" id="jar"
-           depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">
--    <if><equals arg1="${Private.propertyFile}" arg2="none" />
-+    <if><equals arg1="${Private.propertyFile}" arg2="xxx" />
-     	<then><echo>Skipping jar creation</echo></then><else>
- 
-   	
-@@ -685,10 +684,10 @@ all support for previous versions remove
+   	<delete dir="${appjars.dir}/META-INF" />
+     <unjar dest="${appjars.dir}" src="${lib.dir}/${inchi.jar}"/>
+-  	<move file="${appjars.dir}/META-INF/LICENSE" tofile="${appjars.dir}/META-INF/LICENSE-JNI-INCHI"/>
+   	<delete file="${appjars.dir}/META-INF/MANIFEST.MF" />
+     <touch file="build/libjars.timestamp"/>
+   </target>
+@@ -690,10 +688,10 @@ all support for previous versions remove
+     </jar>
  
-     <echo message="Creating Jmol.jar -- if this fails, check to see that build/Jmol.jar is not open." />
  
 -    <antcall target="sign-jar-file">
 +    <!--<antcall target="sign-jar-file">
@@ -106,9 +103,9 @@
 -    </antcall>
 +    </antcall>-->
    	
+     	    <echo message="Creating JmolData.jar -- if this fails, check to see that build/Jmol.jar is not open." />
      <jar destfile="build/JmolData.jar"
-          manifest="manifest/applicationData.txt">
-@@ -724,10 +723,10 @@ all support for previous versions remove
+@@ -730,10 +728,10 @@ all support for previous versions remove
        </fileset>
        <fileset dir="${appjars.dir}" includes="**/cli/** **/naga/**" />
      </jar>
@@ -121,7 +118,7 @@
  
      <copy todir="build">
        <fileset dir=".">
-@@ -755,10 +754,10 @@ all support for previous versions remove
+@@ -761,10 +759,10 @@ all support for previous versions remove
        </fileset>
        <fileset dir="${appjars.dir}" includes="**/*"/>
      </jar>
@@ -134,7 +131,7 @@
    	<!--
      <jar destfile="ChimeToJmol.jar"
           manifest="manifest/chimetojmol.txt">
-@@ -799,7 +798,7 @@ all support for previous versions remove
+@@ -805,7 +803,7 @@ all support for previous versions remove
    
    <target name="applet-jar" id="applet-jar"
            depends="applet-classes">
@@ -143,7 +140,7 @@
      	<then><echo>Skipping applet-jar</echo></then><else>
  	
      <delete dir="build">
-@@ -807,7 +806,6 @@ all support for previous versions remove
+@@ -813,7 +811,6 @@ all support for previous versions remove
      </delete>
  
      <echo message="Creating JmolApplet.jar" />
@@ -151,7 +148,7 @@
  
      <jar destfile="build/JmolApplet.jar"
           manifest="manifest/appletMonolithic.txt" index="true" >
-@@ -1072,7 +1070,7 @@ all support for previous versions remove
+@@ -1078,7 +1075,7 @@ all support for previous versions remove
    </target>
  
    <target name="signed-applet" id="signed-applet" depends="applet-jar">
@@ -160,7 +157,7 @@
      	<then><echo>Skipping applet jar signing</echo></then><else>
  
    	<delete dir="build">
-@@ -1308,17 +1306,17 @@ all support for previous versions remove
+@@ -1314,17 +1311,17 @@ all support for previous versions remove
        	
        </indexjars>
      </jar>
@@ -181,7 +178,7 @@
      	<then><echo>Skipping smiles-applet-jar</echo></then><else>
    	
   <!-- JmolSmilesApplet.jar is skipped for now because it has no HTML5 equivalent
-@@ -1563,13 +1561,6 @@ all support for previous versions remove
+@@ -1568,13 +1565,6 @@ all support for previous versions remove
        </fileset>
      </copy>
  
@@ -195,7 +192,7 @@
      <tar tarfile="build/dist/jmolapisio-${version}.tar.gz"
           compression="gzip" >
        <tarfileset dir="build/dist"
-@@ -1846,7 +1837,7 @@ all support for previous versions remove
+@@ -1854,7 +1844,7 @@ all support for previous versions remove
      <mkdir dir="${test-classes.dir}"/>
      <javac srcdir="test" destdir="${test-classes.dir}"
             debug="off" deprecation="on"
diff --git a/jmol-javadoc.patch b/jmol-javadoc.patch
index c11b569..043f9c5 100644
--- a/jmol-javadoc.patch
+++ b/jmol-javadoc.patch
@@ -1,6 +1,6 @@
---- build.xml.orig	2020-11-20 15:29:39.481736582 -0700
-+++ build.xml	2020-11-20 15:29:51.112729404 -0700
-@@ -1677,7 +1677,7 @@ all support for previous versions remove
+--- build.xml.orig	2021-02-22 16:26:23.668470684 -0700
++++ build.xml	2021-02-22 16:26:47.252461598 -0700
+@@ -1683,7 +1683,7 @@ all support for previous versions remove
               packagenames="org.openscience.*,org.jmol.*"
               excludepackagenames="org.jmol.jcamp.*">
        <classpath refid="project.class.path" />
@@ -9,8 +9,8 @@
        <tag name="j2sIgnore" enabled="false" />
        <tag name="j2sIgnoreSuperConstructor" enabled="false" />
        <tag name="j2sOverride" enabled="false" />
---- src/org/jmol/adapter/readers/cif/CifReader.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/cif/CifReader.java	2020-11-20 15:29:51.156729376 -0700
+--- src/org/jmol/adapter/readers/cif/CifReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/cif/CifReader.java	2021-02-22 16:26:47.253461598 -0700
 @@ -727,7 +727,7 @@ public class CifReader extends AtomSetCo
  
    /**
@@ -20,7 +20,7 @@
     * 
     * @throws Exception
     */
-@@ -1855,7 +1855,7 @@ public class CifReader extends AtomSetCo
+@@ -1854,7 +1854,7 @@ public class CifReader extends AtomSetCo
     * uncertainty (dx) in the record. Note that this also "connects" the atoms
     * that might have been moved in a previous iteration.
     * 
@@ -29,8 +29,8 @@
     * atom.
     * 
     * Then create molecules.
---- src/org/jmol/adapter/readers/cif/MMCifReader.java.orig	2020-11-20 15:29:51.171729367 -0700
-+++ src/org/jmol/adapter/readers/cif/MMCifReader.java	2020-11-20 15:31:08.835681391 -0700
+--- src/org/jmol/adapter/readers/cif/MMCifReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/cif/MMCifReader.java	2021-02-22 16:26:47.254461598 -0700
 @@ -463,7 +463,7 @@ public class MMCifReader extends CifRead
    };
  
@@ -40,8 +40,8 @@
     * @return true
     * @throws Exception
     */
---- src/org/jmol/adapter/readers/cif/MSRdr.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/cif/MSRdr.java	2020-11-20 15:29:51.179729362 -0700
+--- src/org/jmol/adapter/readers/cif/MSRdr.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/cif/MSRdr.java	2021-02-22 16:26:47.254461598 -0700
 @@ -340,7 +340,7 @@ public class MSRdr implements MSInterfac
  
    /**
@@ -51,8 +51,8 @@
     * 
     */
    @Override
---- src/org/jmol/adapter/readers/molxyz/MolReader.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/molxyz/MolReader.java	2020-11-20 15:29:51.180729361 -0700
+--- src/org/jmol/adapter/readers/molxyz/MolReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/molxyz/MolReader.java	2021-02-22 16:26:47.255461597 -0700
 @@ -49,7 +49,7 @@ import org.jmol.util.Logger;
   * 
   * setAtomCoord(atom, x, y, z) applySymmetryAndSetTrajectory()
@@ -62,8 +62,8 @@
   * 
   * load "xxx.mol" FILTER "2D"
   * 
---- src/org/jmol/adapter/readers/molxyz/V3000Rdr.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/molxyz/V3000Rdr.java	2020-11-20 15:29:51.188729357 -0700
+--- src/org/jmol/adapter/readers/molxyz/V3000Rdr.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/molxyz/V3000Rdr.java	2021-02-22 16:26:47.255461597 -0700
 @@ -37,7 +37,7 @@ import org.jmol.adapter.smarter.AtomSetC
   * <p>
   * <a href='http://www.mdli.com/downloads/public/ctfile/ctfile.jsp'>
@@ -73,8 +73,8 @@
   */
  public class V3000Rdr {
    private MolReader mr;
---- src/org/jmol/adapter/readers/more/AFLOWReader.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/more/AFLOWReader.java	2020-11-20 15:29:51.188729357 -0700
+--- src/org/jmol/adapter/readers/more/AFLOWReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/more/AFLOWReader.java	2021-02-22 16:26:47.256461597 -0700
 @@ -22,7 +22,7 @@ import org.jmol.util.Logger;
   * 
   * or, in Jmol, from:
@@ -84,8 +84,8 @@
   * 
   * Unit cells are centered.
   * 
---- src/org/jmol/adapter/readers/more/JcampdxReader.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/more/JcampdxReader.java	2020-11-20 15:29:51.196729352 -0700
+--- src/org/jmol/adapter/readers/more/JcampdxReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/more/JcampdxReader.java	2021-02-22 16:26:47.257461597 -0700
 @@ -51,34 +51,33 @@ import org.jmol.viewer.JC;
   * 
   * specifications (by example here):
@@ -139,8 +139,8 @@
     * delete unreferenced n.m models
     */
    private void processPeakData() {
---- src/org/jmol/adapter/readers/more/MdTopReader.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/more/MdTopReader.java	2020-11-20 15:29:51.197729351 -0700
+--- src/org/jmol/adapter/readers/more/MdTopReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/more/MdTopReader.java	2021-02-22 16:26:47.257461597 -0700
 @@ -34,10 +34,6 @@ import org.jmol.util.Logger;
   * requires subsequent COORD "xxxx.mdcrd" file 
   * 
@@ -161,8 +161,8 @@
   */
  
  public class MdTopReader extends ForceFieldReader {
---- src/org/jmol/adapter/readers/more/Mol2Reader.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/more/Mol2Reader.java	2020-11-20 15:29:51.204729347 -0700
+--- src/org/jmol/adapter/readers/more/Mol2Reader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/more/Mol2Reader.java	2021-02-22 16:26:47.258461596 -0700
 @@ -34,7 +34,7 @@ import org.jmol.api.JmolAdapter;
  /**
   * A minimal multi-file reader for TRIPOS SYBYL mol2 files.
@@ -181,8 +181,8 @@
   */
  
  public class Mol2Reader extends ForceFieldReader {
---- src/org/jmol/adapter/readers/pdb/PdbReader.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/pdb/PdbReader.java	2020-11-20 15:29:51.205729346 -0700
+--- src/org/jmol/adapter/readers/pdb/PdbReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/pdb/PdbReader.java	2021-02-22 16:26:47.259461596 -0700
 @@ -63,7 +63,7 @@ import java.util.Map;
   * 
   * TLS Motion Determination:
@@ -192,8 +192,8 @@
   *    http://skuld.bmsc.washington.edu/~tlsmd
   *    
   * symmetry added by Bob Hanson:
---- src/org/jmol/adapter/readers/pymol/PickleReader.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/pymol/PickleReader.java	2020-11-20 15:29:51.213729341 -0700
+--- src/org/jmol/adapter/readers/pymol/PickleReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/pymol/PickleReader.java	2021-02-22 16:26:47.259461596 -0700
 @@ -21,7 +21,7 @@ import javajs.util.Lst;
   * 2013.04.06 -- added memo functions. PyMOL pickling is using LONG_BINPUT way too often. 
   * This results in a huge unnecessary memory overhead. My only solution is to only
@@ -203,8 +203,8 @@
   * atom generates several items.  
   * 
   * see http://www.picklingtools.com/
---- src/org/jmol/adapter/readers/pymol/PyMOL.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/pymol/PyMOL.java	2020-11-20 15:29:51.235729328 -0700
+--- src/org/jmol/adapter/readers/pymol/PyMOL.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/pymol/PyMOL.java	2021-02-22 16:26:47.261461595 -0700
 @@ -22,7 +22,7 @@ import org.jmol.util.Logger;
   *  with note therein:
   *  
@@ -214,8 +214,8 @@
   *       ( i[1], i[0], ( int( cmd.get_color_tuple(i[0])[0]*255 ), 
   *                       int( cmd.get_color_tuple(i[0])[1]*255 ), 
   *                       int(cmd.get_color_tuple(i[0])[2]*255 ) 
---- src/org/jmol/adapter/readers/pymol/PyMOLReader.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/pymol/PyMOLReader.java	2020-11-20 15:29:51.236729327 -0700
+--- src/org/jmol/adapter/readers/pymol/PyMOLReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/pymol/PyMOLReader.java	2021-02-22 16:26:47.262461595 -0700
 @@ -55,12 +55,12 @@ import javajs.util.V3;
   * development started Feb 2013 Jmol 13.1.13
   * reasonably full implementation May 2013 Jmol 13.1.16
@@ -233,8 +233,8 @@
   *
   * using set LOGFILE, we can dump this to a readable form.
   * 
---- src/org/jmol/adapter/readers/pymol/PyMOLScene.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/pymol/PyMOLScene.java	2020-11-20 15:29:51.309729282 -0700
+--- src/org/jmol/adapter/readers/pymol/PyMOLScene.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/pymol/PyMOLScene.java	2021-02-22 16:26:47.263461594 -0700
 @@ -846,7 +846,7 @@ class PyMOLScene implements JmolSceneGen
     * create all objects for a given molecule or scene
     * @param reps
@@ -244,8 +244,8 @@
     * @param ac
     */
    void createShapeObjects(BS[] reps, boolean allowSurface, int ac0,
---- src/org/jmol/adapter/readers/quantum/AdfReader.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/quantum/AdfReader.java	2020-11-20 15:29:51.327729271 -0700
+--- src/org/jmol/adapter/readers/quantum/AdfReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/quantum/AdfReader.java	2021-02-22 16:26:47.264461594 -0700
 @@ -42,24 +42,24 @@ import java.util.Map;
   * 
   * A reader for ADF output.
@@ -275,8 +275,8 @@
   *
   *
   * @author Bradley A. Smith (yeldar@home.com)
---- src/org/jmol/adapter/readers/quantum/BasisFunctionReader.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/quantum/BasisFunctionReader.java	2020-11-20 15:29:51.328729271 -0700
+--- src/org/jmol/adapter/readers/quantum/BasisFunctionReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/quantum/BasisFunctionReader.java	2021-02-22 16:26:47.264461594 -0700
 @@ -39,7 +39,7 @@ import java.util.Map;
  
  /**
@@ -286,8 +286,8 @@
   */
  public abstract class BasisFunctionReader extends AtomSetCollectionReader {
  
---- src/org/jmol/adapter/readers/quantum/CsfReader.java.orig	2020-11-18 17:45:15.000000000 -0700
-+++ src/org/jmol/adapter/readers/quantum/CsfReader.java	2020-11-20 15:29:51.338729264 -0700
+--- src/org/jmol/adapter/readers/quantum/CsfReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/quantum/CsfReader.java	2021-02-22 16:26:47.265461593 -0700
 @@ -47,7 +47,7 @@ import org.jmol.util.Logger;
   * streamlined CSF dataset reading capabilities 2007/04/09
   * 
@@ -297,8 +297,8 @@
   */
  public class CsfReader extends MopacSlaterReader {
  
---- src/org/jmol/adapter/readers/quantum/MoldenReader.java.orig	2020-11-18 17:45:16.000000000 -0700
-+++ src/org/jmol/adapter/readers/quantum/MoldenReader.java	2020-11-20 15:29:51.339729264 -0700
+--- src/org/jmol/adapter/readers/quantum/MoldenReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/quantum/MoldenReader.java	2021-02-22 16:26:47.266461593 -0700
 @@ -20,11 +20,11 @@ import org.jmol.util.Logger;
   * A molecular structure and orbital reader for MolDen files.
   * See http://www.cmbi.ru.nl/molden/molden_format.html
@@ -313,8 +313,8 @@
   */
  
  public class MoldenReader extends MopacSlaterReader {
---- src/org/jmol/adapter/readers/quantum/MopacGraphfReader.java.orig	2020-11-18 17:45:16.000000000 -0700
-+++ src/org/jmol/adapter/readers/quantum/MopacGraphfReader.java	2020-11-20 15:29:51.346729259 -0700
+--- src/org/jmol/adapter/readers/quantum/MopacGraphfReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/quantum/MopacGraphfReader.java	2021-02-22 16:26:47.266461593 -0700
 @@ -35,7 +35,7 @@ import org.jmol.adapter.smarter.Atom;
  /**
   * Reads Mopac 2007 GRAPHF output files
@@ -324,8 +324,8 @@
   * 
   */
  public class MopacGraphfReader extends MopacSlaterReader {
---- src/org/jmol/adapter/readers/quantum/MopacSlaterReader.java.orig	2020-11-18 17:45:16.000000000 -0700
-+++ src/org/jmol/adapter/readers/quantum/MopacSlaterReader.java	2020-11-20 15:29:51.347729259 -0700
+--- src/org/jmol/adapter/readers/quantum/MopacSlaterReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/quantum/MopacSlaterReader.java	2021-02-22 16:26:47.266461593 -0700
 @@ -25,7 +25,7 @@ package org.jmol.adapter.readers.quantum
  
  /**
@@ -335,8 +335,8 @@
   */
  abstract class MopacSlaterReader extends SlaterReader {
  
---- src/org/jmol/adapter/readers/quantum/QCJSONReader.java.orig	2020-11-18 17:45:16.000000000 -0700
-+++ src/org/jmol/adapter/readers/quantum/QCJSONReader.java	2020-11-20 15:29:51.355729254 -0700
+--- src/org/jmol/adapter/readers/quantum/QCJSONReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/quantum/QCJSONReader.java	2021-02-22 16:26:47.267461593 -0700
 @@ -18,11 +18,11 @@ import org.qcschema.QCSchemaUnits;
   * A molecular structure and orbital reader for MolDen files.
   * See http://www.cmbi.ru.nl/molden/molden_format.html
@@ -351,8 +351,8 @@
   */
  
  public class QCJSONReader extends MoldenReader {
---- src/org/jmol/adapter/readers/quantum/SlaterReader.java.orig	2020-11-18 17:45:16.000000000 -0700
-+++ src/org/jmol/adapter/readers/quantum/SlaterReader.java	2020-11-20 15:29:51.356729253 -0700
+--- src/org/jmol/adapter/readers/quantum/SlaterReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/quantum/SlaterReader.java	2021-02-22 16:26:47.268461592 -0700
 @@ -35,7 +35,7 @@ import java.util.Map;
  
  /**
@@ -373,8 +373,8 @@
     *    
     * @param iAtom now 1-based
     * @param a
---- src/org/jmol/adapter/readers/quantum/WebMOReader.java.orig	2020-11-18 17:45:16.000000000 -0700
-+++ src/org/jmol/adapter/readers/quantum/WebMOReader.java	2020-11-20 15:29:51.363729249 -0700
+--- src/org/jmol/adapter/readers/quantum/WebMOReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/quantum/WebMOReader.java	2021-02-22 16:26:47.268461592 -0700
 @@ -46,7 +46,7 @@ import org.jmol.util.Logger;
   * </a>
   * 
@@ -384,8 +384,8 @@
   */
  public class WebMOReader extends MopacSlaterReader {
  
---- src/org/jmol/adapter/readers/simple/GhemicalMMReader.java.orig	2020-11-18 17:45:16.000000000 -0700
-+++ src/org/jmol/adapter/readers/simple/GhemicalMMReader.java	2020-11-20 15:29:51.364729248 -0700
+--- src/org/jmol/adapter/readers/simple/GhemicalMMReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/simple/GhemicalMMReader.java	2021-02-22 16:26:47.269461592 -0700
 @@ -67,7 +67,7 @@ import org.jmol.api.JmolAdapter;
   * !End
   * </code>
@@ -395,8 +395,8 @@
   */
  public class GhemicalMMReader extends AtomSetCollectionReader {
      
---- src/org/jmol/adapter/readers/simple/HyperChemReader.java.orig	2020-11-18 17:45:16.000000000 -0700
-+++ src/org/jmol/adapter/readers/simple/HyperChemReader.java	2020-11-20 15:29:51.371729244 -0700
+--- src/org/jmol/adapter/readers/simple/HyperChemReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/simple/HyperChemReader.java	2021-02-22 16:26:47.269461592 -0700
 @@ -32,7 +32,7 @@ import org.jmol.api.JmolAdapter;
  /**
   * Support for .hin, HyperChem's native file format.
@@ -417,8 +417,8 @@
   */
  public class HyperChemReader extends AtomSetCollectionReader {
    
---- src/org/jmol/adapter/readers/simple/MopacReader.java.orig	2020-11-18 17:45:16.000000000 -0700
-+++ src/org/jmol/adapter/readers/simple/MopacReader.java	2020-11-20 15:29:51.387729234 -0700
+--- src/org/jmol/adapter/readers/simple/MopacReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/simple/MopacReader.java	2021-02-22 16:26:47.270461591 -0700
 @@ -34,7 +34,7 @@ import org.jmol.util.Logger;
  /**
   * Reads Mopac 93, 6, 7, 2002, or 2009 output files
@@ -428,8 +428,8 @@
   */
  public class MopacReader extends AtomSetCollectionReader {
      
---- src/org/jmol/adapter/readers/xtal/CrystalReader.java.orig	2020-11-18 17:45:16.000000000 -0700
-+++ src/org/jmol/adapter/readers/xtal/CrystalReader.java	2020-11-20 15:29:51.405729223 -0700
+--- src/org/jmol/adapter/readers/xtal/CrystalReader.java.orig	2021-02-05 17:54:49.000000000 -0700
++++ src/org/jmol/adapter/readers/xtal/CrystalReader.java	2021-02-22 16:26:47.271461591 -0700
 @@ -73,7 +73,7 @@ import org.jmol.util.Tensor;
   *          mat4CrystalToPrimitive M4 convenience inverse of
   *          mat4PrimitiveToCrystal
@@ -457,9 +457,9 @@
     * @throws Exception
     */
    private void readLatticeParams(boolean isPrimitive) throws Exception {
---- src/org/jmol/api/JmolViewer.java.orig	2020-11-18 17:45:16.000000000 -0700
-+++ src/org/jmol/api/JmolViewer.java	2020-11-20 15:29:51.418729215 -0700
-@@ -412,7 +412,7 @@ abstract public class JmolViewer {
+--- src/org/jmol/api/JmolViewer.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/api/JmolViewer.java	2021-02-22 16:26:47.271461591 -0700
+@@ -414,7 +414,7 @@ abstract public class JmolViewer {
     * NOTE: THIS METHOD DOES NOT PRESERVE THE STATE
     * 
     * @param arrayData a Vector of models, where each model is either a String
@@ -468,9 +468,9 @@
     * @param isAppend TRUE to append models (no ZAP)
     * @return null or error message
     */
---- src/org/jmol/awt/FileDropper.java.orig	2020-11-18 17:45:17.000000000 -0700
-+++ src/org/jmol/awt/FileDropper.java	2020-11-20 15:29:51.436729204 -0700
-@@ -59,7 +59,7 @@ import org.jmol.viewer.Viewer;
+--- src/org/jmol/awt/FileDropper.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/awt/FileDropper.java	2021-02-22 16:26:47.272461591 -0700
+@@ -55,7 +55,7 @@ import javajs.util.SB;
   * <p>
   * Note that multiple drops ARE thread safe.
   * 
@@ -479,9 +479,9 @@
   */
  public class FileDropper implements DropTargetListener {
    private String fd_oldFileName;
---- src/org/jmol/awtjs2d/Platform.java.orig	2020-11-18 17:45:17.000000000 -0700
-+++ src/org/jmol/awtjs2d/Platform.java	2020-11-20 15:29:51.437729203 -0700
-@@ -25,11 +25,11 @@ import javajs.util.SB;
+--- src/org/jmol/awtjs2d/Platform.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/awtjs2d/Platform.java	2021-02-22 16:26:47.272461591 -0700
+@@ -26,11 +26,11 @@ import javajs.util.SB;
  /**
   * JavaScript 2D canvas version requires Ajax-based URL stream processing.
   * 
@@ -498,8 +498,8 @@
   * (Not fully implemented) 
   * 
   * @author Bob Hanson
---- src/org/jmol/awtjs/swing/SwingController.java.orig	2020-11-18 17:45:17.000000000 -0700
-+++ src/org/jmol/awtjs/swing/SwingController.java	2020-11-20 15:29:51.444729199 -0700
+--- src/org/jmol/awtjs/swing/SwingController.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/awtjs/swing/SwingController.java	2021-02-22 16:26:47.273461590 -0700
 @@ -26,7 +26,7 @@ public interface SwingController {
     *   var component = Jmol.Swing.htDialogs[element.id];
     *   var info = component.toString();
@@ -509,8 +509,8 @@
     *     component.selected = element.checked;
     * var id = $("div.JDialog:has(#" + element.id + ")")[0].id
     * var dialog = Jmol.Swing.htDialogs[id];
---- src/org/jmol/bspt/Bspt.java.orig	2020-11-18 17:45:17.000000000 -0700
-+++ src/org/jmol/bspt/Bspt.java	2020-11-20 15:29:51.444729199 -0700
+--- src/org/jmol/bspt/Bspt.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/bspt/Bspt.java	2021-02-22 16:26:47.273461590 -0700
 @@ -46,13 +46,15 @@ import javajs.util.T3;
   * We are working with three dimensions. For the purposes of the Bspt code these
   * dimensions are stored as 0, 1, or 2. Each node of the tree splits along the
@@ -529,8 +529,8 @@
   * the right branch. If searchValue == splitValue then the search must proceed
   * down both branches.
   *</p>
---- src/org/jmol/bspt/PointIterator.java.orig	2020-11-18 17:45:17.000000000 -0700
-+++ src/org/jmol/bspt/PointIterator.java	2020-11-20 15:29:51.452729194 -0700
+--- src/org/jmol/bspt/PointIterator.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/bspt/PointIterator.java	2021-02-22 16:26:47.274461590 -0700
 @@ -39,7 +39,7 @@ public class PointIterator {
     * @param pt  if not null and pt.x == Float.NaN, this is an internal comparison, to return a "cleaned" list of points
     * @param ap3 the list of points, required
@@ -540,8 +540,8 @@
     * @return T.nada, T.string, T.array, T.list, T.point 
     */
    public static int withinDistPoints(float distance, P3 pt, P3[] ap3, P3[] ap31, Object[] ret) {
---- src/org/jmol/dssx/AnnotationParser.java.orig	2020-11-18 17:45:17.000000000 -0700
-+++ src/org/jmol/dssx/AnnotationParser.java	2020-11-20 15:29:51.472729181 -0700
+--- src/org/jmol/dssx/AnnotationParser.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/dssx/AnnotationParser.java	2021-02-22 16:26:47.274461590 -0700
 @@ -310,7 +310,7 @@ public class AnnotationParser implements
    }
  
@@ -551,8 +551,8 @@
     * data(float[]), modelIndex (Integer), isGroup (Boolean);
     * 
     */
---- src/org/jmol/dssx/DSSP.java.orig	2020-11-18 17:45:17.000000000 -0700
-+++ src/org/jmol/dssx/DSSP.java	2020-11-20 15:29:51.522729151 -0700
+--- src/org/jmol/dssx/DSSP.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/dssx/DSSP.java	2021-02-22 16:26:47.275461590 -0700
 @@ -363,9 +363,9 @@ public class DSSP {
     * the interatomic distance from A to B. In chemical units, r is in angstroms,
     * the dimensional factor f = 332, and E is in kcal/mol. We ... assign an H
@@ -578,8 +578,8 @@
     * one residue is indicated by "X." ... Residues bracketed by the hydrogen bond
     * are marked "T," unless they are part of an n-helix (defined below). 
     * 
---- src/org/jmol/i18n/Language.java.orig	2020-11-18 17:45:18.000000000 -0700
-+++ src/org/jmol/i18n/Language.java	2020-11-20 15:29:51.550729133 -0700
+--- src/org/jmol/i18n/Language.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/i18n/Language.java	2021-02-22 16:26:47.275461590 -0700
 @@ -135,7 +135,7 @@ public class Language {
     * @param nativeLanguage Language name in its own language (see ISO 639-1 for the values)
     * @param display True if this language has a good percentage of translations done
@@ -589,8 +589,8 @@
     */
    private Language(String code, String language, String nativeLanguage, boolean display) {
      this.code = code;
---- src/org/jmol/jvxl/api/VertexDataServer.java.orig	2020-11-18 17:45:18.000000000 -0700
-+++ src/org/jmol/jvxl/api/VertexDataServer.java	2020-11-20 15:29:51.569729122 -0700
+--- src/org/jmol/jvxl/api/VertexDataServer.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/jvxl/api/VertexDataServer.java	2021-02-22 16:26:47.276461589 -0700
 @@ -42,7 +42,7 @@ public interface VertexDataServer {
     * where fraction is generally calculated as:
     * 
@@ -600,48 +600,50 @@
     *  fraction = (-cutoff - valueA) / (valueB - valueA);
     *  
     *  This method is also used by MarchingCubes to deliver the appropriate
---- src/org/jmol/jvxl/data/JvxlCoder.java.orig	2020-11-18 17:45:18.000000000 -0700
-+++ src/org/jmol/jvxl/data/JvxlCoder.java	2020-11-20 15:29:51.585729112 -0700
-@@ -431,12 +431,12 @@ public class JvxlCoder {
- 
-   /**
-    * contour data are appended to a string buffer in the form of a 
--   * <jmolContourData count="[nContours]">
--   *   <jmolContour index="0" value="-0.033" color="[xff0000]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>
--   *   <jmolContour index="1" value=" 0.000" color="[xffff00]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>
--   *   <jmolContour index="2" value=" 0.033" color="[x00ffff]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>
-+   * &lt;jmolContourData count="[nContours]"&gt;
-+   *   &lt;jmolContour index="0" value="-0.033" color="[xff0000]" encoding="base90iff1" data="fractional data"&gt;triangle bitset data&lt;/jmolContour&gt;
-+   *   &lt;jmolContour index="1" value=" 0.000" color="[xffff00]" encoding="base90iff1" data="fractional data"&gt;triangle bitset data&lt;/jmolContour&gt;
-+   *   &lt;jmolContour index="2" value=" 0.033" color="[x00ffff]" encoding="base90iff1" data="fractional data"&gt;triangle bitset data&lt;/jmolContour&gt;
-    *   ...
--   * </jmolContourData>
-+   * &lt;/jmolContourData&gt;
-    * 
-    * One presumes an ordered set of triangles.
-    * The contour intersects these triangles along two edges or at two vertices. 
-@@ -672,7 +672,7 @@ public class JvxlCoder {
-    *    
-    *    ASCII:
-    *    -30       -20       -10         0       +10       +20       +30      
--   *    <=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|
-+   *    &lt;=&gt;?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|
-    *    
-    *    So the above sequence would simply be:
-    *    
-@@ -780,8 +780,8 @@ public class JvxlCoder {
-    * 
-    * The tag will indicate the minimum and maximum values:
-    * 
--   * <jvxlVertexData count="150" min="(15.218472, -28.304049, 34.71112)"
--   * max="(97.8228, 54.011948, 109.95208)" data="...."> </jvxlVertexData>
-+   * &lt;jvxlVertexData count="150" min="(15.218472, -28.304049, 34.71112)"
-+   * max="(97.8228, 54.011948, 109.95208)" data="...."&gt; &lt;/jvxlVertexData&gt;
-    * 
-    * The resultant string is really two strings of length nData where the first
-    * string lists the "high" part of the positions, and the second string lists
---- src/org/jmol/jvxl/data/VolumeData.java.orig	2020-11-18 17:45:18.000000000 -0700
-+++ src/org/jmol/jvxl/data/VolumeData.java	2020-11-20 15:29:51.603729101 -0700
+--- src/org/jmol/jvxl/data/JvxlCoder.java.orig	2021-02-22 16:26:47.277461589 -0700
++++ src/org/jmol/jvxl/data/JvxlCoder.java	2021-02-22 16:35:31.850218324 -0700
+@@ -449,12 +449,14 @@ public class JvxlCoder {
+ 
+   /**
+    * contour data are appended to a string buffer in the form of a 
+-   * <jmolContourData count="[nContours]">
+-   *   <jmolContour index="0" value="-0.033" color="[xff0000]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>
+-   *   <jmolContour index="1" value=" 0.000" color="[xffff00]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>
+-   *   <jmolContour index="2" value=" 0.033" color="[x00ffff]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>
++   * <pre>
++   * &lt;jmolContourData count="[nContours]"&gt;
++   *   &lt;jmolContour index="0" value="-0.033" color="[xff0000]" encoding="base90iff1" data="fractional data"&gt;triangle bitset data&lt;/jmolContour&gt;
++   *   &lt;jmolContour index="1" value=" 0.000" color="[xffff00]" encoding="base90iff1" data="fractional data"&gt;triangle bitset data&lt;/jmolContour&gt;
++   *   &lt;jmolContour index="2" value=" 0.033" color="[x00ffff]" encoding="base90iff1" data="fractional data"&gt;triangle bitset data&lt;/jmolContour&gt;
+    *   ...
+-   * </jmolContourData>
++   * &lt;/jmolContourData&gt;
++   * </pre>
+    * 
+    * One presumes an ordered set of triangles.
+    * The contour intersects these triangles along two edges or at two vertices. 
+@@ -690,7 +692,7 @@ public class JvxlCoder {
+    *    
+    *    ASCII:
+    *    -30       -20       -10         0       +10       +20       +30      
+-   *    <=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|
++   *    &lt;=&gt;?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|
+    *    
+    *    So the above sequence would simply be:
+    *    
+@@ -798,8 +800,8 @@ public class JvxlCoder {
+    * 
+    * The tag will indicate the minimum and maximum values:
+    * 
+-   * <jvxlVertexData count="150" min="(15.218472, -28.304049, 34.71112)"
+-   * max="(97.8228, 54.011948, 109.95208)" data="...."> </jvxlVertexData>
++   * &lt;jvxlVertexData count="150" min="(15.218472, -28.304049, 34.71112)"
++   * max="(97.8228, 54.011948, 109.95208)" data="...."&gt; &lt;/jvxlVertexData&gt;
+    * 
+    * The resultant string is really two strings of length nData where the first
+    * string lists the "high" part of the positions, and the second string lists
+--- src/org/jmol/jvxl/data/VolumeData.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/jvxl/data/VolumeData.java	2021-02-22 16:26:47.278461588 -0700
 @@ -428,7 +428,7 @@ public class VolumeData {
     * periodic grids should have val[0] == val[xMax]
     * 
@@ -651,8 +653,8 @@
     * 
     * @param x
     * @param xMax
---- src/org/jmol/jvxl/readers/BCifDensityReader.java.orig	2020-11-18 17:45:18.000000000 -0700
-+++ src/org/jmol/jvxl/readers/BCifDensityReader.java	2020-11-20 15:29:51.611729096 -0700
+--- src/org/jmol/jvxl/readers/BCifDensityReader.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/jvxl/readers/BCifDensityReader.java	2021-02-22 16:26:47.278461588 -0700
 @@ -45,7 +45,7 @@ import org.jmol.util.Logger;
   * Binary CIF density reader. See https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box, 
   * for example:
@@ -662,8 +664,8 @@
   *  
   * Reads a MessagePack file and extracts either 2Fo-Fc or Fo-Fc.
   *
---- src/org/jmol/jvxl/readers/CifDensityReader.java.orig	2020-11-18 17:45:18.000000000 -0700
-+++ src/org/jmol/jvxl/readers/CifDensityReader.java	2020-11-20 15:29:51.612729095 -0700
+--- src/org/jmol/jvxl/readers/CifDensityReader.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/jvxl/readers/CifDensityReader.java	2021-02-22 16:26:47.279461588 -0700
 @@ -36,7 +36,7 @@ import javajs.util.PT;
   * CIF density reader. See https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box, 
   * for example:
@@ -673,37 +675,37 @@
   *  
   * Extends BCifDensityReader just enough to handle nonbinary CIF data.
   *
---- src/org/jmol/jvxl/readers/JvxlXmlReader.java.orig	2020-11-18 17:45:18.000000000 -0700
-+++ src/org/jmol/jvxl/readers/JvxlXmlReader.java	2020-11-20 15:29:51.619729091 -0700
-@@ -735,7 +735,7 @@ public class JvxlXmlReader extends Volum
- 
-   /**
-    * retrieve Jvxl 2.0 format vertex/triangle/edge/color data found
--   * within <jvxlSurfaceData> element 
-+   * within &lt;jvxlSurfaceData&gt; element 
-    * 
-    * @throws Exception
-    */
-@@ -777,7 +777,7 @@ public class JvxlXmlReader extends Volum
-   }
- 
-   /**
--   * decode vertex data found within <jvxlVertexData> element as created by
-+   * decode vertex data found within &lt;jvxlVertexData&gt; element as created by
-    * jvxlEncodeVertexData (see above)
-    * 
-    * @param data
-@@ -842,7 +842,7 @@ public class JvxlXmlReader extends Volum
-   }
- 
-   /**
--   * decode triangle data found within <jvxlTriangleData> element as created
-+   * decode triangle data found within &lt;jvxlTriangleData&gt; element as created
-    * with jvxlEncodeTriangleData (see above)
-    * 
-    * @param tdata
---- src/org/jmol/jvxl/readers/KinemageReader.java.orig	2020-11-18 17:45:18.000000000 -0700
-+++ src/org/jmol/jvxl/readers/KinemageReader.java	2020-11-20 15:29:51.627729086 -0700
+--- src/org/jmol/jvxl/readers/JvxlXmlReader.java.orig	2021-02-22 16:26:47.280461588 -0700
++++ src/org/jmol/jvxl/readers/JvxlXmlReader.java	2021-02-22 16:36:38.761178291 -0700
+@@ -748,7 +748,7 @@ public class JvxlXmlReader extends Volum
+ 
+   /**
+    * retrieve Jvxl 2.0 format vertex/triangle/edge/color data found
+-   * within <jvxlSurfaceData> element 
++   * within &lt;jvxlSurfaceData&gt; element 
+    * 
+    * @throws Exception
+    */
+@@ -790,7 +790,7 @@ public class JvxlXmlReader extends Volum
+   }
+ 
+   /**
+-   * decode vertex data found within <jvxlVertexData> element as created by
++   * decode vertex data found within &lt;jvxlVertexData&gt; element as created by
+    * jvxlEncodeVertexData (see above)
+    * 
+    * @param data
+@@ -855,7 +855,7 @@ public class JvxlXmlReader extends Volum
+   }
+ 
+   /**
+-   * decode triangle data found within <jvxlTriangleData> element as created
++   * decode triangle data found within &lt;jvxlTriangleData&gt; element as created
+    * with jvxlEncodeTriangleData (see above)
+    * 
+    * @param tdata
+--- src/org/jmol/jvxl/readers/KinemageReader.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/jvxl/readers/KinemageReader.java	2021-02-22 16:26:47.280461588 -0700
 @@ -219,7 +219,7 @@ class KinemageReader extends PmeshReader
       */
  
@@ -713,8 +715,8 @@
       * so technically we are off by a smidgeon. But they are the
       * reference numbers, so we will use them inclusively instead.
       * 
---- src/org/jmol/minimize/forcefield/ForceFieldMMFF.java.orig	2020-11-18 17:45:18.000000000 -0700
-+++ src/org/jmol/minimize/forcefield/ForceFieldMMFF.java	2020-11-20 15:29:51.647729074 -0700
+--- src/org/jmol/minimize/forcefield/ForceFieldMMFF.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/minimize/forcefield/ForceFieldMMFF.java	2021-02-22 16:26:47.281461587 -0700
 @@ -64,7 +64,7 @@ import org.jmol.viewer.JmolAsyncExceptio
   *   
   *    T. A. Halgren; "Merck Molecular Force Field. V. Extension of MMFF94 
@@ -747,8 +749,8 @@
   *    T. A. Halgren; "MMFF VII. Characterization of MMFF94, MMFF94s, 
   *      and Other Widely Available Force Fields for Conformational Energies 
   *      and for Intermolecular-Interaction Energies and Geometries", 
---- src/org/jmol/minimize/Util.java.orig	2020-11-18 17:45:18.000000000 -0700
-+++ src/org/jmol/minimize/Util.java	2020-11-20 15:29:51.654729069 -0700
+--- src/org/jmol/minimize/Util.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/minimize/Util.java	2021-02-22 16:26:47.281461587 -0700
 @@ -119,7 +119,7 @@ public class Util {
  
    /**
@@ -758,8 +760,8 @@
     * highly distorted trigonal pyramidal situations 
     * 
     * @param a
---- src/org/jmol/modelkit/ModelKitPopup.java.orig	2020-11-18 17:45:19.000000000 -0700
-+++ src/org/jmol/modelkit/ModelKitPopup.java	2020-11-20 15:29:51.685729050 -0700
+--- src/org/jmol/modelkit/ModelKitPopup.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/modelkit/ModelKitPopup.java	2021-02-22 16:26:47.282461587 -0700
 @@ -1307,7 +1307,6 @@ abstract public class ModelKitPopup exte
     * 
     * @param pressed
@@ -768,8 +770,8 @@
     * @param countPlusIndices
     * @return true if handled here
     */
---- src/org/jmol/modelsetbio/AlphaPolymer.java.orig	2020-11-18 17:45:19.000000000 -0700
-+++ src/org/jmol/modelsetbio/AlphaPolymer.java	2020-11-20 15:29:51.746729013 -0700
+--- src/org/jmol/modelsetbio/AlphaPolymer.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/modelsetbio/AlphaPolymer.java	2021-02-22 16:26:47.282461587 -0700
 @@ -143,12 +143,13 @@ public class AlphaPolymer extends BioPol
    /////////////////////////////////////////////////////////////
    
@@ -788,8 +790,8 @@
     *<p>
     * <a
     * href='http://csb.stanford.edu/levitt/Levitt_JMB77_Secondary_structure.pdf'>
---- src/org/jmol/modelsetbio/AminoPolymer.java.orig	2020-11-18 17:45:19.000000000 -0700
-+++ src/org/jmol/modelsetbio/AminoPolymer.java	2020-11-20 15:29:51.761729003 -0700
+--- src/org/jmol/modelsetbio/AminoPolymer.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/modelsetbio/AminoPolymer.java	2021-02-22 16:26:47.282461587 -0700
 @@ -279,7 +279,7 @@ public class AminoPolymer extends AlphaP
     * checkDistances: 
     * 
@@ -799,8 +801,8 @@
     * is less than 3 Angstroms. Otherwise that's just too strange 
     * a hydrogen bond. (We get hydrogen bonds from i to i+2, for example)
     * 
---- src/org/jmol/modelsetbio/BioResolver.java.orig	2020-11-18 17:45:19.000000000 -0700
-+++ src/org/jmol/modelsetbio/BioResolver.java	2020-11-20 15:29:51.770728998 -0700
+--- src/org/jmol/modelsetbio/BioResolver.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/modelsetbio/BioResolver.java	2021-02-22 16:26:47.283461586 -0700
 @@ -1529,7 +1529,7 @@ public final class BioResolver implement
     * FF8060 - light tomato
     * 00FF7F - springgreen
@@ -810,8 +812,8 @@
     ****************************************************************/
  
    private final static int[] argbsChainAtom = {
---- src/org/jmol/modelsetbio/Monomer.java.orig	2020-11-18 17:45:19.000000000 -0700
-+++ src/org/jmol/modelsetbio/Monomer.java	2020-11-20 15:29:51.778728993 -0700
+--- src/org/jmol/modelsetbio/Monomer.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/modelsetbio/Monomer.java	2021-02-22 16:26:47.283461586 -0700
 @@ -55,7 +55,7 @@ import java.util.Map;
  public abstract class Monomer extends Group {
  
@@ -821,8 +823,8 @@
     */
  
    public Monomer() {  
---- src/org/jmol/modelset/Group.java.orig	2020-11-18 17:45:19.000000000 -0700
-+++ src/org/jmol/modelset/Group.java	2020-11-20 15:29:51.779728992 -0700
+--- src/org/jmol/modelset/Group.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/modelset/Group.java	2021-02-22 16:26:47.283461586 -0700
 @@ -92,7 +92,7 @@ public class Group implements Structure
  
  
@@ -832,8 +834,8 @@
     */
    public Group() {}
    
---- src/org/jmol/modelset/ModelLoader.java.orig	2020-11-18 17:45:19.000000000 -0700
-+++ src/org/jmol/modelset/ModelLoader.java	2020-11-20 15:29:51.791728985 -0700
+--- src/org/jmol/modelset/ModelLoader.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/modelset/ModelLoader.java	2021-02-22 16:26:47.284461586 -0700
 @@ -672,7 +672,7 @@ public final class ModelLoader {
     * file * 1000000 + modelInFile (1-based)
     * 
@@ -843,9 +845,9 @@
     * 
     * String modelNumberDotted
     * 
---- src/org/jmol/modelset/ModelSet.java.orig	2020-11-18 17:45:19.000000000 -0700
-+++ src/org/jmol/modelset/ModelSet.java	2020-11-20 15:29:51.813728971 -0700
-@@ -3800,7 +3800,7 @@ public class ModelSet extends BondCollec
+--- src/org/jmol/modelset/ModelSet.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/modelset/ModelSet.java	2021-02-22 16:26:47.285461586 -0700
+@@ -3723,7 +3723,7 @@ public class ModelSet extends BondCollec
     * 
     * @param pt point to invert around if not null
     * @param plane plane to invert across if not null
@@ -854,8 +856,8 @@
     * @param bsAtoms atoms to switch for the atom option
     */
    public void invertSelected(P3 pt, P4 plane, int iAtom, BS bsAtoms) {
---- src/org/jmol/multitouch/sparshui/TwoPointGesture.java.orig	2020-11-18 17:45:19.000000000 -0700
-+++ src/org/jmol/multitouch/sparshui/TwoPointGesture.java	2020-11-20 15:29:51.814728971 -0700
+--- src/org/jmol/multitouch/sparshui/TwoPointGesture.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/multitouch/sparshui/TwoPointGesture.java	2021-02-22 16:26:47.285461586 -0700
 @@ -29,8 +29,8 @@ import com.sparshui.server.TouchPoint;
   * 
   * v00 from pt(1,0) to pt(2,0)
@@ -879,8 +881,8 @@
   *    
   * Bob Hanson 12/13/2009
   * 
---- src/org/jmol/popup/JmolPopup.java.orig	2020-11-18 17:45:19.000000000 -0700
-+++ src/org/jmol/popup/JmolPopup.java	2020-11-20 15:29:51.815728970 -0700
+--- src/org/jmol/popup/JmolPopup.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/popup/JmolPopup.java	2021-02-22 16:26:47.286461585 -0700
 @@ -255,7 +255,7 @@ abstract public class JmolPopup extends
    }
  
@@ -890,8 +892,8 @@
     * 
     * @param item
     * 
---- src/org/jmol/quantum/NciCalculation.java.orig	2020-11-18 17:45:19.000000000 -0700
-+++ src/org/jmol/quantum/NciCalculation.java	2020-11-20 15:29:51.816728969 -0700
+--- src/org/jmol/quantum/NciCalculation.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/quantum/NciCalculation.java	2021-02-22 16:26:47.286461585 -0700
 @@ -362,7 +362,7 @@ public class NciCalculation extends Quan
     *  that are too far away to make a difference before we waste 
     *  time doing exponentiation.
@@ -901,8 +903,8 @@
     *  molecularity based on promolecular density. This is needed for 
     *  applying intra- and inter-molecular filters to SCF CUBE data.
     * 
---- src/org/jmol/quantum/NMRCalculation.java.orig	2020-11-18 17:45:19.000000000 -0700
-+++ src/org/jmol/quantum/NMRCalculation.java	2020-11-20 15:29:51.817728969 -0700
+--- src/org/jmol/quantum/NMRCalculation.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/quantum/NMRCalculation.java	2021-02-22 16:26:47.287461585 -0700
 @@ -314,7 +314,7 @@ public class NMRCalculation implements J
    /**
     * Creates the data set necessary for doing NMR calculations. Values are
@@ -912,8 +914,8 @@
     * 
     */
    @SuppressWarnings("resource")
---- src/org/jmol/quantum/NMRNoeMatrix.java.orig	2020-11-18 17:45:19.000000000 -0700
-+++ src/org/jmol/quantum/NMRNoeMatrix.java	2020-11-20 15:29:51.818728968 -0700
+--- src/org/jmol/quantum/NMRNoeMatrix.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/quantum/NMRNoeMatrix.java	2021-02-22 16:26:47.287461585 -0700
 @@ -87,7 +87,7 @@ import org.jmol.viewer.Viewer;
   * if the atoms have not been set up properly.
   * 
@@ -923,9 +925,9 @@
   */
  public class NMRNoeMatrix {
    
---- src/org/jmol/scriptext/MathExt.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/scriptext/MathExt.java	2020-11-20 15:29:51.826728963 -0700
-@@ -1711,7 +1711,7 @@ public class MathExt {
+--- src/org/jmol/scriptext/MathExt.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/scriptext/MathExt.java	2021-02-22 16:26:47.288461585 -0700
+@@ -1887,7 +1887,7 @@ public class MathExt {
     * _(key) prepends "auxiliaryInfo.models", delivering a modelCount-length
     * array of information
     * 
@@ -934,7 +936,7 @@
     * 
     * 
     * {atomset}._(key) selects for model Auxiliary info related to models of the
-@@ -1722,9 +1722,9 @@ public class MathExt {
+@@ -1898,9 +1898,9 @@ public class MathExt {
     * 
     * Examples:
     * 
@@ -946,7 +948,7 @@
     * 
     * @param mp
     * @param args
-@@ -1941,7 +1941,7 @@ public class MathExt {
+@@ -2121,7 +2121,7 @@ public class MathExt {
    }
  
    /**
@@ -955,8 +957,8 @@
     * 
     * @param listIn
     * @param formatList
---- src/org/jmol/script/ScriptCompiler.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/script/ScriptCompiler.java	2020-11-20 15:29:51.828728962 -0700
+--- src/org/jmol/script/ScriptCompiler.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/script/ScriptCompiler.java	2021-02-22 16:26:47.289461584 -0700
 @@ -1081,7 +1081,7 @@ public class ScriptCompiler extends Scri
     * 
     * Check for special parameters, including:
@@ -984,9 +986,9 @@
     *        characters not involving white space. echo, hover, message, and
     *        pause are odd-valued; no initial parsing of variables for them.
     * 
---- src/org/jmol/script/ScriptEval.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/script/ScriptEval.java	2020-11-20 15:29:51.832728960 -0700
-@@ -488,7 +488,7 @@ public class ScriptEval extends ScriptEx
+--- src/org/jmol/script/ScriptEval.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/script/ScriptEval.java	2021-02-22 16:26:47.290461584 -0700
+@@ -482,7 +482,7 @@ public class ScriptEval extends ScriptEx
     * program counter is incremented to skip the initiating statement, and all
     * parent contexts up the line are set with mustResumeEval = true.
     * 
@@ -995,9 +997,9 @@
     */
  
    @Override
---- src/org/jmol/script/ScriptParam.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/script/ScriptParam.java	2020-11-20 15:29:51.833728959 -0700
-@@ -1070,7 +1070,7 @@ abstract public class ScriptParam extend
+--- src/org/jmol/script/ScriptParam.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/script/ScriptParam.java	2021-02-22 16:26:47.290461584 -0700
+@@ -1062,7 +1062,7 @@ abstract public class ScriptParam extend
    }
  
    /**
@@ -1006,8 +1008,8 @@
     * + (m % 0x1F)
     * 
     * @param bondOrderInteger
---- src/org/jmol/shapebio/BioShape.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/shapebio/BioShape.java	2020-11-20 15:29:51.834728958 -0700
+--- src/org/jmol/shapebio/BioShape.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/shapebio/BioShape.java	2021-02-22 16:26:47.291461583 -0700
 @@ -120,32 +120,32 @@ public class BioShape extends AtomShape
     * <a href='http://www.rcsb.org/pdb/lists/pdb-l/200303/000609.html'>
     * http://www.rcsb.org/pdb/lists/pdb-l/200303/000609.html
@@ -1085,28 +1087,28 @@
     *
     * @param bFactor100
     * @return ?
---- src/org/jmol/shapespecial/Polyhedra.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/shapespecial/Polyhedra.java	2020-11-20 15:29:51.835728958 -0700
+--- src/org/jmol/shapespecial/Polyhedra.java.orig	2021-02-22 16:26:47.291461583 -0700
++++ src/org/jmol/shapespecial/Polyhedra.java	2021-02-22 16:37:40.418141391 -0700
 @@ -645,7 +645,7 @@ public class Polyhedra extends AtomShape
-   /**
-    * 
-    * @param id  may be null
--   * @param iatom  may be < 0 to (along with id==null) to get matching polyhedron 
-+   * @param iatom  may be &lt; 0 to (along with id==null) to get matching polyhedron 
-    * @param allowCollapsed
-    * @return Polyhedron or null
-    */
+   /**
+    * 
+    * @param id  may be null
+-   * @param iatom  may be < 0 to (along with id==null) to get matching polyhedron 
++   * @param iatom  may be &lt; 0 to (along with id==null) to get matching polyhedron 
+    * @param allowCollapsed
+    * @return Polyhedron or null
+    */
 @@ -1382,7 +1382,7 @@ public class Polyhedra extends AtomShape
-    * Objective is to find all triangles with *essentially* the same normal and to 
-    * then group them into a face. But we have to be careful here; not everything is 
-    * perfect. We can have be so slightly off in a 4- or 6-face, and we still want it
--   * to be called a face. We allow a normal dot product (i.e. cos(theta)) to be < 0.05.
-+   * to be called a face. We allow a normal dot product (i.e. cos(theta)) to be &lt; 0.05.
-    * This empirically seems to work.  
-    *  
-    * @param triangles
---- src/org/jmol/shapesurface/IsosurfaceMesh.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/shapesurface/IsosurfaceMesh.java	2020-11-20 15:29:51.836728957 -0700
+    * Objective is to find all triangles with *essentially* the same normal and to 
+    * then group them into a face. But we have to be careful here; not everything is 
+    * perfect. We can have be so slightly off in a 4- or 6-face, and we still want it
+-   * to be called a face. We allow a normal dot product (i.e. cos(theta)) to be < 0.05.
++   * to be called a face. We allow a normal dot product (i.e. cos(theta)) to be &lt; 0.05.
+    * This empirically seems to work.  
+    *  
+    * @param triangles
+--- src/org/jmol/shapesurface/IsosurfaceMesh.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/shapesurface/IsosurfaceMesh.java	2021-02-22 16:26:47.292461583 -0700
 @@ -77,7 +77,6 @@ public class IsosurfaceMesh extends Mesh
  
    /**
@@ -1148,251 +1150,251 @@
     * tested.
     * 
     * @param vertexValues
---- src/org/jmol/smiles/package.html.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/smiles/package.html	2020-11-20 15:29:51.837728956 -0700
+--- src/org/jmol/smiles/package.html.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/smiles/package.html	2021-02-22 16:26:47.292461583 -0700
 @@ -63,7 +63,7 @@ the term <a href="#aromaticity">aromatic
- 
- 
- <br><br>     
-- <h3>Comparision to <a target="_blank" href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">Daylight SMILES</a></h3>
-+ <h2>Comparision to <a target="_blank" href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">Daylight SMILES</a></h2>
-  All single-component aspects of Daylight SMILES are implemented, including
-     aromaticity and atom- and bond-based stereochemistry ("chirality").
- <br><br>     
+ 
+ 
+ <br><br>     
+- <h3>Comparision to <a target="_blank" href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">Daylight SMILES</a></h3>
++ <h2>Comparison to <a target="_blank" href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">Daylight SMILES</a></h2>
+  All single-component aspects of Daylight SMILES are implemented, including
+     aromaticity and atom- and bond-based stereochemistry ("chirality").
+ <br><br>     
 @@ -83,7 +83,8 @@ and may dramatically increase processing
- Jmol SMILES adds the following two aspects to Daylight SMILES:
- <br>
- <br>
--<table border="1" cellpadding="5" width="500">
-+<table border="1">
-+<caption>Daylight SMILES aspects</caption>
- <tr><td valign="top"><b>%(n)</b></td><td>Jmol SMILES adds unlimited branching. Daylight SMILES 
- allows indication of "rings" using the digits 1-9, for example, <b>C1CCCC1</b>. Actually, these numbers
- do not necessarily indicate rings. Rather, in association with "." component notation, 
+ Jmol SMILES adds the following two aspects to Daylight SMILES:
+ <br>
+ <br>
+-<table border="1" cellpadding="5" width="500">
++<table border="1">
++<caption>Daylight SMILES aspects</caption>
+ <tr><td valign="top"><b>%(n)</b></td><td>Jmol SMILES adds unlimited branching. Daylight SMILES 
+ allows indication of "rings" using the digits 1-9, for example, <b>C1CCCC1</b>. Actually, these numbers
+ do not necessarily indicate rings. Rather, in association with "." component notation, 
 @@ -136,7 +137,8 @@ the Jmol version used for its creation a
- Jmol bioSMILES adds the following to Jmol SMILES:
- <br>
- <br>
--<table border="1" cellpadding="5" width="500">
-+<table border="1">
-+<caption>bioSMILES additions</caption>
- <tr><td valign=top>~X~</td><td>
- Jmol bioSMILES separates all protein, nucleic, and carbohydrate polymers into separate SMILES components,
- separated by ".". 
+ Jmol bioSMILES adds the following to Jmol SMILES:
+ <br>
+ <br>
+-<table border="1" cellpadding="5" width="500">
++<table border="1">
++<caption>bioSMILES additions</caption>
+ <tr><td valign=top>~X~</td><td>
+ Jmol bioSMILES separates all protein, nucleic, and carbohydrate polymers into separate SMILES components,
+ separated by ".". 
 @@ -196,7 +198,7 @@ indicating a branched manose hexamer. No
- <br>
- 
- 
-- <h3>Comparision to <a target="_blank" href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">Daylight SMARTS</a></h3>
-+ <h2>Comparision to <a target="_blank" href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">Daylight SMARTS</a></h2>
- <ul>
- <li>[H1] interpreted as [*H1] -- "an atom with one connected H atom".
- 
+ <br>
+ 
+ 
+- <h3>Comparision to <a target="_blank" href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">Daylight SMARTS</a></h3>
++ <h2>Comparison to <a target="_blank" href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">Daylight SMARTS</a></h2>
+ <ul>
+ <li>[H1] interpreted as [*H1] -- "an atom with one connected H atom".
+ 
 @@ -227,7 +229,6 @@ Note that these variables are any string
- </pre>
-     Note that $(...) need not be within [...], and 
-     wherever it is, it always means "just the first atom".
--</li>
- 
- </li><li>All primitives that are not element names, <b>*</b>, <b>A</b>, or <b>a</b> must be 
-     enclosed in brackets. In addition, the following elements must be enclosed in brackets
+ </pre>
+     Note that $(...) need not be within [...], and 
+     wherever it is, it always means "just the first atom".
+-</li>
+ 
+ </li><li>All primitives that are not element names, <b>*</b>, <b>A</b>, or <b>a</b> must be 
+     enclosed in brackets. In addition, the following elements must be enclosed in brackets
 @@ -236,10 +237,10 @@ Note that these variables are any string
-     
- </li><li>Allows any order of bracketed primitives: [H2C13] same as [13CH2].
-  
--</li><li>All atom and bond logic implemented: [X,!X,X&X,X&X&X;X&X]-,=X
-+</li><li>All atom and bond logic implemented: [X,!X,X&amp;X,X&amp;X&amp;X;X&amp;X]-,=X
-  
--</li><li>"&" is optional: [13CH2] same as [13&C&H2]
--    except in cases of ambiguity with element symbols: [Rh] is rhodium, not [R&h].
-+</li><li>"&amp;" is optional: [13CH2] same as [13&amp;C&amp;H2]
-+    except in cases of ambiguity with element symbols: [Rh] is rhodium, not [R&amp;h].
-  
- </li><li>Jmol SMARTS does NOT implement:
- <ul><li> "zero-level parentheses", since the match is 
+     
+ </li><li>Allows any order of bracketed primitives: [H2C13] same as [13CH2].
+  
+-</li><li>All atom and bond logic implemented: [X,!X,X&X,X&X&X;X&X]-,=X
++</li><li>All atom and bond logic implemented: [X,!X,X&amp;X,X&amp;X&amp;X;X&amp;X]-,=X
+  
+-</li><li>"&" is optional: [13CH2] same as [13&C&H2]
+-    except in cases of ambiguity with element symbols: [Rh] is rhodium, not [R&h].
++</li><li>"&amp;" is optional: [13CH2] same as [13&amp;C&amp;H2]
++    except in cases of ambiguity with element symbols: [Rh] is rhodium, not [R&amp;h].
+  
+ </li><li>Jmol SMARTS does NOT implement:
+ <ul><li> "zero-level parentheses", since the match is 
 @@ -259,7 +260,8 @@ Note that these variables are any string
- <br><br>
- All Daylight SMARTS primitives are implemented. These include:
- <br>
--<table border="1" cellpadding="5" width="500">
-+<table border="1">
-+<caption>Daylight SMARTS primitives</caption>
- <tr><td>[Element]</td><td>capitalized - standard notation Na, Si, etc. -- specific non-aromatic atom</td></tr>
- <tr><td>[element]</td><td>uncapitalized - specific aromatic atom (as for standard notation, no limitations)</td></tr>
- <tr><td>*</td><td>any atom</td></tr>
+ <br><br>
+ All Daylight SMARTS primitives are implemented. These include:
+ <br>
+-<table border="1" cellpadding="5" width="500">
++<table border="1">
++<caption>Daylight SMARTS primitives</caption>
+ <tr><td>[Element]</td><td>capitalized - standard notation Na, Si, etc. -- specific non-aromatic atom</td></tr>
+ <tr><td>[element]</td><td>uncapitalized - specific aromatic atom (as for standard notation, no limitations)</td></tr>
+ <tr><td>*</td><td>any atom</td></tr>
 @@ -282,20 +284,21 @@ All Daylight SMARTS primitives are imple
- Jmol SMARTS adds the following primitives:
- <br>
- <br>
--<table border="1" cellpadding="5" width="800">
-+<table border="1">
-+<caption>SMARTS primitives</caption>
- <tr><td>d</td><td>non-hydrogen degree -- number of non-hydrogen connections</td></tr>
- <tr><td>=</td><td>Jmol atom index, for example: [=23]</td></tr>
- <tr><td>"xxx"</td><td>atom type, in double quotes, for example: ["39"r5] (After <b>calculate partialcharge</b> this will be the MMFF94 atom type. [Jmol 12.3.24]</td></tr>
--<tr><td>$(select xxx)"</td><td>external selection method. For Jmol, this is an atom expression. For example: [c$(select temperature>10)] [Jmol 12.3.26]</td></tr>
-+<tr><td>$(select xxx)"</td><td>external selection method. For Jmol, this is an atom expression. For example: [c$(select temperature&gt;10)] [Jmol 12.3.26]</td></tr>
- <tr><td>r500</td><td>a specifically aromatic 5-membered ring [Jmol 12.3.24]</td></tr>
- <tr><td>r600</td><td>a specifically aromatic 6-membered ring [Jmol 12.3.24]</td></tr>
- <tr><td>number?</td><td>mass number or undefined (so, for example, [C12?] means any carbon that isn't explicitly C13 or C14</td></tr>
- <tr><td>$n(pattern)</td><td>A specific number of occurances of <b>pattern</b>. For example, <b>C[$3(C=C)]C</b> is synonymous with <b>CC=CC=CC=CC</b>.</td></tr>
- <tr><td>$min-max(pattern)</td><td>A variable number of occurances of <b>pattern</b>. 
- For example: <b>A[$0-2(C:G)]A</b> is synonymous with <b>AA</b> or <b>AC(:G)A</b> or <b>AC(:G)C(:G)A</b>.</td></tr>
--<tr><td>residueName#resno^insCode.atomName#atomicNumber</b> </td><td>
-+<tr><td><b>residueName#resno^insCode.atomName#atomicNumber</b> </td><td>
- All five fields are optional; only the period itself is required.
--This primitive may appear with other primitives provided (a) it is first, and (b) it is followed by an operator ("," ,"&", or ";").
-+This primitive may appear with other primitives provided (a) it is first, and (b) it is followed by an operator ("," ,"&amp;", or ";").
- This allows searching a bioSMILES string using SMARTS patterns that only involve standard atom types. In the above example, 
- notice that the connecting atoms to protein chains within the non-bioSEQUENCE component indicates the
- connections to the protein using this extended notation. Thus, both the actual 3D model and the bioSMARTS string for 1d66
+ Jmol SMARTS adds the following primitives:
+ <br>
+ <br>
+-<table border="1" cellpadding="5" width="800">
++<table border="1">
++<caption>SMARTS primitives</caption>
+ <tr><td>d</td><td>non-hydrogen degree -- number of non-hydrogen connections</td></tr>
+ <tr><td>=</td><td>Jmol atom index, for example: [=23]</td></tr>
+ <tr><td>"xxx"</td><td>atom type, in double quotes, for example: ["39"r5] (After <b>calculate partialcharge</b> this will be the MMFF94 atom type. [Jmol 12.3.24]</td></tr>
+-<tr><td>$(select xxx)"</td><td>external selection method. For Jmol, this is an atom expression. For example: [c$(select temperature>10)] [Jmol 12.3.26]</td></tr>
++<tr><td>$(select xxx)"</td><td>external selection method. For Jmol, this is an atom expression. For example: [c$(select temperature&gt;10)] [Jmol 12.3.26]</td></tr>
+ <tr><td>r500</td><td>a specifically aromatic 5-membered ring [Jmol 12.3.24]</td></tr>
+ <tr><td>r600</td><td>a specifically aromatic 6-membered ring [Jmol 12.3.24]</td></tr>
+ <tr><td>number?</td><td>mass number or undefined (so, for example, [C12?] means any carbon that isn't explicitly C13 or C14</td></tr>
+ <tr><td>$n(pattern)</td><td>A specific number of occurances of <b>pattern</b>. For example, <b>C[$3(C=C)]C</b> is synonymous with <b>CC=CC=CC=CC</b>.</td></tr>
+ <tr><td>$min-max(pattern)</td><td>A variable number of occurances of <b>pattern</b>. 
+ For example: <b>A[$0-2(C:G)]A</b> is synonymous with <b>AA</b> or <b>AC(:G)A</b> or <b>AC(:G)C(:G)A</b>.</td></tr>
+-<tr><td>residueName#resno^insCode.atomName#atomicNumber</b> </td><td>
++<tr><td><b>residueName#resno^insCode.atomName#atomicNumber</b> </td><td>
+ All five fields are optional; only the period itself is required.
+-This primitive may appear with other primitives provided (a) it is first, and (b) it is followed by an operator ("," ,"&", or ";").
++This primitive may appear with other primitives provided (a) it is first, and (b) it is followed by an operator ("," ,"&amp;", or ";").
+ This allows searching a bioSMILES string using SMARTS patterns that only involve standard atom types. In the above example, 
+ notice that the connecting atoms to protein chains within the non-bioSEQUENCE component indicates the
+ connections to the protein using this extended notation. Thus, both the actual 3D model and the bioSMARTS string for 1d66
 @@ -312,7 +315,8 @@ the phosphorus atom in nucleic acids, or
- Jmol SMARTS adds the following in-line options:
- <br>
- <br>
--<table border="1" cellpadding="5" width="500">
-+<table border="1">
-+<caption>SMARTS in-line options</caption>
- <tr><td valign=top>
- /..../</td><td>
- <b>processing directives</b> Jmol recognizes <b>/..../</b> at the beginning of a pattern as processing directives.
+ Jmol SMARTS adds the following in-line options:
+ <br>
+ <br>
+-<table border="1" cellpadding="5" width="500">
++<table border="1">
++<caption>SMARTS in-line options</caption>
+ <tr><td valign=top>
+ /..../</td><td>
+ <b>processing directives</b> Jmol recognizes <b>/..../</b> at the beginning of a pattern as processing directives.
 @@ -322,7 +326,7 @@ These directives can be introduced indiv
- <b>invertStereo</b> reverses the sense of chirality (R-, S- stereochemistry). Double-bond stereochemistry is not reverse.  
- <b>noStereo</b> turns off all stereochemical checking.  
- </li><li><b>aromaticDouble</b> allows for using "=" between two aromatic atoms to indicate an explicitly double aromatic bond.
--To specify an explicitly single aromatic bond, use <b>@&!=</b>. 
-+To specify an explicitly single aromatic bond, use <b>{@literal @}&amp;!=</b>. 
- <b>aromaticStrict</b> uses a 6-electron Hueckel model for specifying aromaticity.
- </li><li><b>noAromatic</b> turns off all aromaticity checks.It may be desirable when no distinction between
- aromatic and nonaromatic atoms is desired. For large biomolecules /noAromatic/ can 
+ <b>invertStereo</b> reverses the sense of chirality (R-, S- stereochemistry). Double-bond stereochemistry is not reverse.  
+ <b>noStereo</b> turns off all stereochemical checking.  
+ </li><li><b>aromaticDouble</b> allows for using "=" between two aromatic atoms to indicate an explicitly double aromatic bond.
+-To specify an explicitly single aromatic bond, use <b>@&!=</b>. 
++	To specify an explicitly single aromatic bond, use <b>{@literal @}&amp;!=</b>. 
+ <b>aromaticStrict</b> uses a 6-electron Hueckel model for specifying aromaticity.
+ </li><li><b>noAromatic</b> turns off all aromaticity checks.It may be desirable when no distinction between
+ aromatic and nonaromatic atoms is desired. For large biomolecules /noAromatic/ can 
 @@ -419,7 +423,8 @@ in this case being equivalent to (and sl
- Jmol bioSMARTS adds the following pattern options to Jmol SMARTS:
- <br>
- <br>
--<table border="1" cellpadding="5" width="500">
-+<table border="1">
-+<caption>bioSMARTS pattern options</caption>
- <tr><td>
- <b>"~"</b> 
- </td><td>Any biopolymer.
+ Jmol bioSMARTS adds the following pattern options to Jmol SMARTS:
+ <br>
+ <br>
+-<table border="1" cellpadding="5" width="500">
++<table border="1">
++<caption>bioSMARTS pattern options</caption>
+ <tr><td>
+ <b>"~"</b> 
+ </td><td>Any biopolymer.
 @@ -497,7 +502,7 @@ includes:
-   
- 
- <br><br>     
--<a name="smilesspecs"><h3>Detailed Jmol SMILES/bioSMILES Specification</h3></a>
-+<h2><a id="smilesspecs">Detailed Jmol SMILES/bioSMILES Specification</a></h2>
- <br><br>
- <pre> 
-       # note: prior to parsing, all white space is removed
+   
+ 
+ <br><br>     
+-<a name="smilesspecs"><h3>Detailed Jmol SMILES/bioSMILES Specification</h3></a>
++<h2><a id="smilesspecs">Detailed Jmol SMILES/bioSMILES Specification</a></h2>
+ <br><br>
+ <pre> 
+       # note: prior to parsing, all white space is removed
 @@ -521,7 +526,7 @@ includes:
-                              | "[" [bracketedExpression] "]" }
-    
-    [unbracketedAtomType] == [atomType] 
--                                 & ! { "Ac" | "Ba" | "Ca" | "Na" | "Pa" | "Sc"
-+                                 &amp; ! { "Ac" | "Ba" | "Ca" | "Na" | "Pa" | "Sc"
-                                      | "ac" | "ba" | "ca" | "na" | "pa" | "sc" }
-       # note: Brackets are required for these elements: [Na], [Ca], etc.
-       #       These elements Xy are instead interpreted as "X" "y", a single-letter
+                              | "[" [bracketedExpression] "]" }
+    
+    [unbracketedAtomType] == [atomType] 
+-                                 & ! { "Ac" | "Ba" | "Ca" | "Na" | "Pa" | "Sc"
++                                 &amp; ! { "Ac" | "Ba" | "Ca" | "Na" | "Pa" | "Sc"
+                                      | "ac" | "ba" | "ca" | "na" | "pa" | "sc" }
+       # note: Brackets are required for these elements: [Na], [Ca], etc.
+       #       These elements Xy are instead interpreted as "X" "y", a single-letter
 @@ -558,7 +563,7 @@ includes:
-       #       and must be preceded by an atomExpression for the 
-       #       first occurance and either an atomExpression or a bond
-       #       for the second occurance
--      # note: Jmol bioSMARTS extends the possible number of rings to > 100 by 
-+      # note: Jmol bioSMARTS extends the possible number of rings to &gt; 100 by 
-       #       allowing %(n)
- 
-    [connections] == [connection] | NULL }
+       #       and must be preceded by an atomExpression for the 
+       #       first occurance and either an atomExpression or a bond
+       #       for the second occurance
+-      # note: Jmol bioSMARTS extends the possible number of rings to > 100 by 
++      # note: Jmol bioSMARTS extends the possible number of rings to &gt; 100 by 
+       #       allowing %(n)
+ 
+    [connections] == [connection] | NULL }
 @@ -590,7 +595,7 @@ includes:
- </pre>
- <br><br>
- 
--<a name="specs"><h3>Detailed Jmol SMARTS/Jmol bioSMARTS Specification</h3></a>
-+<h2><a id="specs">Detailed Jmol SMARTS/Jmol bioSMARTS Specification</a></h2>
- <br><br>
- <pre> 
- 
+ </pre>
+ <br><br>
+ 
+-<a name="specs"><h3>Detailed Jmol SMARTS/Jmol bioSMARTS Specification</h3></a>
++<h2><a id="specs">Detailed Jmol SMARTS/Jmol bioSMARTS Specification</a></h2>
+ <br><br>
+ <pre> 
+ 
 @@ -638,7 +643,7 @@ includes:
-    
-    
-    [unbracketedAtomType] == [atomType] 
--                                 & ! { "Ac" | "Ba" | "Ca" | "Na" | "Pa" | "Sc"
-+                                 &amp; ! { "Ac" | "Ba" | "Ca" | "Na" | "Pa" | "Sc"
-                                      | "ac" | "ba" | "ca" | "na" | "pa" | "sc" }
-       # note: Brackets are required for these elements: [Na], [Ca], etc.
-       #       These elements Xy are instead interpreted as "X" "y", a single-letter
+    
+    
+    [unbracketedAtomType] == [atomType] 
+-                                 & ! { "Ac" | "Ba" | "Ca" | "Na" | "Pa" | "Sc"
++                                 &amp; ! { "Ac" | "Ba" | "Ca" | "Na" | "Pa" | "Sc"
+                                      | "ac" | "ba" | "ca" | "na" | "pa" | "sc" }
+       # note: Brackets are required for these elements: [Na], [Ca], etc.
+       #       These elements Xy are instead interpreted as "X" "y", a single-letter
 @@ -653,21 +658,21 @@ includes:
-    [bracketedExpression] == "[" { [atomOrSet] | [atomOrSet] ";" [atomAndSet] } "]" 
-    
-    [atomOrSet] == { [atomAndSet] | [atomAndSet] "," [atomAndSet] }
--   [atomAndSet] == { [atomPrimitives] | [atomPrimitives] "&" [atomAndSet]
-+   [atomAndSet] == { [atomPrimitives] | [atomPrimitives] "&amp;" [atomAndSet]
-                               | "!" [atomPrimitive] 
--                              | "!" [atomPrimitive] "&" [atomAndSet] }
-+                              | "!" [atomPrimitive] "&amp;" [atomAndSet] }
-                               
-  ######## ATOM PRIMITIVES ########
- 
-    [atomPrimitives] == { [atomPrimitive] | [atomPrimitive] [atomPrimitives] }
--       # note -- if & is not used, certain combinations of primitiveDescritors
-+       # note -- if &amp; is not used, certain combinations of primitiveDescritors
-        #         are not allowed. Specifically, combinations that together
-        #         form the symbol for an element will be read as the element (Ar, Rh, etc.)
-        #         when NOT followed by a digit and no element has already been defined 
--       #         So, for example, [Ar] is argon, [Ar3] is [A&r3], [ORh] is [O&R&h],  
--       #         but [Ard2] is [Ar&d2] -- "argon with two non-hydrogen connections"
--       #         Also, "!" may not be use with implied "&". 
--       #         Thus, [!a], [!a&!h2], and [h2&!a] are all valid, but [!ah2] is invalid.             
-+       #         So, for example, [Ar] is argon, [Ar3] is [A&amp;r3], [ORh] is [O&amp;R&amp;h],  
-+       #         but [Ard2] is [Ar&amp;d2] -- "argon with two non-hydrogen connections"
-+       #         Also, "!" may not be use with implied "&amp;". 
-+       #         Thus, [!a], [!a&amp;!h2], and [h2&amp;!a] are all valid, but [!ah2] is invalid.             
-    [atomPrimitive] == { [isotope] | [atomType] | [charge] | [stereochemistry]
-                               | [a_Prop] | [A_Prop] | [D_Prop] | [H_Prop] | [h_Prop] 
-                               | [R_Prop] | [r_Prop] | [v_Prop] | [X_Prop]
+    [bracketedExpression] == "[" { [atomOrSet] | [atomOrSet] ";" [atomAndSet] } "]" 
+    
+    [atomOrSet] == { [atomAndSet] | [atomAndSet] "," [atomAndSet] }
+-   [atomAndSet] == { [atomPrimitives] | [atomPrimitives] "&" [atomAndSet]
++   [atomAndSet] == { [atomPrimitives] | [atomPrimitives] "&amp;" [atomAndSet]
+                               | "!" [atomPrimitive] 
+-                              | "!" [atomPrimitive] "&" [atomAndSet] }
++                              | "!" [atomPrimitive] "&amp;" [atomAndSet] }
+                               
+  ######## ATOM PRIMITIVES ########
+ 
+    [atomPrimitives] == { [atomPrimitive] | [atomPrimitive] [atomPrimitives] }
+-       # note -- if & is not used, certain combinations of primitiveDescritors
++       # note -- if &amp; is not used, certain combinations of primitiveDescriptors
+        #         are not allowed. Specifically, combinations that together
+        #         form the symbol for an element will be read as the element (Ar, Rh, etc.)
+        #         when NOT followed by a digit and no element has already been defined 
+-       #         So, for example, [Ar] is argon, [Ar3] is [A&r3], [ORh] is [O&R&h],  
+-       #         but [Ard2] is [Ar&d2] -- "argon with two non-hydrogen connections"
+-       #         Also, "!" may not be use with implied "&". 
+-       #         Thus, [!a], [!a&!h2], and [h2&!a] are all valid, but [!ah2] is invalid.             
++       #         So, for example, [Ar] is argon, [Ar3] is [A&amp;r3], [ORh] is [O&amp;R&amp;h],  
++       #         but [Ard2] is [Ar&amp;d2] -- "argon with two non-hydrogen connections"
++       #         Also, "!" may not be use with implied "&amp;". 
++       #         Thus, [!a], [!a&amp;!h2], and [h2&amp;!a] are all valid, but [!ah2] is invalid.             
+    [atomPrimitive] == { [isotope] | [atomType] | [charge] | [stereochemistry]
+                               | [a_Prop] | [A_Prop] | [D_Prop] | [H_Prop] | [h_Prop] 
+                               | [R_Prop] | [r_Prop] | [v_Prop] | [X_Prop]
 @@ -786,9 +791,9 @@ includes:
-    [bondExpression] == { [bondOrSet] | [bondOrSet] ";" [bondAndSet] } 
-    
-    [bondOrSet] == { [bondAndSet] | [bondAndSet] "," [bondAndSet] }
--   [bondAndSet] == { [bondPrimitives] | [bondPrimitives] "&" [bondAndSet]
-+   [bondAndSet] == { [bondPrimitives] | [bondPrimitives] "&amp;" [bondAndSet]
-                               | "!" [bondPrimitive] 
--                              | "!" [bondPrimitive] "&" [bondAndSet] }
-+                              | "!" [bondPrimitive] "&amp;" [bondAndSet] }
-                                               
-  ######## BOND PRIMITIVES ########
-                               
+    [bondExpression] == { [bondOrSet] | [bondOrSet] ";" [bondAndSet] } 
+    
+    [bondOrSet] == { [bondAndSet] | [bondAndSet] "," [bondAndSet] }
+-   [bondAndSet] == { [bondPrimitives] | [bondPrimitives] "&" [bondAndSet]
++   [bondAndSet] == { [bondPrimitives] | [bondPrimitives] "&amp;" [bondAndSet]
+                               | "!" [bondPrimitive] 
+-                              | "!" [bondPrimitive] "&" [bondAndSet] }
++                              | "!" [bondPrimitive] "&amp;" [bondAndSet] }
+                                               
+  ######## BOND PRIMITIVES ########
+                               
 @@ -797,9 +802,9 @@ includes:
-       # note: All bondExpressions are not valid. Stereochemistry should not 
-       #       be mixed with the others, as it represents a single bond always.
-       #       In addition, "." ("no bond") cannot be mixed with any bond type.
--      #       Nothing would be retrieved by "-&=", as a bond cannot be both single
-+      #       Nothing would be retrieved by "-&amp;=", as a bond cannot be both single
-       #       and double. However, "-@" is potentially very useful -- "ring single-bonds"
--      #       or "=&!@" -- "doubly-bonded atoms where the double bond is not in a ring"
-+      #       or "=&amp;!@" -- "doubly-bonded atoms where the double bond is not in a ring"
-       # note: Jmol will not match two totally independent molecular pieces. For example,
-       #       Jmol will not math [Na+].[Cl-]
-       # note: "+" indicates "adjacent biomolecular groups in a chain"
+       # note: All bondExpressions are not valid. Stereochemistry should not 
+       #       be mixed with the others, as it represents a single bond always.
+       #       In addition, "." ("no bond") cannot be mixed with any bond type.
+-      #       Nothing would be retrieved by "-&=", as a bond cannot be both single
++      #       Nothing would be retrieved by "-&amp;=", as a bond cannot be both single
+       #       and double. However, "-@" is potentially very useful -- "ring single-bonds"
+-      #       or "=&!@" -- "doubly-bonded atoms where the double bond is not in a ring"
++      #       or "=&amp;!@" -- "doubly-bonded atoms where the double bond is not in a ring"
+       # note: Jmol will not match two totally independent molecular pieces. For example,
+       #       Jmol will not math [Na+].[Cl-]
+       # note: "+" indicates "adjacent biomolecular groups in a chain"
 @@ -822,7 +827,7 @@ includes:
- </pre>
- <br><br>
- 
--<a name="aromaticity"><h3>Jmol SMILES and Jmol SMARTS Definition of "aromatic"</h3></a>
-+<h2><a id="aromaticity">Jmol SMILES and Jmol SMARTS Definition of "aromatic"</a></h2>
- 
- <br><br>
- 
+ </pre>
+ <br><br>
+ 
+-<a name="aromaticity"><h3>Jmol SMILES and Jmol SMARTS Definition of "aromatic"</h3></a>
++<h2><a id="aromaticity">Jmol SMILES and Jmol SMARTS Definition of "aromatic"</a></h2>
+ 
+ <br><br>
+ 
 @@ -878,7 +883,7 @@ assume a bonding scheme (PDB, GAUSSIAN,
-  <br>updated 8/26/2015: switch to HTML5; added measure option for multiple ranges 
-  <br>updated 5/21/2012: added $(select...)
-  <br>updated 5/13/2012: added /aromaticStrict/ and /aromaticDouble/ 
-- <br>updated 5/13/2012: added [&lt;atomType>] 
-+ <br>updated 5/13/2012: added [&lt;atomType&gt;] 
-  <br>updated 4/10/2012: fix for [$(...)n] and [$(...)min-max]
-  <br>original5/19/2010
-  <br><br>
---- src/org/jmol/smiles/SmilesAromatic.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/smiles/SmilesAromatic.java	2020-11-20 15:29:51.838728956 -0700
+  <br>updated 8/26/2015: switch to HTML5; added measure option for multiple ranges 
+  <br>updated 5/21/2012: added $(select...)
+  <br>updated 5/13/2012: added /aromaticStrict/ and /aromaticDouble/ 
+- <br>updated 5/13/2012: added [&lt;atomType>] 
++ <br>updated 5/13/2012: added [&lt;atomType&gt;] 
+  <br>updated 4/10/2012: fix for [$(...)n] and [$(...)min-max]
+  <br>original5/19/2010
+  <br><br>
+--- src/org/jmol/smiles/SmilesAromatic.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/smiles/SmilesAromatic.java	2021-02-22 16:26:47.292461583 -0700
 @@ -336,7 +336,7 @@ public class SmilesAromatic {
     * @param vMean
     * @param n
@@ -1402,8 +1404,8 @@
     */
    private final static boolean checkStandardDeviation(V3[] vNorms, V3 vMean,
                                                        int n, float cutoff) {
---- src/org/jmol/smiles/SmilesMatcher.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/smiles/SmilesMatcher.java	2020-11-20 15:29:51.839728955 -0700
+--- src/org/jmol/smiles/SmilesMatcher.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/smiles/SmilesMatcher.java	2021-02-22 16:26:47.293461583 -0700
 @@ -57,13 +57,13 @@ import org.jmol.viewer.JC;
   * 
   * Specification for this implementation can be found in package.html.
@@ -1420,8 +1422,8 @@
   * 
   * BitSet[] find  -- finds one or more occurances of a SMILES or SMARTS string within a SMILES string
   * 
---- src/org/jmol/smiles/SmilesParser.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/smiles/SmilesParser.java	2020-11-20 15:29:51.840728954 -0700
+--- src/org/jmol/smiles/SmilesParser.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/smiles/SmilesParser.java	2021-02-22 16:26:47.293461583 -0700
 @@ -119,7 +119,7 @@ public class SmilesParser {
     * 
     * @param pattern
@@ -1440,8 +1442,8 @@
     * @param isBranchAtom
     * @return New atom
     * @throws InvalidSmilesException
---- src/org/jmol/symmetry/CIPChirality.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/symmetry/CIPChirality.java	2020-11-20 15:29:51.841728954 -0700
+--- src/org/jmol/symmetry/CIPChirality.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/symmetry/CIPChirality.java	2021-02-22 16:26:47.293461583 -0700
 @@ -68,7 +68,7 @@ import org.jmol.viewer.JC;
   * 
   * - implemented in Java (Jmol) and JavaScript (JSmol)
@@ -1491,8 +1493,8 @@
       */
      private char auxChirality = '~';
  
---- src/org/jmol/symmetry/SpaceGroup.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/symmetry/SpaceGroup.java	2020-11-20 15:29:51.843728953 -0700
+--- src/org/jmol/symmetry/SpaceGroup.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/symmetry/SpaceGroup.java	2021-02-22 16:26:47.294461582 -0700
 @@ -162,7 +162,7 @@ class SpaceGroup {
    /**
     * 
@@ -1502,8 +1504,8 @@
     * @return a new SpaceGroup if successful or null
     */
    private static SpaceGroup createSGFromList(String name, Lst<?> data) {
---- src/org/jmol/symmetry/Symmetry.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/symmetry/Symmetry.java	2020-11-20 15:29:51.844728952 -0700
+--- src/org/jmol/symmetry/Symmetry.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/symmetry/Symmetry.java	2021-02-22 16:26:47.294461582 -0700
 @@ -166,8 +166,8 @@ public class Symmetry implements Symmetr
     * 
     * @param desiredSpaceGroupIndex
@@ -1515,8 +1517,8 @@
     * @return true if a known space group
     */
    @Override
---- src/org/jmol/symmetry/UnitCellIterator.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/symmetry/UnitCellIterator.java	2020-11-20 15:29:51.844728952 -0700
+--- src/org/jmol/symmetry/UnitCellIterator.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/symmetry/UnitCellIterator.java	2021-02-22 16:26:47.294461582 -0700
 @@ -44,7 +44,7 @@ public class UnitCellIterator implements
     * @param atoms
     * @param bsAtoms
@@ -1526,8 +1528,8 @@
     *        point
     * @return this
     */
---- src/org/jmol/thread/SpinThread.java.orig	2020-11-18 17:45:20.000000000 -0700
-+++ src/org/jmol/thread/SpinThread.java	2020-11-20 15:29:51.845728952 -0700
+--- src/org/jmol/thread/SpinThread.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/thread/SpinThread.java	2021-02-22 16:26:47.294461582 -0700
 @@ -101,8 +101,8 @@ public class SpinThread extends JmolThre
     * 
     * JavaScript:
@@ -1539,8 +1541,8 @@
     * run1(FINISH) and return
     * 
     */
---- src/org/jmol/util/BSUtil.java.orig	2020-11-18 17:45:21.000000000 -0700
-+++ src/org/jmol/util/BSUtil.java	2020-11-20 15:29:51.845728952 -0700
+--- src/org/jmol/util/BSUtil.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/util/BSUtil.java	2021-02-22 16:26:47.295461582 -0700
 @@ -110,8 +110,8 @@ final public class BSUtil {
     * For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if
     * a is not set, then add to a all set bits of b
@@ -1570,8 +1572,8 @@
     * 
     * @param bs
     * @param bsAdded
---- src/org/jmol/util/ColorEncoder.java.orig	2020-11-18 17:45:21.000000000 -0700
-+++ src/org/jmol/util/ColorEncoder.java	2020-11-20 15:29:51.851728948 -0700
+--- src/org/jmol/util/ColorEncoder.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/util/ColorEncoder.java	2021-02-22 16:26:47.295461582 -0700
 @@ -172,7 +172,7 @@ import javajs.util.P3;
     * @param name
     * @param scale  if null, then this is a reset.
@@ -1581,8 +1583,8 @@
     */
    private synchronized int makeColorScheme(String name, int[] scale,
                                                    boolean isOverloaded) {
---- src/org/jmol/util/CommandHistory.java.orig	2020-11-18 17:45:21.000000000 -0700
-+++ src/org/jmol/util/CommandHistory.java	2020-11-20 15:29:51.852728947 -0700
+--- src/org/jmol/util/CommandHistory.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/util/CommandHistory.java	2021-02-22 16:26:47.295461582 -0700
 @@ -169,9 +169,9 @@ final public class CommandHistory {
    /**
     * Options include:
@@ -1595,8 +1597,8 @@
     *   just clear                     -2
     *   clear and turn off; return ""   0
     *   clear and turn on; return ""    Integer.MIN_VALUE;  
---- src/org/jmol/util/Elements.java.orig	2020-11-18 17:45:21.000000000 -0700
-+++ src/org/jmol/util/Elements.java	2020-11-20 15:29:51.862728941 -0700
+--- src/org/jmol/util/Elements.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/util/Elements.java	2021-02-22 16:26:47.295461582 -0700
 @@ -883,7 +883,7 @@ public class Elements {
     * that contains the atomic number, the charge, and the radius in two
     * consecutive values, encoded as follows:
@@ -1606,8 +1608,8 @@
     * 
     * That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius
     * 
---- src/org/jmol/util/MeshCapper.java.orig	2020-11-18 17:45:21.000000000 -0700
-+++ src/org/jmol/util/MeshCapper.java	2020-11-20 15:29:51.866728938 -0700
+--- src/org/jmol/util/MeshCapper.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/util/MeshCapper.java	2021-02-22 16:26:47.295461582 -0700
 @@ -37,7 +37,7 @@ import javajs.util.V3;
   * - no push/pop stacks
   * 
@@ -1626,8 +1628,8 @@
     */
    private boolean checkWinding(CapVertex v0, CapVertex v1, CapVertex v2) {
      return (v1.x - v0.x) * (v2.y - v0.y) > (v1.y - v0.y) * (v2.x - v0.x);
---- src/org/jmol/util/Modulation.java.orig	2020-11-18 17:45:21.000000000 -0700
-+++ src/org/jmol/util/Modulation.java	2020-11-20 15:29:51.879728931 -0700
+--- src/org/jmol/util/Modulation.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/util/Modulation.java	2021-02-22 16:26:47.296461581 -0700
 @@ -305,7 +305,7 @@ public class Modulation {
    }
  
@@ -1637,8 +1639,8 @@
     * 
     * @param x4
     * @return true only if x4 is in the (possibly folded) range of left and right
---- src/org/jmol/util/Node.java.orig	2020-11-18 17:45:21.000000000 -0700
-+++ src/org/jmol/util/Node.java	2020-11-20 15:29:51.879728931 -0700
+--- src/org/jmol/util/Node.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/util/Node.java	2021-02-22 16:26:47.296461581 -0700
 @@ -73,7 +73,7 @@ public interface Node extends SimpleNode
    public int getModelIndex();
    public int getAtomNumber();
@@ -1648,8 +1650,8 @@
     * 
     * @return number of missing H atoms
     */
---- src/org/jmol/util/SimpleUnitCell.java.orig	2020-11-18 17:45:21.000000000 -0700
-+++ src/org/jmol/util/SimpleUnitCell.java	2020-11-20 15:29:51.901728917 -0700
+--- src/org/jmol/util/SimpleUnitCell.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/util/SimpleUnitCell.java	2021-02-22 16:26:47.296461581 -0700
 @@ -381,16 +381,16 @@ public class SimpleUnitCell {
    /**
     * Expanded cell notation:
@@ -1671,8 +1673,8 @@
     * @param kcode
     *        Generally the multiplier is just {ijk ijk scale}, but when we have
     *        1iiijjjkkk 1iiijjjkkk scale, floats lose kkk due to Java float
---- src/org/jmol/util/Tensor.java.orig	2020-11-18 17:45:21.000000000 -0700
-+++ src/org/jmol/util/Tensor.java	2020-11-20 15:29:51.912728910 -0700
+--- src/org/jmol/util/Tensor.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/util/Tensor.java	2021-02-22 16:26:47.296461581 -0700
 @@ -289,7 +289,7 @@ public class Tensor {
    /**
     * width of the signal; |e2 - e0|
@@ -1698,8 +1700,8 @@
     * 
     * which amounts to the same thing and is prettier. (Think about it!)
     * 
---- src/org/jmol/util/Vibration.java.orig	2020-11-18 17:45:21.000000000 -0700
-+++ src/org/jmol/util/Vibration.java	2020-11-20 15:29:51.913728909 -0700
+--- src/org/jmol/util/Vibration.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/util/Vibration.java	2021-02-22 16:26:47.296461581 -0700
 @@ -26,7 +26,7 @@ public class Vibration extends V3 {
   // public static final int TYPE_DISPLACEMENT = -3; // not used
  
@@ -1709,8 +1711,8 @@
     */
    public int modDim = TYPE_VIBRATION;
    public float modScale = Float.NaN; // modulation only
---- src/org/jmol/viewer/OutputManager.java.orig	2020-11-18 17:45:22.000000000 -0700
-+++ src/org/jmol/viewer/OutputManager.java	2020-11-20 15:29:51.931728899 -0700
+--- src/org/jmol/viewer/OutputManager.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/viewer/OutputManager.java	2021-02-22 16:26:47.296461581 -0700
 @@ -630,7 +630,7 @@ abstract class OutputManager {
     * jmolStatusListener interface
     * 
@@ -1720,8 +1722,8 @@
     *        JPG, etc.; text: String to output; bytes: byte[] or null if an
     *        image; scripts for scenes; quality: for JPG and PNG; width: image
     *        width; height: image height; fullPath: String[] return
---- src/org/jmol/viewer/TransformManager.java.orig	2020-11-18 17:45:22.000000000 -0700
-+++ src/org/jmol/viewer/TransformManager.java	2020-11-20 15:29:51.946728889 -0700
+--- src/org/jmol/viewer/TransformManager.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/viewer/TransformManager.java	2021-02-22 16:26:47.297461581 -0700
 @@ -2190,8 +2190,8 @@ public class TransformManager {
    }
  
@@ -1751,9 +1753,9 @@
     * 
     * @param seconds
     * @param x
---- src/org/jmol/viewer/Viewer.java.orig	2020-11-18 17:45:22.000000000 -0700
-+++ src/org/jmol/viewer/Viewer.java	2020-11-20 15:29:51.979728869 -0700
-@@ -721,9 +721,9 @@ public class Viewer extends JmolViewer i
+--- src/org/jmol/viewer/Viewer.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/jmol/viewer/Viewer.java	2021-02-22 16:26:47.297461581 -0700
+@@ -722,9 +722,9 @@ public class Viewer extends JmolViewer i
     * 
     * disables command threading
     * 
@@ -1765,7 +1767,7 @@
     */
  
    public boolean headless;
-@@ -3035,7 +3035,7 @@ public class Viewer extends JmolViewer i
+@@ -3040,7 +3040,7 @@ public class Viewer extends JmolViewer i
     * 
     *        data[1] -- string or float[] or float[][] or float[][][]
     * 
@@ -1774,7 +1776,7 @@
     * 
     *        data[3] -- arrayDepth 0(String),1(float[]),2(float[][]),3(float[][][]) or -1
     *        to indidate that it is set by data type
-@@ -3099,7 +3099,7 @@ public class Viewer extends JmolViewer i
+@@ -3104,7 +3104,7 @@ public class Viewer extends JmolViewer i
     * 
     *         data[1] -- string or float[] or float[][] or float[][][]
     * 
@@ -1783,7 +1785,7 @@
     * 
     *         data[3] -- arrayDepth
     *         0(String),1(float[]),2(float[][]),3(float[][][]) or -1 to indicate
-@@ -7890,7 +7890,7 @@ public class Viewer extends JmolViewer i
+@@ -7895,7 +7895,7 @@ public class Viewer extends JmolViewer i
    }
  
    /**
@@ -1792,7 +1794,7 @@
     * then this reads a full set of Double[][] in one function call. Otherwise it
     * reads the values using individual function calls, which each return Double.
     * 
-@@ -8112,8 +8112,8 @@ public class Viewer extends JmolViewer i
+@@ -8117,8 +8117,8 @@ public class Viewer extends JmolViewer i
    }
  
    /**
@@ -1803,7 +1805,7 @@
     * return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;
     * 
     * @param howFarBack
-@@ -8690,9 +8690,9 @@ public class Viewer extends JmolViewer i
+@@ -8695,9 +8695,9 @@ public class Viewer extends JmolViewer i
     * 
     * @param eval
     * @param steps
@@ -1815,7 +1817,7 @@
     * @param bsSelected
     * @param bsFixed
     * @param rangeFixed
-@@ -9434,10 +9434,10 @@ public class Viewer extends JmolViewer i
+@@ -9439,10 +9439,10 @@ public class Viewer extends JmolViewer i
     * 
     * 
     * @param id
@@ -1828,7 +1830,7 @@
     * 
     * @param isAssign
     *        from a file reader, not a select query
-@@ -9873,7 +9873,7 @@ public class Viewer extends JmolViewer i
+@@ -9878,7 +9878,7 @@ public class Viewer extends JmolViewer i
     * @param options
     *        if nonzero, a option, currently just T.offset, indicating that pt1
     *        is an {i j k} offset from cell 555
@@ -1837,8 +1839,8 @@
     */
    public Object getSymmetryInfo(int iatom, String xyz, int iOp, P3 pt1, P3 pt2,
                                  int type, String desc, float scaleFactor,
---- src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java.orig	2020-11-18 17:45:23.000000000 -0700
-+++ src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java	2020-11-20 15:29:52.001728855 -0700
+--- src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java.orig	2021-02-05 17:54:50.000000000 -0700
++++ src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java	2021-02-22 16:26:47.298461581 -0700
 @@ -173,7 +173,7 @@ import naga.packetwriter.RawPacketWriter
   *
   *   sync 30000 "backgrund blue"
diff --git a/jmol.spec b/jmol.spec
index 707953a..d58ab70 100644
--- a/jmol.spec
+++ b/jmol.spec
@@ -6,8 +6,8 @@
 # JDK in Fedora is JDK 11, we target that release.
 
 Name:           jmol
-Version:        14.31.18
-Release:        2%{?dist}
+Version:        14.31.31
+Release:        1%{?dist}
 Summary:        Java viewer for chemical structures in 3D
 
 # JSpecView, JMol, and Sparsh-UI are all LGPLv2+.
@@ -40,6 +40,7 @@ BuildRequires:  gettext
 BuildRequires:  java-devel
 BuildRequires:  java-javadoc
 BuildRequires:  javapackages-tools
+BuildRequires:  jni-inchi
 BuildRequires:  junit
 BuildRequires:  libxslt
 BuildRequires:  naga
@@ -50,6 +51,7 @@ Requires:       hicolor-icon-theme
 Requires:       java
 Requires:       javapackages-filesystem
 Requires:       javapackages-tools
+Requires:       jni-inchi
 Requires:       naga
 
 # The upstreams for JSpecView and JMol are the same.  The JSpecView site appears
@@ -123,6 +125,7 @@ rm doc/*.zip
 
 # Link the system jars
 build-jar-repository -p -s jars commons-cli junit naga-3_0
+ln -s %{_jnidir}/jni-inchi/jni-inchi.jar jars
 
 # Handle netscape.jar.  See the comment at the top of the spec file.
 sed -i '/netscape\.jar/d' build.xml
@@ -162,7 +165,7 @@ install -D -p -m 644 build/{Jmol{,Data,Lib},Jvxl}.jar \
         %{buildroot}%{_javadir}/%{name}
 
 # Install wrapper script
-%jpackage_script org.openscience.jmol.app.Jmol "" "" naga:commons-cli:jmol/Jmol %{name} 1
+%jpackage_script org.openscience.jmol.app.Jmol "" "" naga:commons-cli:jni-inchi/jni-inchi:jmol/Jmol %{name} 1
 
 # Install the icon
 install -D -p -m 644 %{SOURCE1} \
@@ -172,8 +175,8 @@ install -D -p -m 644 %{SOURCE1} \
 desktop-file-install --dir=%{buildroot}%{_datadir}/applications jmol.desktop
 
 # Javadoc files
-mkdir -p %{buildroot}%{_javadocdir}/%{name}
-cp -rp build/javadoc/* %{buildroot}%{_javadocdir}/%{name}
+mkdir -p %{buildroot}%{_javadocdir}
+cp -a build/doc %{buildroot}%{_javadocdir}/%{name}
 
 # Install the parts of jsmol needed by sagemath
 mkdir -p %{buildroot}%{_jsdir}/jsmol
@@ -220,6 +223,9 @@ cd ../..
 %license COPYRIGHT.txt LICENSE.txt
 
 %changelog
+* Mon Feb 22 2021 Jerry James <loganjerry@gmail.com> - 14.31.31-1
+- Version 14.31.31
+
 * Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 14.31.18-2
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
 
diff --git a/sources b/sources
index 9e08780..d41eeff 100644
--- a/sources
+++ b/sources
@@ -1,2 +1,2 @@
-SHA512 (Jmol-14.31.18-full.tar.gz) = 519cfe24620778982b1367b0ad1ce3cd72e64e5ba4bd824f6a22e044d3aca1ec63e10e029e29bdcdb49faa8683dbe56c9cf00549b55a514612d888af733e1a6f
+SHA512 (Jmol-14.31.31-full.tar.gz) = 2087729d7e1a72313930f83e5e0fb3a7e790e21f430b2587c4c770731b190b6835d93dc4eb400f3c67b1eb00644bd45050d12a171f8108779548e4cbb0993e49
 SHA512 (Jmol_icon13.svg) = 116b94f19e94e822cae9679d4eab7bab8841144b0cf85ba70de31cf59f3e6c82b478a5a38c4afe6c1c34f684667ce3c51fc0487df63673145060a34934fff785