diff --git a/jmol-java9.patch b/jmol-java9.patch index 63766f7..da28413 100644 --- a/jmol-java9.patch +++ b/jmol-java9.patch @@ -1,27 +1,27 @@ ---- src/javajs/util/DebugJS.java.orig 2020-09-26 11:17:38.000000000 -0600 -+++ src/javajs/util/DebugJS.java 2020-09-29 17:20:02.175710733 -0600 +--- src/javajs/util/DebugJS.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/javajs/util/DebugJS.java 2021-03-17 09:19:41.334232243 -0600 @@ -12,7 +12,7 @@ public class DebugJS { - * @param msg - * - */ -- public static void _(String msg) { -+ public static void x(String msg) { - /** - * @j2sNative - * ---- src/jspecview/api/JSVTreeNode.java.orig 2020-09-26 11:17:38.000000000 -0600 -+++ src/jspecview/api/JSVTreeNode.java 2020-09-29 17:20:02.176710733 -0600 + * @param msg + * + */ +- public static void _(String msg) { ++ public static void x(String msg) { + /** + * @j2sNative + * +--- src/jspecview/api/JSVTreeNode.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/jspecview/api/JSVTreeNode.java 2021-03-17 09:24:33.767864924 -0600 @@ -17,7 +17,7 @@ public interface JSVTreeNode { - - PanelNode getPanelNode(); - -- Enumeration children(); -+ Enumeration children(); - - int getIndex(); - ---- src/jspecview/common/JSViewer.java.orig 2020-09-26 11:17:38.000000000 -0600 -+++ src/jspecview/common/JSViewer.java 2020-09-29 17:20:02.177710733 -0600 + + PanelNode getPanelNode(); + +- Enumeration children(); ++ Enumeration children(); + + int getIndex(); + +--- src/jspecview/common/JSViewer.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/jspecview/common/JSViewer.java 2021-03-17 09:21:02.335130481 -0600 @@ -1507,14 +1507,14 @@ public class JSViewer implements Platfor JSVTreeNode rootNode = spectraTree.getRootNode(); String fileName = (source == null ? null : source.getFilePath()); @@ -41,67 +41,67 @@ toDelete.addLast(childNode); panelNodes.removeObj(childNode.getPanelNode()); } ---- src/jspecview/dialog/ViewsDialog.java.orig 2020-09-26 11:17:38.000000000 -0600 -+++ src/jspecview/dialog/ViewsDialog.java 2020-09-29 17:20:02.178710732 -0600 +--- src/jspecview/dialog/ViewsDialog.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/jspecview/dialog/ViewsDialog.java 2021-03-17 09:22:31.142018932 -0600 @@ -74,9 +74,9 @@ public class ViewsDialog extends JSVDial - } - - private void addCheckBoxes(JSVTreeNode rootNode, int level, boolean isViews) { -- Enumeration enume = rootNode.children(); -+ Enumeration enume = rootNode.children(); - while (enume.hasMoreElements()) { -- JSVTreeNode treeNode = enume.nextElement(); -+ JSVTreeNode treeNode = JSVTreeNode.class.cast(enume.nextElement()); - PanelNode node = treeNode.getPanelNode(); - if (node.isView != isViews) - continue; + } + + private void addCheckBoxes(JSVTreeNode rootNode, int level, boolean isViews) { +- Enumeration enume = rootNode.children(); ++ Enumeration enume = rootNode.children(); + while (enume.hasMoreElements()) { +- JSVTreeNode treeNode = enume.nextElement(); ++ JSVTreeNode treeNode = JSVTreeNode.class.cast(enume.nextElement()); + PanelNode node = treeNode.getPanelNode(); + if (node.isView != isViews) + continue; @@ -122,9 +122,9 @@ public class ViewsDialog extends JSVDial - node.getPanelNode().isSelected = true; - checking = false; - } -- Enumeration enume = node.children(); -+ Enumeration enume = node.children(); - while (enume.hasMoreElements()) { -- JSVTreeNode treeNode = enume.nextElement(); -+ JSVTreeNode treeNode = JSVTreeNode.class.cast(enume.nextElement()); - dialog.setSelected(checkBoxes.get(treeNode.getIndex()), isSelected); - treeNode.getPanelNode().isSelected = isSelected; - node.getPanelNode().isSelected = isSelected; ---- src/org/jmol/util/JmolAudio.java.orig 2020-09-26 11:17:40.000000000 -0600 -+++ src/org/jmol/util/JmolAudio.java 2020-09-29 17:20:02.179710733 -0600 + node.getPanelNode().isSelected = true; + checking = false; + } +- Enumeration enume = node.children(); ++ Enumeration enume = node.children(); + while (enume.hasMoreElements()) { +- JSVTreeNode treeNode = enume.nextElement(); ++ JSVTreeNode treeNode = JSVTreeNode.class.cast(enume.nextElement()); + dialog.setSelected(checkBoxes.get(treeNode.getIndex()), isSelected); + treeNode.getPanelNode().isSelected = isSelected; + node.getPanelNode().isSelected = isSelected; +--- src/org/jmol/util/JmolAudio.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/util/JmolAudio.java 2021-03-17 09:23:58.925908678 -0600 @@ -23,6 +23,8 @@ - */ - package org.jmol.util; - -+import java.io.ByteArrayInputStream; -+ - import java.util.Map; - - import javajs.J2SIgnoreImport; + */ + package org.jmol.util; + ++import java.io.ByteArrayInputStream; ++ + import java.util.Map; + + import javajs.J2SIgnoreImport; @@ -39,14 +41,11 @@ import javax.sound.sampled.Clip; - import javax.sound.sampled.Line; - import javax.sound.sampled.LineEvent; - import javax.sound.sampled.LineListener; --import sun.audio.AudioData; --import sun.audio.AudioDataStream; - - @J2SIgnoreImport({ javax.sound.sampled.AudioInputStream.class, - javax.sound.sampled.AudioSystem.class, javax.sound.sampled.Clip.class, - javax.sound.sampled.Line.class, javax.sound.sampled.LineEvent.class, -- javax.sound.sampled.LineListener.class, sun.audio.AudioData.class, -- sun.audio.AudioDataStream.class }) -+ javax.sound.sampled.LineListener.class }) - public class JmolAudio implements javax.sound.sampled.LineListener, JmolAudioPlayer { - - public JmolAudio() { + import javax.sound.sampled.Line; + import javax.sound.sampled.LineEvent; + import javax.sound.sampled.LineListener; +-import sun.audio.AudioData; +-import sun.audio.AudioDataStream; + + @J2SIgnoreImport({ javax.sound.sampled.AudioInputStream.class, + javax.sound.sampled.AudioSystem.class, javax.sound.sampled.Clip.class, + javax.sound.sampled.Line.class, javax.sound.sampled.LineEvent.class, +- javax.sound.sampled.LineListener.class, sun.audio.AudioData.class, +- sun.audio.AudioDataStream.class }) ++ javax.sound.sampled.LineListener.class }) + public class JmolAudio implements javax.sound.sampled.LineListener, JmolAudioPlayer { + + public JmolAudio() { @@ -114,8 +113,8 @@ public class JmolAudio implements javax. - } - myClip = (Clip) AudioSystem.getLine(new Line.Info(Clip.class)); - myClip.addLineListener(this); -- AudioInputStream ais = AudioSystem.getAudioInputStream(new AudioDataStream( -- new AudioData((byte[]) data))); -+ AudioInputStream ais = AudioSystem.getAudioInputStream( -+ new ByteArrayInputStream((byte[]) data)); - myClip.open(ais); - } - + } + myClip = (Clip) AudioSystem.getLine(new Line.Info(Clip.class)); + myClip.addLineListener(this); +- AudioInputStream ais = AudioSystem.getAudioInputStream(new AudioDataStream( +- new AudioData((byte[]) data))); ++ AudioInputStream ais = AudioSystem.getAudioInputStream( ++ new ByteArrayInputStream((byte[]) data)); + myClip.open(ais); + } + diff --git a/jmol-javadoc.patch b/jmol-javadoc.patch index 043f9c5..ddbc308 100644 --- a/jmol-javadoc.patch +++ b/jmol-javadoc.patch @@ -1,36 +1,25 @@ ---- 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.*"> - -- -+ - - - ---- 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 +--- src/org/jmol/adapter/readers/cif/CifReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/cif/CifReader.java 2021-03-17 09:35:59.148003859 -0600 @@ -727,7 +727,7 @@ public class CifReader extends AtomSetCo - - /** - * -- * the PDB transformation matrix cartesian --> fractional -+ * the PDB transformation matrix cartesian → fractional - * - * @throws Exception - */ + + /** + * +- * the PDB transformation matrix cartesian --> fractional ++ * the PDB transformation matrix cartesian → fractional + * + * @throws Exception + */ @@ -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. - * -- * Also connect H atoms based on a distance <= 1.1 Angstrom from a nearby -+ * Also connect H atoms based on a distance ≤ 1.1 Angstrom from a nearby - * atom. - * - * Then create molecules. ---- 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 + * uncertainty (dx) in the record. Note that this also "connects" the atoms + * that might have been moved in a previous iteration. + * +- * Also connect H atoms based on a distance <= 1.1 Angstrom from a nearby ++ * Also connect H atoms based on a distance ≤ 1.1 Angstrom from a nearby + * atom. + * + * Then create molecules. +--- src/org/jmol/adapter/readers/cif/MMCifReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/cif/MMCifReader.java 2021-03-17 09:35:59.149003858 -0600 @@ -463,7 +463,7 @@ public class MMCifReader extends CifRead }; @@ -40,8 +29,8 @@ * @return true * @throws Exception */ ---- 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 +--- src/org/jmol/adapter/readers/cif/MSRdr.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/cif/MSRdr.java 2021-03-17 09:35:59.149003858 -0600 @@ -340,7 +340,7 @@ public class MSRdr implements MSInterfac /** @@ -51,8 +40,8 @@ * */ @Override ---- 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 +--- src/org/jmol/adapter/readers/molxyz/MolReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/molxyz/MolReader.java 2021-03-17 09:35:59.150003856 -0600 @@ -49,7 +49,7 @@ import org.jmol.util.Logger; * * setAtomCoord(atom, x, y, z) applySymmetryAndSetTrajectory() @@ -62,138 +51,138 @@ * * load "xxx.mol" FILTER "2D" * ---- 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 +--- src/org/jmol/adapter/readers/molxyz/V3000Rdr.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/molxyz/V3000Rdr.java 2021-03-17 09:35:59.150003856 -0600 @@ -37,7 +37,7 @@ import org.jmol.adapter.smarter.AtomSetC - *

- * - * http://www.mdli.com/downloads/public/ctfile/ctfile.jsp -- *

-+ *

- */ - public class V3000Rdr { - private MolReader mr; ---- 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 + *

+ * + * http://www.mdli.com/downloads/public/ctfile/ctfile.jsp +- *

++ *

+ */ + public class V3000Rdr { + private MolReader mr; +--- src/org/jmol/adapter/readers/more/AFLOWReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/more/AFLOWReader.java 2021-03-17 09:35:59.151003855 -0600 @@ -22,7 +22,7 @@ import org.jmol.util.Logger; - * - * or, in Jmol, from: - * -- * print load("http://aflowlib.mems.duke.edu/php/apool.php?POST?job=awrapper_apool&lattice=all&alloy=AgAu") -+ * print load("http://aflowlib.mems.duke.edu/php/apool.php?POST?job=awrapper_apool&lattice=all&alloy=AgAu") - * - * Unit cells are centered. - * ---- 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 + * + * or, in Jmol, from: + * +- * print load("http://aflowlib.mems.duke.edu/php/apool.php?POST?job=awrapper_apool&lattice=all&alloy=AgAu") ++ * print load("http://aflowlib.mems.duke.edu/php/apool.php?POST?job=awrapper_apool&lattice=all&alloy=AgAu") + * + * Unit cells are centered. + * +--- src/org/jmol/adapter/readers/more/JcampdxReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/more/JcampdxReader.java 2021-03-17 09:35:59.152003853 -0600 @@ -51,34 +51,33 @@ import org.jmol.viewer.JC; - * - * specifications (by example here): - * -- * ##$MODELS= acetophenone -+ * ##$MODELS= <Models> <ModelData id="acetophenone" type="MOL"> acetophenone - * DSViewer 3D 0 - * -- * 17 17 0 0 0 0 0 0 0 0999 V2000 ... 17 14 1 0 0 0 M END -- * 17 1 Energy: -1454.38826 Freq: 3199.35852 C -1.693100 -- * 0.007800 0.000000 -0.000980 0.000120 0.000000 ... -+ * 17 17 0 0 0 0 0 0 0 0999 V2000 ... 17 14 1 0 0 0 M END </ModelData> -+ * <ModelData id="irvibs" type="XYZVIB" baseModel="acetophenone" -+ * vibrationScale="0.1"> 17 1 Energy: -1454.38826 Freq: 3199.35852 C -1.693100 -+ * 0.007800 0.000000 -0.000980 0.000120 0.000000 ... </ModelData> </Models> - * - * -- All XML data should be line-oriented in the above fashion. Leading spaces -- * will be ignored. -- Any number of segments can be present -- The -+ * will be ignored. -- Any number of <ModelData> segments can be present -- The - * first model is referred to as the "base" model -- The base model: -- will - * generally be of type MOL, but any known type is acceptable -- will be used to - * generate bonding for later models that have no bonding information -- will be - * the only model for NMR -- Additional models can represent vibrations (XYZ - * format) or MS fragmentation (MOL format, probably) - * -- * ##$PEAKS= ... -+ * /> ... </Peaks> - * - * -- peak record must be a single line of information because Jmol will use - * line.trim() as a key to pass information to JSpecView. - * - * -- *

- */ - - public class JcampdxReader extends MolReader implements JmolJDXMOLReader { + * + * specifications (by example here): + * +- * ##$MODELS= acetophenone ++ * ##$MODELS= <Models> <ModelData id="acetophenone" type="MOL"> acetophenone + * DSViewer 3D 0 + * +- * 17 17 0 0 0 0 0 0 0 0999 V2000 ... 17 14 1 0 0 0 M END +- * 17 1 Energy: -1454.38826 Freq: 3199.35852 C -1.693100 +- * 0.007800 0.000000 -0.000980 0.000120 0.000000 ... ++ * 17 17 0 0 0 0 0 0 0 0999 V2000 ... 17 14 1 0 0 0 M END </ModelData> ++ * <ModelData id="irvibs" type="XYZVIB" baseModel="acetophenone" ++ * vibrationScale="0.1"> 17 1 Energy: -1454.38826 Freq: 3199.35852 C -1.693100 ++ * 0.007800 0.000000 -0.000980 0.000120 0.000000 ... </ModelData> </Models> + * + * -- All XML data should be line-oriented in the above fashion. Leading spaces +- * will be ignored. -- Any number of segments can be present -- The ++ * will be ignored. -- Any number of <ModelData> segments can be present -- The + * first model is referred to as the "base" model -- The base model: -- will + * generally be of type MOL, but any known type is acceptable -- will be used to + * generate bonding for later models that have no bonding information -- will be + * the only model for NMR -- Additional models can represent vibrations (XYZ + * format) or MS fragmentation (MOL format, probably) + * +- * ##$PEAKS= ... ++ * /> ... </Peaks> + * + * -- peak record must be a single line of information because Jmol will use + * line.trim() as a key to pass information to JSpecView. + * + * +- *

+ */ + + public class JcampdxReader extends MolReader implements JmolJDXMOLReader { @@ -311,7 +310,7 @@ public class JcampdxReader extends MolRe - } - - /** -- * integrate the records into the associated models, and -+ * integrate the <PeakAssignment> records into the associated models, and - * delete unreferenced n.m models - */ - private void processPeakData() { ---- 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 + } + + /** +- * integrate the records into the associated models, and ++ * integrate the <PeakAssignment> records into the associated models, and + * delete unreferenced n.m models + */ + private void processPeakData() { +--- src/org/jmol/adapter/readers/more/MdTopReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/more/MdTopReader.java 2021-03-17 09:35:59.152003853 -0600 @@ -34,10 +34,6 @@ import org.jmol.util.Logger; - * requires subsequent COORD "xxxx.mdcrd" file - * - *

-- * -- * -- * -- * - * PDB note: - * - * Note that topology format does not include chain designations, + * requires subsequent COORD "xxxx.mdcrd" file + * + *

+- * +- * +- * +- * + * PDB note: + * + * Note that topology format does not include chain designations, @@ -49,7 +45,7 @@ import org.jmol.util.Logger; - * In principal we could use average atomic mass. - * - * -- *

-+ *

- */ - - public class MdTopReader extends ForceFieldReader { ---- 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 + * In principal we could use average atomic mass. + * + * +- *

++ *

+ */ + + public class MdTopReader extends ForceFieldReader { +--- src/org/jmol/adapter/readers/more/Mol2Reader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/more/Mol2Reader.java 2021-03-17 09:35:59.153003853 -0600 @@ -34,7 +34,7 @@ import org.jmol.api.JmolAdapter; - /** - * A minimal multi-file reader for TRIPOS SYBYL mol2 files. - *

-- * -+ * - * http://www.tripos.com/data/support/mol2.pdf - * - * + /** + * A minimal multi-file reader for TRIPOS SYBYL mol2 files. + *

+- * ++ * + * http://www.tripos.com/data/support/mol2.pdf + * + * @@ -48,7 +48,7 @@ import org.jmol.api.JmolAdapter; - * - * Chains based on numbering reset just labeled A B C D .... Z a b c d .... z - * -- *

-+ *

- */ - - public class Mol2Reader extends ForceFieldReader { ---- 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 + * + * Chains based on numbering reset just labeled A B C D .... Z a b c d .... z + * +- *

++ *

+ */ + + public class Mol2Reader extends ForceFieldReader { +--- src/org/jmol/adapter/readers/pdb/PdbReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/pdb/PdbReader.java 2021-03-17 09:35:59.154003851 -0600 @@ -63,7 +63,7 @@ import java.util.Map; - * - * TLS Motion Determination: - * -- * J Painter & E A Merritt (2006) Acta Cryst. D62, 439-450 -+ * J Painter & E A Merritt (2006) Acta Cryst. D62, 439-450 - * http://skuld.bmsc.washington.edu/~tlsmd - * - * symmetry added by Bob Hanson: ---- 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 + * + * TLS Motion Determination: + * +- * J Painter & E A Merritt (2006) Acta Cryst. D62, 439-450 ++ * J Painter & E A Merritt (2006) Acta Cryst. D62, 439-450 + * http://skuld.bmsc.washington.edu/~tlsmd + * + * symmetry added by Bob Hanson: +--- src/org/jmol/adapter/readers/pymol/PickleReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/pymol/PickleReader.java 2021-03-17 09:35:59.154003851 -0600 @@ -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 +192,8 @@ * atom generates several items. * * see http://www.picklingtools.com/ ---- 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 +--- src/org/jmol/adapter/readers/pymol/PyMOL.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/pymol/PyMOL.java 2021-03-17 09:35:59.156003849 -0600 @@ -22,7 +22,7 @@ import org.jmol.util.Logger; * with note therein: * @@ -214,8 +203,8 @@ * ( 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 2021-02-05 17:54:49.000000000 -0700 -+++ src/org/jmol/adapter/readers/pymol/PyMOLReader.java 2021-02-22 16:26:47.262461595 -0700 +--- src/org/jmol/adapter/readers/pymol/PyMOLReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/pymol/PyMOLReader.java 2021-03-17 09:35:59.157003847 -0600 @@ -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 +222,8 @@ * * using set LOGFILE, we can dump this to a readable form. * ---- 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 +--- src/org/jmol/adapter/readers/pymol/PyMOLScene.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/pymol/PyMOLScene.java 2021-03-17 09:35:59.158003846 -0600 @@ -846,7 +846,7 @@ class PyMOLScene implements JmolSceneGen * create all objects for a given molecule or scene * @param reps @@ -244,232 +233,232 @@ * @param ac */ void createShapeObjects(BS[] reps, boolean allowSurface, int ac0, ---- 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 +--- src/org/jmol/adapter/readers/quantum/AdfReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/quantum/AdfReader.java 2021-03-17 09:35:59.159003845 -0600 @@ -42,24 +42,24 @@ import java.util.Map; - * - * A reader for ADF output. - * Amsterdam Density Functional (ADF) is a quantum chemistry program -- * by Scientific Computing & Modelling NV (SCM) -+ * by Scientific Computing & Modelling NV (SCM) - * (http://www.scm.com/). - * - *

Molecular coordinates, energies, and normal coordinates of - * vibrations are read. Each set of coordinates is added to the - * ChemFile in the order they are found. Energies and vibrations -- * are associated with the previously read set of coordinates. -+ * are associated with the previously read set of coordinates.

- * - *

This reader was developed from a small set of - * example output files, and therefore, is not guaranteed to - * properly read all ADF output. If you have problems, - * please contact the author of this code, not the developers -- * of ADF. -+ * of ADF.

- * - *

Added note (Bob Hanson) -- 1/1/2010 -- - * Trying to implement reading of orbitals; ran into the problem - * that the atomic Slater description uses Cartesian orbitals, -- * but the MO refers to spherical orbitals. -+ * but the MO refers to spherical orbitals.

- * - * - * @author Bradley A. Smith (yeldar@home.com) ---- 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 + * + * A reader for ADF output. + * Amsterdam Density Functional (ADF) is a quantum chemistry program +- * by Scientific Computing & Modelling NV (SCM) ++ * by Scientific Computing & Modelling NV (SCM) + * (http://www.scm.com/). + * + *

Molecular coordinates, energies, and normal coordinates of + * vibrations are read. Each set of coordinates is added to the + * ChemFile in the order they are found. Energies and vibrations +- * are associated with the previously read set of coordinates. ++ * are associated with the previously read set of coordinates.

+ * + *

This reader was developed from a small set of + * example output files, and therefore, is not guaranteed to + * properly read all ADF output. If you have problems, + * please contact the author of this code, not the developers +- * of ADF. ++ * of ADF.

+ * + *

Added note (Bob Hanson) -- 1/1/2010 -- + * Trying to implement reading of orbitals; ran into the problem + * that the atomic Slater description uses Cartesian orbitals, +- * but the MO refers to spherical orbitals. ++ * but the MO refers to spherical orbitals.

+ * + * + * @author Bradley A. Smith (yeldar@home.com) +--- src/org/jmol/adapter/readers/quantum/BasisFunctionReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/quantum/BasisFunctionReader.java 2021-03-17 09:35:59.159003845 -0600 @@ -39,7 +39,7 @@ import java.util.Map; - - /** - * -- * @author hansonr -+ * @author hansonr <hansonr@stolaf.edu> - */ - public abstract class BasisFunctionReader extends AtomSetCollectionReader { - ---- 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 + + /** + * +- * @author hansonr ++ * @author hansonr <hansonr@stolaf.edu> + */ + public abstract class BasisFunctionReader extends AtomSetCollectionReader { + +--- src/org/jmol/adapter/readers/quantum/CsfReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/quantum/CsfReader.java 2021-03-17 09:35:59.160003844 -0600 @@ -47,7 +47,7 @@ import org.jmol.util.Logger; - * streamlined CSF dataset reading capabilities 2007/04/09 - * - * -- * @author hansonr -+ * @author hansonr <hansonr@stolaf.edu> - */ - public class CsfReader extends MopacSlaterReader { - ---- 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 + * streamlined CSF dataset reading capabilities 2007/04/09 + * + * +- * @author hansonr ++ * @author hansonr <hansonr@stolaf.edu> + */ + public class CsfReader extends MopacSlaterReader { + +--- src/org/jmol/adapter/readers/quantum/MoldenReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/quantum/MoldenReader.java 2021-03-17 09:35:59.160003844 -0600 @@ -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 - * -- * updated by Bob Hanson for Jmol 12.0/12.1 -+ * updated by Bob Hanson <hansonr@stolaf.edu> for Jmol 12.0/12.1 - * - * adding [spacegroup] [operators] [cell] [cellaxes] for Jmol 14.3.7 - * -- * @author Matthew Zwier -+ * @author Matthew Zwier <mczwier@gmail.com> - */ - - public class MoldenReader extends MopacSlaterReader { ---- 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 + * A molecular structure and orbital reader for MolDen files. + * See http://www.cmbi.ru.nl/molden/molden_format.html + * +- * updated by Bob Hanson for Jmol 12.0/12.1 ++ * updated by Bob Hanson <hansonr@stolaf.edu> for Jmol 12.0/12.1 + * + * adding [spacegroup] [operators] [cell] [cellaxes] for Jmol 14.3.7 + * +- * @author Matthew Zwier ++ * @author Matthew Zwier <mczwier@gmail.com> + */ + + public class MoldenReader extends MopacSlaterReader { +--- src/org/jmol/adapter/readers/quantum/MopacGraphfReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/quantum/MopacGraphfReader.java 2021-03-17 09:35:59.161003842 -0600 @@ -35,7 +35,7 @@ import org.jmol.adapter.smarter.Atom; - /** - * Reads Mopac 2007 GRAPHF output files - * -- * @author Bob Hanson -+ * @author Bob Hanson <hansonr@stolaf.edu> - * - */ - public class MopacGraphfReader extends MopacSlaterReader { ---- 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 + /** + * Reads Mopac 2007 GRAPHF output files + * +- * @author Bob Hanson ++ * @author Bob Hanson <hansonr@stolaf.edu> + * + */ + public class MopacGraphfReader extends MopacSlaterReader { +--- src/org/jmol/adapter/readers/quantum/MopacSlaterReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/quantum/MopacSlaterReader.java 2021-03-17 09:35:59.161003842 -0600 @@ -25,7 +25,7 @@ package org.jmol.adapter.readers.quantum - - /** - * -- * @author hansonr -+ * @author hansonr <hansonr@stolaf.edu> - */ - abstract class MopacSlaterReader extends SlaterReader { - ---- 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 + + /** + * +- * @author hansonr ++ * @author hansonr <hansonr@stolaf.edu> + */ + abstract class MopacSlaterReader extends SlaterReader { + +--- src/org/jmol/adapter/readers/quantum/QCJSONReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/quantum/QCJSONReader.java 2021-03-17 09:35:59.162003841 -0600 @@ -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 - * -- * updated by Bob Hanson for Jmol 12.0/12.1 -+ * updated by Bob Hanson <hansonr@stolaf.edu> for Jmol 12.0/12.1 - * - * adding [spacegroup] [operators] [cell] [cellaxes] for Jmol 14.3.7 - * -- * @author Matthew Zwier -+ * @author Matthew Zwier <mczwier@gmail.com> - */ - - public class QCJSONReader extends MoldenReader { ---- 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 + * A molecular structure and orbital reader for MolDen files. + * See http://www.cmbi.ru.nl/molden/molden_format.html + * +- * updated by Bob Hanson for Jmol 12.0/12.1 ++ * updated by Bob Hanson <hansonr@stolaf.edu> for Jmol 12.0/12.1 + * + * adding [spacegroup] [operators] [cell] [cellaxes] for Jmol 14.3.7 + * +- * @author Matthew Zwier ++ * @author Matthew Zwier <mczwier@gmail.com> + */ + + public class QCJSONReader extends MoldenReader { +--- src/org/jmol/adapter/readers/quantum/SlaterReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/quantum/SlaterReader.java 2021-03-17 09:35:59.163003840 -0600 @@ -35,7 +35,7 @@ import java.util.Map; - - /** - * -- * @author hansonr -+ * @author hansonr <hansonr@stolaf.edu> - */ - abstract class SlaterReader extends BasisFunctionReader { - + + /** + * +- * @author hansonr ++ * @author hansonr <hansonr@stolaf.edu> + */ + abstract class SlaterReader extends BasisFunctionReader { + @@ -60,8 +60,8 @@ abstract class SlaterReader extends Basi - * - * psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) - * -- * Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) -- * and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r) -+ * Mopac: a == -2 → z^2 → (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) -+ * and: b == -2 → (coef)(x^2-y^2)(r^d)exp(-zeta*r) - * - * @param iAtom now 1-based - * @param a ---- 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 + * + * psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) + * +- * Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) +- * and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r) ++ * Mopac: a == -2 → z^2 → (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) ++ * and: b == -2 → (coef)(x^2-y^2)(r^d)exp(-zeta*r) + * + * @param iAtom now 1-based + * @param a +--- src/org/jmol/adapter/readers/quantum/WebMOReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/quantum/WebMOReader.java 2021-03-17 09:35:59.163003840 -0600 @@ -46,7 +46,7 @@ import org.jmol.util.Logger; - * - * - * right now WebMO files don't allow for multiple MOS, but we will assume here that that may change. -- *

-+ *

- */ - public class WebMOReader extends MopacSlaterReader { - ---- 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 + * + * + * right now WebMO files don't allow for multiple MOS, but we will assume here that that may change. +- *

++ *

+ */ + public class WebMOReader extends MopacSlaterReader { + +--- src/org/jmol/adapter/readers/simple/GhemicalMMReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/simple/GhemicalMMReader.java 2021-03-17 09:35:59.164003839 -0600 @@ -67,7 +67,7 @@ import org.jmol.api.JmolAdapter; - * !End - * - * -- * @author Egon Willighagen -+ * @author Egon Willighagen <egonw@sci.kun.nl> - */ - public class GhemicalMMReader extends AtomSetCollectionReader { - ---- 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 + * !End + * + * +- * @author Egon Willighagen ++ * @author Egon Willighagen <egonw@sci.kun.nl> + */ + public class GhemicalMMReader extends AtomSetCollectionReader { + +--- src/org/jmol/adapter/readers/simple/HyperChemReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/simple/HyperChemReader.java 2021-03-17 09:35:59.164003839 -0600 @@ -32,7 +32,7 @@ import org.jmol.api.JmolAdapter; - /** - * Support for .hin, HyperChem's native file format. - * http://www.hyper.com -- *

-+ *

- * Record format is: - * - * atom 1 - C ** - -0.06040 0.00000 0.00000 0.00000 3 2 a 6 a 38 s + /** + * Support for .hin, HyperChem's native file format. + * http://www.hyper.com +- *

++ *

+ * Record format is: + * + * atom 1 - C ** - -0.06040 0.00000 0.00000 0.00000 3 2 a 6 a 38 s @@ -40,8 +40,8 @@ import org.jmol.api.JmolAdapter; - * atom 67 - H ** - 0.17710 -7.10260 -3.74840 2.24660 1 34 s - * endmol 1 - * -- * interesting fields are partialCharge, x, y, z, bondCount
-- * bonds are atom number and s/d/t/a for single/double/triple/aromatic -+ * interesting fields are partialCharge, x, y, z, bondCount
-+ * bonds are atom number and s/d/t/a for single/double/triple/aromatic

- */ - public class HyperChemReader extends AtomSetCollectionReader { - ---- 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 + * atom 67 - H ** - 0.17710 -7.10260 -3.74840 2.24660 1 34 s + * endmol 1 + * +- * interesting fields are partialCharge, x, y, z, bondCount
+- * bonds are atom number and s/d/t/a for single/double/triple/aromatic ++ * interesting fields are partialCharge, x, y, z, bondCount
++ * bonds are atom number and s/d/t/a for single/double/triple/aromatic

+ */ + public class HyperChemReader extends AtomSetCollectionReader { + +--- src/org/jmol/adapter/readers/simple/MopacReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/simple/MopacReader.java 2021-03-17 09:35:59.164003839 -0600 @@ -34,7 +34,7 @@ import org.jmol.util.Logger; - /** - * Reads Mopac 93, 6, 7, 2002, or 2009 output files - * -- * @author Egon Willighagen -+ * @author Egon Willighagen <egonw@jmol.org> - */ - public class MopacReader extends AtomSetCollectionReader { - ---- 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 + /** + * Reads Mopac 93, 6, 7, 2002, or 2009 output files + * +- * @author Egon Willighagen ++ * @author Egon Willighagen <egonw@jmol.org> + */ + public class MopacReader extends AtomSetCollectionReader { + +--- src/org/jmol/adapter/readers/xtal/CrystalReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/adapter/readers/xtal/CrystalReader.java 2021-03-17 09:35:59.166003836 -0600 @@ -73,7 +73,7 @@ import org.jmol.util.Tensor; - * mat4CrystalToPrimitive M4 convenience inverse of - * mat4PrimitiveToCrystal - * -- * fileSymmetryOperations List symmetry operators (primitive) -+ * fileSymmetryOperations List<String> symmetry operators (primitive) - * - * Drawing primitive unitcell operations: - * + * mat4CrystalToPrimitive M4 convenience inverse of + * mat4PrimitiveToCrystal + * +- * fileSymmetryOperations List symmetry operators (primitive) ++ * fileSymmetryOperations List<String> symmetry operators (primitive) + * + * Drawing primitive unitcell operations: + * @@ -95,7 +95,7 @@ import org.jmol.util.Tensor; - * - * load "xxx.out" n - * -- * as for all readers, where n is an integer > 0 -+ * as for all readers, where n is an integer > 0 - * - * for final optimized geometry use - * + * + * load "xxx.out" n + * +- * as for all readers, where n is an integer > 0 ++ * as for all readers, where n is an integer > 0 + * + * for final optimized geometry use + * @@ -1047,7 +1047,7 @@ public class CrystalReader extends AtomS - /** - * Read the lattice parameters. - * -- * @param isNewSet -+ * @param isPrimitive - * @throws Exception - */ - private void readLatticeParams(boolean isPrimitive) throws Exception { ---- 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 + /** + * Read the lattice parameters. + * +- * @param isNewSet ++ * @param isPrimitive + * @throws Exception + */ + private void readLatticeParams(boolean isPrimitive) throws Exception { +--- src/org/jmol/api/JmolViewer.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/api/JmolViewer.java 2021-03-17 09:35:59.166003836 -0600 @@ -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 -- * or a String[] or a Vector -+ * or a String[] or a Vector<String> - * @param isAppend TRUE to append models (no ZAP) - * @return null or error message - */ ---- 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 + * NOTE: THIS METHOD DOES NOT PRESERVE THE STATE + * + * @param arrayData a Vector of models, where each model is either a String +- * or a String[] or a Vector ++ * or a String[] or a Vector<String> + * @param isAppend TRUE to append models (no ZAP) + * @return null or error message + */ +--- src/org/jmol/awt/FileDropper.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/awt/FileDropper.java 2021-03-17 09:35:59.167003835 -0600 @@ -55,7 +55,7 @@ import javajs.util.SB; *

* Note that multiple drops ARE thread safe. @@ -479,8 +468,8 @@ */ public class FileDropper implements DropTargetListener { private String fd_oldFileName; ---- 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 +--- src/org/jmol/awtjs2d/Platform.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/awtjs2d/Platform.java 2021-03-17 09:35:59.167003835 -0600 @@ -26,11 +26,11 @@ import javajs.util.SB; /** * JavaScript 2D canvas version requires Ajax-based URL stream processing. @@ -498,8 +487,8 @@ * (Not fully implemented) * * @author Bob Hanson ---- 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 +--- src/org/jmol/awtjs/swing/SwingController.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/awtjs/swing/SwingController.java 2021-03-17 09:35:59.168003834 -0600 @@ -26,7 +26,7 @@ public interface SwingController { * var component = Jmol.Swing.htDialogs[element.id]; * var info = component.toString(); @@ -509,99 +498,99 @@ * 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 2021-02-05 17:54:50.000000000 -0700 -+++ src/org/jmol/bspt/Bspt.java 2021-02-22 16:26:47.273461590 -0700 +--- src/org/jmol/bspt/Bspt.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/bspt/Bspt.java 2021-03-17 09:35:59.168003834 -0600 @@ -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 - * next dimension, wrapping around to 0. -+ *

- * - * 
-  * mySplitDimension = (parentSplitDimension + 1) % 3;
-  *
- * -- * A split value is stored in the node. Values which are <= splitValue are -- * stored down the left branch. Values which are >= splitValue are stored down -+ *

-+ * A split value is stored in the node. Values which are ≤ splitValue are -+ * stored down the left branch. Values which are ≥ splitValue are stored down - * the right branch. If searchValue == splitValue then the search must proceed - * down both branches. - *

---- 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 + * 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 + * next dimension, wrapping around to 0. ++ *

+ * + * 
+  * mySplitDimension = (parentSplitDimension + 1) % 3;
+  *
+ * +- * A split value is stored in the node. Values which are <= splitValue are +- * stored down the left branch. Values which are >= splitValue are stored down ++ *

++ * A split value is stored in the node. Values which are ≤ splitValue are ++ * stored down the left branch. Values which are ≥ splitValue are stored down + * the right branch. If searchValue == splitValue then the search must proceed + * down both branches. + *

+--- src/org/jmol/bspt/PointIterator.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/bspt/PointIterator.java 2021-03-17 09:35:59.168003834 -0600 @@ -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 - * @param ap31 a second list of points, optional -- * @param ret null, "", int[], Lst, or P3 -+ * @param ret null, "", int[], Lst<T3>, or P3 - * @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 2021-02-05 17:54:50.000000000 -0700 -+++ src/org/jmol/dssx/AnnotationParser.java 2021-02-22 16:26:47.274461590 -0700 + * @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 + * @param ap31 a second list of points, optional +- * @param ret null, "", int[], Lst, or P3 ++ * @param ret null, "", int[], Lst<T3>, or P3 + * @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 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/dssx/AnnotationParser.java 2021-03-17 09:35:59.169003832 -0600 @@ -310,7 +310,7 @@ public class AnnotationParser implements - } - - /** -- * Returns a Lst of property data in the form name(String), -+ * Returns a Lst<Object> of property data in the form name(String), - * data(float[]), modelIndex (Integer), isGroup (Boolean); - * - */ ---- 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 + } + + /** +- * Returns a Lst of property data in the form name(String), ++ * Returns a Lst<Object> of property data in the form name(String), + * data(float[]), modelIndex (Integer), isGroup (Boolean); + * + */ +--- src/org/jmol/dssx/DSSP.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/dssx/DSSP.java 2021-03-17 09:35:59.169003832 -0600 @@ -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 - * bond between C=O of residue i and N-H of residue j if E is less than the -- * cutoff, i.e., "Hbond(i,j) =: [E < -0.5 kcal/mol]." -+ * cutoff, i.e., "Hbond(i,j) =: [E < -0.5 kcal/mol]." - * -- * @return array of dual-minmum NH-->O=C H bonds -+ * @return array of dual-minmum NH→O=C H bonds - * - */ - private int[][][][] getDualHydrogenBondArray() { + * 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 + * bond between C=O of residue i and N-H of residue j if E is less than the +- * cutoff, i.e., "Hbond(i,j) =: [E < -0.5 kcal/mol]." ++ * cutoff, i.e., "Hbond(i,j) =: [E < -0.5 kcal/mol]." + * +- * @return array of dual-minmum NH-->O=C H bonds ++ * @return array of dual-minmum NH→O=C H bonds + * + */ + private int[][][][] getDualHydrogenBondArray() { @@ -704,9 +704,9 @@ public class DSSP { - * - * A basic turn pattern (Fig. 2) is a single H bond of type (i,i+n). We - * assign an n-turn at residue i if there is an H bond from CO(i) to NH(i+n).... -- * When the pattern is found, the ends of the H bond are indicated using ">" at i -- * and "<" at i+n...; the residues bracketed by the H bond are noted "3," "4," or "5" -- * unless they are also end points of other H bonds. Coincidence of ">" and "<" at -+ * When the pattern is found, the ends of the H bond are indicated using ">" at i -+ * and "<" at i+n...; the residues bracketed by the H bond are noted "3," "4," or "5" -+ * unless they are also end points of other H bonds. Coincidence of ">" and "<" at - * 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 2021-02-05 17:54:50.000000000 -0700 -+++ src/org/jmol/i18n/Language.java 2021-02-22 16:26:47.275461590 -0700 + * + * A basic turn pattern (Fig. 2) is a single H bond of type (i,i+n). We + * assign an n-turn at residue i if there is an H bond from CO(i) to NH(i+n).... +- * When the pattern is found, the ends of the H bond are indicated using ">" at i +- * and "<" at i+n...; the residues bracketed by the H bond are noted "3," "4," or "5" +- * unless they are also end points of other H bonds. Coincidence of ">" and "<" at ++ * When the pattern is found, the ends of the H bond are indicated using ">" at i ++ * and "<" at i+n...; the residues bracketed by the H bond are noted "3," "4," or "5" ++ * unless they are also end points of other H bonds. Coincidence of ">" and "<" at + * 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 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/i18n/Language.java 2021-03-17 09:35:59.169003832 -0600 @@ -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 - * -- * {@link "http://en.wikipedia.org/wiki/List_of_ISO_639-1_codes"} -+ * See the list of ISO-639-1 codes. - */ - private Language(String code, String language, String nativeLanguage, boolean display) { - this.code = code; ---- 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 + * @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 + * +- * {@link "http://en.wikipedia.org/wiki/List_of_ISO_639-1_codes"} ++ * See the list of ISO-639-1 codes. + */ + private Language(String code, String language, String nativeLanguage, boolean display) { + this.code = code; +--- src/org/jmol/jvxl/api/VertexDataServer.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/jvxl/api/VertexDataServer.java 2021-03-17 09:35:59.170003831 -0600 @@ -42,7 +42,7 @@ public interface VertexDataServer { - * where fraction is generally calculated as: - * - * fraction = (cutoff - valueA) / (valueB - valueA); -- * if (isCutoffAbsolute && (fraction < 0 || fraction > 1)) -+ * if (isCutoffAbsolute && (fraction < 0 || fraction > 1)) - * fraction = (-cutoff - valueA) / (valueB - valueA); - * - * This method is also used by MarchingCubes to deliver the appropriate ---- 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 + * where fraction is generally calculated as: + * + * fraction = (cutoff - valueA) / (valueB - valueA); +- * if (isCutoffAbsolute && (fraction < 0 || fraction > 1)) ++ * if (isCutoffAbsolute && (fraction < 0 || fraction > 1)) + * fraction = (-cutoff - valueA) / (valueB - valueA); + * + * This method is also used by MarchingCubes to deliver the appropriate +--- src/org/jmol/jvxl/data/JvxlCoder.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/jvxl/data/JvxlCoder.java 2021-03-17 09:35:59.170003831 -0600 @@ -449,12 +449,14 @@ public class JvxlCoder { /** @@ -642,41 +631,41 @@ * * 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 +--- src/org/jmol/jvxl/data/VolumeData.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/jvxl/data/VolumeData.java 2021-03-17 09:35:59.171003830 -0600 @@ -428,7 +428,7 @@ public class VolumeData { - * periodic grids should have val[0] == val[xMax] - * - * voxelCount: 1....2....3....4....5 xMax/index: 0....1....2....3....4.... -- * nonper. ^ ---> [0,0] ^ --> [4, 4] periodic ^ ---> [3,4] ^ --> [0, 1] -+ * nonper. ^ → [0,0] ^ → [4, 4] periodic ^ → [3,4] ^ → [0, 1] - * - * @param x - * @param xMax ---- 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 + * periodic grids should have val[0] == val[xMax] + * + * voxelCount: 1....2....3....4....5 xMax/index: 0....1....2....3....4.... +- * nonper. ^ ---> [0,0] ^ --> [4, 4] periodic ^ ---> [3,4] ^ --> [0, 1] ++ * nonper. ^ → [0,0] ^ → [4, 4] periodic ^ → [3,4] ^ → [0, 1] + * + * @param x + * @param xMax +--- src/org/jmol/jvxl/readers/BCifDensityReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/jvxl/readers/BCifDensityReader.java 2021-03-17 09:35:59.171003830 -0600 @@ -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: - * -- * https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box/-4.413,55.607,64.124/-0.4130001,59.607,68.124?space=cartesian&encoding=bcif -+ * https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box/-4.413,55.607,64.124/-0.4130001,59.607,68.124?space=cartesian&encoding=bcif - * - * Reads a MessagePack file and extracts either 2Fo-Fc or Fo-Fc. - * ---- 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 + * Binary CIF density reader. See https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box, + * for example: + * +- * https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box/-4.413,55.607,64.124/-0.4130001,59.607,68.124?space=cartesian&encoding=bcif ++ * https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box/-4.413,55.607,64.124/-0.4130001,59.607,68.124?space=cartesian&encoding=bcif + * + * Reads a MessagePack file and extracts either 2Fo-Fc or Fo-Fc. + * +--- src/org/jmol/jvxl/readers/CifDensityReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/jvxl/readers/CifDensityReader.java 2021-03-17 09:35:59.172003829 -0600 @@ -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: - * -- * https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box/-4.413,55.607,64.124/-0.4130001,59.607,68.124?space=cartesian&encoding=cif -+ * https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box/-4.413,55.607,64.124/-0.4130001,59.607,68.124?space=cartesian&encoding=cif - * - * Extends BCifDensityReader just enough to handle nonbinary CIF data. - * ---- 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 + * CIF density reader. See https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box, + * for example: + * +- * https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box/-4.413,55.607,64.124/-0.4130001,59.607,68.124?space=cartesian&encoding=cif ++ * https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box/-4.413,55.607,64.124/-0.4130001,59.607,68.124?space=cartesian&encoding=cif + * + * Extends BCifDensityReader just enough to handle nonbinary CIF data. + * +--- src/org/jmol/jvxl/readers/JvxlXmlReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/jvxl/readers/JvxlXmlReader.java 2021-03-17 09:35:59.172003829 -0600 @@ -748,7 +748,7 @@ public class JvxlXmlReader extends Volum /** @@ -704,64 +693,64 @@ * 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 +--- src/org/jmol/jvxl/readers/KinemageReader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/jvxl/readers/KinemageReader.java 2021-03-17 09:35:59.172003829 -0600 @@ -219,7 +219,7 @@ class KinemageReader extends PmeshReader - */ - - /** -- * C++ code gives these as " value > x.x ? "xxxxx", etc. -+ * C++ code gives these as " value > x.x ? "xxxxx", etc., - * 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 2021-02-05 17:54:50.000000000 -0700 -+++ src/org/jmol/minimize/forcefield/ForceFieldMMFF.java 2021-02-22 16:26:47.281461587 -0700 + */ + + /** +- * C++ code gives these as " value > x.x ? "xxxxx", etc. ++ * C++ code gives these as " value > x.x ? "xxxxx", etc., + * 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 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/minimize/forcefield/ForceFieldMMFF.java 2021-03-17 09:35:59.173003827 -0600 @@ -64,7 +64,7 @@ import org.jmol.viewer.JmolAsyncExceptio - * - * T. A. Halgren; "Merck Molecular Force Field. V. Extension of MMFF94 - * Using Experimental Data, Additional Computational Data, -- * and Empirical Rules", J. Comp. Chem. 5 & 6 616-641 (1996). -+ * and Empirical Rules", J. Comp. Chem. 5 & 6 616-641 (1996). - * - * Parameter files are clipped from the original Wiley FTP site supplemental material: - * + * + * T. A. Halgren; "Merck Molecular Force Field. V. Extension of MMFF94 + * Using Experimental Data, Additional Computational Data, +- * and Empirical Rules", J. Comp. Chem. 5 & 6 616-641 (1996). ++ * and Empirical Rules", J. Comp. Chem. 5 & 6 616-641 (1996). + * + * Parameter files are clipped from the original Wiley FTP site supplemental material: + * @@ -73,17 +73,17 @@ import org.jmol.viewer.JmolAsyncExceptio - * Original work, as listed at http://towhee.sourceforge.net/forcefields/mmff94.html: - * - * T. A. Halgren; "Merck Molecular Force Field. I. Basis, Form, Scope, -- * Parameterization, and Performance of MMFF94", J. Comp. Chem. 5 & 6 490-519 (1996). -+ * Parameterization, and Performance of MMFF94", J. Comp. Chem. 5 & 6 490-519 (1996). - * T. A. Halgren; "Merck Molecular Force Field. II. MMFF94 van der Waals - * and Electrostatic Parameters for Intermolecular Interactions", -- * J. Comp. Chem. 5 & 6 520-552 (1996). -+ * J. Comp. Chem. 5 & 6 520-552 (1996). - * T. A. Halgren; "Merck Molecular Force Field. III. Molecular Geometries and -- * Vibrational Frequencies for MMFF94", J. Comp. Chem. 5 & 6 553-586 (1996). -+ * Vibrational Frequencies for MMFF94", J. Comp. Chem. 5 & 6 553-586 (1996). - * T. A. Halgren; R. B. Nachbar; "Merck Molecular Force Field. IV. -- * Conformational Energies and Geometries for MMFF94", J. Comp. Chem. 5 & 6 587-615 (1996). -+ * Conformational Energies and Geometries for MMFF94", J. Comp. Chem. 5 & 6 587-615 (1996). - * T. A. Halgren; "Merck Molecular Force Field. V. Extension of MMFF94 - * Using Experimental Data, Additional Computational Data, -- * and Empirical Rules", J. Comp. Chem. 5 & 6 616-641 (1996). -+ * and Empirical Rules", J. Comp. Chem. 5 & 6 616-641 (1996). - * 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 2021-02-05 17:54:50.000000000 -0700 -+++ src/org/jmol/minimize/Util.java 2021-02-22 16:26:47.281461587 -0700 + * Original work, as listed at http://towhee.sourceforge.net/forcefields/mmff94.html: + * + * T. A. Halgren; "Merck Molecular Force Field. I. Basis, Form, Scope, +- * Parameterization, and Performance of MMFF94", J. Comp. Chem. 5 & 6 490-519 (1996). ++ * Parameterization, and Performance of MMFF94", J. Comp. Chem. 5 & 6 490-519 (1996). + * T. A. Halgren; "Merck Molecular Force Field. II. MMFF94 van der Waals + * and Electrostatic Parameters for Intermolecular Interactions", +- * J. Comp. Chem. 5 & 6 520-552 (1996). ++ * J. Comp. Chem. 5 & 6 520-552 (1996). + * T. A. Halgren; "Merck Molecular Force Field. III. Molecular Geometries and +- * Vibrational Frequencies for MMFF94", J. Comp. Chem. 5 & 6 553-586 (1996). ++ * Vibrational Frequencies for MMFF94", J. Comp. Chem. 5 & 6 553-586 (1996). + * T. A. Halgren; R. B. Nachbar; "Merck Molecular Force Field. IV. +- * Conformational Energies and Geometries for MMFF94", J. Comp. Chem. 5 & 6 587-615 (1996). ++ * Conformational Energies and Geometries for MMFF94", J. Comp. Chem. 5 & 6 587-615 (1996). + * T. A. Halgren; "Merck Molecular Force Field. V. Extension of MMFF94 + * Using Experimental Data, Additional Computational Data, +- * and Empirical Rules", J. Comp. Chem. 5 & 6 616-641 (1996). ++ * and Empirical Rules", J. Comp. Chem. 5 & 6 616-641 (1996). + * 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 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/minimize/Util.java 2021-03-17 09:35:59.173003827 -0600 @@ -119,7 +119,7 @@ public class Util { - - /** - * -- * calculates angle of a to plane bcd, returning a value > pi/2 in -+ * calculates angle of a to plane bcd, returning a value > pi/2 in - * highly distorted trigonal pyramidal situations - * - * @param a ---- 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 + + /** + * +- * calculates angle of a to plane bcd, returning a value > pi/2 in ++ * calculates angle of a to plane bcd, returning a value > pi/2 in + * highly distorted trigonal pyramidal situations + * + * @param a +--- src/org/jmol/modelkit/ModelKitPopup.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/modelkit/ModelKitPopup.java 2021-03-17 09:35:59.173003827 -0600 @@ -1307,7 +1307,6 @@ abstract public class ModelKitPopup exte * * @param pressed @@ -770,94 +759,94 @@ * @param countPlusIndices * @return true if handled here */ ---- 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 +--- src/org/jmol/modelsetbio/AlphaPolymer.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/modelsetbio/AlphaPolymer.java 2021-03-17 09:35:59.173003827 -0600 @@ -143,12 +143,13 @@ public class AlphaPolymer extends BioPol - ///////////////////////////////////////////////////////////// - - /** -- * Uses Levitt & Greer algorithm to calculate protein secondary -+ * Uses Levitt & Greer algorithm to calculate protein secondary - * structures using only alpha-carbon atoms. - *

-- * Levitt and Greer
-- * Automatic Identification of Secondary Structure in Globular Proteins
-- * J.Mol.Biol.(1977) 114, 181-293
-+ * Levitt and Greer
-+ * Automatic Identification of Secondary Structure in Globular Proteins
-+ * J.Mol.Biol.(1977) 114, 181-293 -+ *

- *

- * ---- 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 + ///////////////////////////////////////////////////////////// + + /** +- * Uses Levitt & Greer algorithm to calculate protein secondary ++ * Uses Levitt & Greer algorithm to calculate protein secondary + * structures using only alpha-carbon atoms. + *

+- * Levitt and Greer
+- * Automatic Identification of Secondary Structure in Globular Proteins
+- * J.Mol.Biol.(1977) 114, 181-293
++ * Levitt and Greer
++ * Automatic Identification of Secondary Structure in Globular Proteins
++ * J.Mol.Biol.(1977) 114, 181-293 ++ *

+ *

+ * +--- src/org/jmol/modelsetbio/AminoPolymer.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/modelsetbio/AminoPolymer.java 2021-03-17 09:35:59.173003827 -0600 @@ -279,7 +279,7 @@ public class AminoPolymer extends AlphaP - * checkDistances: - * - * When we are seriously looking for H bonds, we want to -- * also check that distCN > distCH and that the OH distance -+ * also check that distCN > distCH and that the OH distance - * 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 2021-02-05 17:54:50.000000000 -0700 -+++ src/org/jmol/modelsetbio/BioResolver.java 2021-02-22 16:26:47.283461586 -0700 + * checkDistances: + * + * When we are seriously looking for H bonds, we want to +- * also check that distCN > distCH and that the OH distance ++ * also check that distCN > distCH and that the OH distance + * 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 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/modelsetbio/BioResolver.java 2021-03-17 09:35:59.173003827 -0600 @@ -1529,7 +1529,7 @@ public final class BioResolver implement - * FF8060 - light tomato - * 00FF7F - springgreen - * --cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off -+cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off - ****************************************************************/ - - private final static int[] argbsChainAtom = { ---- 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 + * FF8060 - light tomato + * 00FF7F - springgreen + * +-cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off ++cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off + ****************************************************************/ + + private final static int[] argbsChainAtom = { +--- src/org/jmol/modelsetbio/Monomer.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/modelsetbio/Monomer.java 2021-03-17 09:35:59.174003826 -0600 @@ -55,7 +55,7 @@ import java.util.Map; - public abstract class Monomer extends Group { - - /** -- * @j2sIngore -+ * @j2sIgnore - */ - - public Monomer() { ---- 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 + public abstract class Monomer extends Group { + + /** +- * @j2sIngore ++ * @j2sIgnore + */ + + public Monomer() { +--- src/org/jmol/modelset/Group.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/modelset/Group.java 2021-03-17 09:35:59.174003826 -0600 @@ -92,7 +92,7 @@ public class Group implements Structure - - - /** -- * @j2sIngore -+ * @j2sIgnore - */ - public Group() {} - ---- 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 + + + /** +- * @j2sIngore ++ * @j2sIgnore + */ + public Group() {} + +--- src/org/jmol/modelset/ModelLoader.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/modelset/ModelLoader.java 2021-03-17 09:35:59.174003826 -0600 @@ -672,7 +672,7 @@ public final class ModelLoader { - * file * 1000000 + modelInFile (1-based) - * - * Used all over the place. Note that if there is only one file, then -- * modelFileNumber < 1000000. -+ * modelFileNumber < 1000000. - * - * String modelNumberDotted - * ---- 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 + * file * 1000000 + modelInFile (1-based) + * + * Used all over the place. Note that if there is only one file, then +- * modelFileNumber < 1000000. ++ * modelFileNumber < 1000000. + * + * String modelNumberDotted + * +--- src/org/jmol/modelset/ModelSet.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/modelset/ModelSet.java 2021-03-17 09:35:59.174003826 -0600 @@ -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 -- * @param iAtom atom to switch two groups on if >= 0 -+ * @param iAtom atom to switch two groups on if ≥ 0 - * @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 2021-02-05 17:54:50.000000000 -0700 -+++ src/org/jmol/multitouch/sparshui/TwoPointGesture.java 2021-02-22 16:26:47.285461586 -0700 + * + * @param pt point to invert around if not null + * @param plane plane to invert across if not null +- * @param iAtom atom to switch two groups on if >= 0 ++ * @param iAtom atom to switch two groups on if ≥ 0 + * @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 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/multitouch/sparshui/TwoPointGesture.java 2021-03-17 09:35:59.174003826 -0600 @@ -29,8 +29,8 @@ import com.sparshui.server.TouchPoint; * * v00 from pt(1,0) to pt(2,0) @@ -881,41 +870,41 @@ * * Bob Hanson 12/13/2009 * ---- 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 +--- src/org/jmol/popup/JmolPopup.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/popup/JmolPopup.java 2021-03-17 09:35:59.175003825 -0600 @@ -255,7 +255,7 @@ abstract public class JmolPopup extends - } - - /** -- * (1) setOption --> set setOption true or set setOption false -+ * (1) setOption → set setOption true or set setOption false - * - * @param item - * ---- 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 + } + + /** +- * (1) setOption --> set setOption true or set setOption false ++ * (1) setOption → set setOption true or set setOption false + * + * @param item + * +--- src/org/jmol/quantum/NciCalculation.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/quantum/NciCalculation.java 2021-03-17 09:35:59.175003825 -0600 @@ -362,7 +362,7 @@ public class NciCalculation extends Quan - * that are too far away to make a difference before we waste - * time doing exponentiation. - * -- * If index >= 0, then this is just a check for intra- vs. inter- -+ * If index ≥ 0, then this is just a check for intra- vs. inter- - * 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 2021-02-05 17:54:50.000000000 -0700 -+++ src/org/jmol/quantum/NMRCalculation.java 2021-02-22 16:26:47.287461585 -0700 + * that are too far away to make a difference before we waste + * time doing exponentiation. + * +- * If index >= 0, then this is just a check for intra- vs. inter- ++ * If index ≥ 0, then this is just a check for intra- vs. inter- + * 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 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/quantum/NMRCalculation.java 2021-03-17 09:35:59.175003825 -0600 @@ -314,7 +314,7 @@ public class NMRCalculation implements J - /** - * Creates the data set necessary for doing NMR calculations. Values are - * retrievable using getProperty "nmrInfo" "Xx"; each entry is -- * float[+/-isotopeNumber, g, Q], where [0] < 0 for the default value. -+ * float[+/-isotopeNumber, g, Q], where [0] < 0 for the default value. - * - */ - @SuppressWarnings("resource") ---- 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 + /** + * Creates the data set necessary for doing NMR calculations. Values are + * retrievable using getProperty "nmrInfo" "Xx"; each entry is +- * float[+/-isotopeNumber, g, Q], where [0] < 0 for the default value. ++ * float[+/-isotopeNumber, g, Q], where [0] < 0 for the default value. + * + */ + @SuppressWarnings("resource") +--- src/org/jmol/quantum/NMRNoeMatrix.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/quantum/NMRNoeMatrix.java 2021-03-17 09:35:59.175003825 -0600 @@ -87,7 +87,7 @@ import org.jmol.viewer.Viewer; * if the atoms have not been set up properly. * @@ -925,8 +914,8 @@ */ public class NMRNoeMatrix { ---- 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 +--- src/org/jmol/scriptext/MathExt.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/scriptext/MathExt.java 2021-03-17 09:35:59.175003825 -0600 @@ -1887,7 +1887,7 @@ public class MathExt { * _(key) prepends "auxiliaryInfo.models", delivering a modelCount-length * array of information @@ -957,48 +946,48 @@ * * @param listIn * @param formatList ---- 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 +--- src/org/jmol/script/ScriptCompiler.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/script/ScriptCompiler.java 2021-03-17 09:35:59.176003824 -0600 @@ -1081,7 +1081,7 @@ public class ScriptCompiler extends Scri - * - * Check for special parameters, including: - * -- * +, -, \, *, /, &, |, =, period, or [, single or double quote, -+ * +, -, \, *, /, &, |, =, period, or [, single or double quote, - * command-specific parameters, $.... identifiers, exponential notation, - * decimal numbers, sequence codes, integers, bitsets ({....}) or [{....}], or - * matrices + * + * Check for special parameters, including: + * +- * +, -, \, *, /, &, |, =, period, or [, single or double quote, ++ * +, -, \, *, /, &, |, =, period, or [, single or double quote, + * command-specific parameters, $.... identifiers, exponential notation, + * decimal numbers, sequence codes, integers, bitsets ({....}) or [{....}], or + * matrices @@ -2505,7 +2505,7 @@ public class ScriptCompiler extends Scri - /** - * - * look for end-of-line character \r, \n, or ; that is not within a command -- * such as for (var i=0;i < 10; i++) -+ * such as {@code for (var i=0;i < 10; i++)} - * - * @param ch - * @return true if end of line + /** + * + * look for end-of-line character \r, \n, or ; that is not within a command +- * such as for (var i=0;i < 10; i++) ++ * such as {@code for (var i=0;i < 10; i++)} + * + * @param ch + * @return true if end of line @@ -2680,7 +2680,7 @@ public class ScriptCompiler extends Scri - * An "implied string" is a parameter that is not quoted but because of its - * position in a command is implied to be a string. First we must exclude the - * -- * @xxxx. Then we consume the entire math syntax @{......} or any set of -+ * {@literal @}xxxx. Then we consume the entire math syntax {@literal @}{......} or any set of - * 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 2021-02-05 17:54:50.000000000 -0700 -+++ src/org/jmol/script/ScriptEval.java 2021-02-22 16:26:47.290461584 -0700 + * An "implied string" is a parameter that is not quoted but because of its + * position in a command is implied to be a string. First we must exclude the + * +- * @xxxx. Then we consume the entire math syntax @{......} or any set of ++ * {@literal @}xxxx. Then we consume the entire math syntax {@literal @}{......} or any set of + * 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 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/script/ScriptEval.java 2021-03-17 09:35:59.177003822 -0600 @@ -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. - * -- * @param sc -+ * @param sco - */ - - @Override ---- 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 + * program counter is incremented to skip the initiating statement, and all + * parent contexts up the line are set with mustResumeEval = true. + * +- * @param sc ++ * @param sco + */ + + @Override +--- src/org/jmol/script/ScriptParam.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/script/ScriptParam.java 2021-03-17 09:35:59.177003822 -0600 @@ -1062,7 +1062,7 @@ abstract public class ScriptParam extend } @@ -1008,87 +997,87 @@ * + (m % 0x1F) * * @param bondOrderInteger ---- 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 +--- src/org/jmol/shapebio/BioShape.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/shapebio/BioShape.java 2021-03-17 09:35:59.177003822 -0600 @@ -120,32 +120,32 @@ public class BioShape extends AtomShape - * - * http://www.rcsb.org/pdb/lists/pdb-l/200303/000609.html - * -- * -- * > -----Original Message----- -- * > From: pdb-l-admin@sdsc.edu [mailto:pdb-l-admin@sdsc.edu] On -- * > Behalf Of Philipp Heuser -- * > Sent: Thursday, March 27, 2003 6:05 AM -- * > To: pdb-l@sdsc.edu -- * > Subject: pdb-l: temperature factor; occupancy -- * > -- * > -- * > Hi all! -- * > -- * > Does anyone know where to find proper definitions for the -- * > temperature factors -- * > and the values for occupancy? -- * > -- * > Alright I do know, that the atoms with high temperature -- * > factors are more -- * > disordered than others, but what does a temperature factor of -- * > a specific -- * > value mean exactly. -- * > -- * > -- * > Thanks in advance! -- * > -- * > Philipp -- * > -+ * 


-+   * > -----Original Message-----
-+   * > From: pdb-l-admin@sdsc.edu [mailto:pdb-l-admin@sdsc.edu] On 
-+   * > Behalf Of Philipp Heuser
-+   * > Sent: Thursday, March 27, 2003 6:05 AM
-+   * > To: pdb-l@sdsc.edu
-+   * > Subject: pdb-l: temperature factor; occupancy
-+   * > 
-+   * > 
-+   * > Hi all!
-+   * > 
-+   * > Does anyone know where to find proper definitions for the 
-+   * > temperature factors 
-+   * > and the values for occupancy?
-+   * > 
-+   * > Alright I do know, that the atoms with high temperature 
-+   * > factors are more 
-+   * > disordered than others, but what does a temperature factor of 
-+   * > a specific 
-+   * > value mean exactly.
-+   * > 
-+   * > 
-+   * > Thanks in advance!
-+   * > 
-+   * > Philipp
-+   * > 
-    * pdb-l: temperature factor; occupancy
-    * Bernhard Rupp br@llnl.gov
-    * Thu, 27 Mar 2003 08:01:29 -0800
+    * 
+    * http://www.rcsb.org/pdb/lists/pdb-l/200303/000609.html
+    * 
+-   * 
+-   * > -----Original Message-----
+-   * > From: pdb-l-admin@sdsc.edu [mailto:pdb-l-admin@sdsc.edu] On 
+-   * > Behalf Of Philipp Heuser
+-   * > Sent: Thursday, March 27, 2003 6:05 AM
+-   * > To: pdb-l@sdsc.edu
+-   * > Subject: pdb-l: temperature factor; occupancy
+-   * > 
+-   * > 
+-   * > Hi all!
+-   * > 
+-   * > Does anyone know where to find proper definitions for the 
+-   * > temperature factors 
+-   * > and the values for occupancy?
+-   * > 
+-   * > Alright I do know, that the atoms with high temperature 
+-   * > factors are more 
+-   * > disordered than others, but what does a temperature factor of 
+-   * > a specific 
+-   * > value mean exactly.
+-   * > 
+-   * > 
+-   * > Thanks in advance!
+-   * > 
+-   * > Philipp
+-   * > 
++   * 

++   * > -----Original Message-----
++   * > From: pdb-l-admin@sdsc.edu [mailto:pdb-l-admin@sdsc.edu] On 
++   * > Behalf Of Philipp Heuser
++   * > Sent: Thursday, March 27, 2003 6:05 AM
++   * > To: pdb-l@sdsc.edu
++   * > Subject: pdb-l: temperature factor; occupancy
++   * > 
++   * > 
++   * > Hi all!
++   * > 
++   * > Does anyone know where to find proper definitions for the 
++   * > temperature factors 
++   * > and the values for occupancy?
++   * > 
++   * > Alright I do know, that the atoms with high temperature 
++   * > factors are more 
++   * > disordered than others, but what does a temperature factor of 
++   * > a specific 
++   * > value mean exactly.
++   * > 
++   * > 
++   * > Thanks in advance!
++   * > 
++   * > Philipp
++   * > 
+    * pdb-l: temperature factor; occupancy
+    * Bernhard Rupp br@llnl.gov
+    * Thu, 27 Mar 2003 08:01:29 -0800
 @@ -154,7 +154,7 @@ public class BioShape extends AtomShape
-    * * Next message: pdb-l: Structural alignment?
-    * * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
-    * 
--   * Isotropic B is defined as 8*pi**2.
-+   * Isotropic B is defined as 8*pi**2<u**2>.
-    * 
-    * Meaning: eight pi squared =79
-    * 
+    * * Next message: pdb-l: Structural alignment?
+    * * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
+    * 
+-   * Isotropic B is defined as 8*pi**2.
++   * Isotropic B is defined as 8*pi**2<u**2>.
+    * 
+    * Meaning: eight pi squared =79
+    * 
 @@ -174,7 +174,7 @@ public class BioShape extends AtomShape
-    * for more examples.
-    * 
-    * BR
--   *
-+   *

-    *
-    * @param bFactor100
-    * @return ?
---- 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
+    * for more examples.
+    * 
+    * BR
+-   *
++   *
+ * + * @param bFactor100 + * @return ? +--- src/org/jmol/shapespecial/Polyhedra.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/shapespecial/Polyhedra.java 2021-03-17 09:35:59.177003822 -0600 @@ -645,7 +645,7 @@ public class Polyhedra extends AtomShape /** * @@ -1107,8 +1096,8 @@ * 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 +--- src/org/jmol/shapesurface/IsosurfaceMesh.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/shapesurface/IsosurfaceMesh.java 2021-03-17 09:35:59.177003822 -0600 @@ -77,7 +77,6 @@ public class IsosurfaceMesh extends Mesh /** @@ -1150,8 +1139,8 @@ * tested. * * @param vertexValues ---- 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 +--- src/org/jmol/smiles/package.html.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/smiles/package.html 2021-03-17 09:35:59.178003821 -0600 @@ -63,7 +63,7 @@ the term aromatic @@ -1393,8 +1382,8 @@
updated 4/10/2012: fix for [$(...)n] and [$(...)min-max]
original5/19/2010

---- 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 +--- src/org/jmol/smiles/SmilesAromatic.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/smiles/SmilesAromatic.java 2021-03-17 09:35:59.178003821 -0600 @@ -336,7 +336,7 @@ public class SmilesAromatic { * @param vMean * @param n @@ -1404,8 +1393,8 @@ */ private final static boolean checkStandardDeviation(V3[] vNorms, V3 vMean, int n, float cutoff) { ---- 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 +--- src/org/jmol/smiles/SmilesMatcher.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/smiles/SmilesMatcher.java 2021-03-17 09:35:59.178003821 -0600 @@ -57,13 +57,13 @@ import org.jmol.viewer.JC; * * Specification for this implementation can be found in package.html. @@ -1422,79 +1411,79 @@ * * BitSet[] find -- finds one or more occurances of a SMILES or SMARTS string within a SMILES string * ---- 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 +--- src/org/jmol/smiles/SmilesParser.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/smiles/SmilesParser.java 2021-03-17 09:35:59.178003821 -0600 @@ -119,7 +119,7 @@ public class SmilesParser { - * - * @param pattern - * SMILES String -- * @return Molecule corresponding pattern -+ * @return Molecule corresponding pattern - * @throws InvalidSmilesException - */ - SmilesSearch parse(String pattern) throws InvalidSmilesException { + * + * @param pattern + * SMILES String +- * @return Molecule corresponding pattern ++ * @return Molecule corresponding pattern + * @throws InvalidSmilesException + */ + SmilesSearch parse(String pattern) throws InvalidSmilesException { @@ -863,7 +863,7 @@ public class SmilesParser { - * @param isBracketed - * true if a bracketed definition [...] - * @param isAND -- * being called from checkLogic for & or ; -+ * being called from checkLogic for & or ; - * @param isBranchAtom - * @return New atom - * @throws InvalidSmilesException ---- 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 + * @param isBracketed + * true if a bracketed definition [...] + * @param isAND +- * being called from checkLogic for & or ; ++ * being called from checkLogic for & or ; + * @param isBranchAtom + * @return New atom + * @throws InvalidSmilesException +--- src/org/jmol/symmetry/CIPChirality.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/symmetry/CIPChirality.java 2021-03-17 09:35:59.179003820 -0600 @@ -68,7 +68,7 @@ import org.jmol.viewer.JC; - * - * - implemented in Java (Jmol) and JavaScript (JSmol) - * -- * - only a few Java classes; < 1000 lines -+ * - only a few Java classes; < 1000 lines - * - * - efficient, one-pass process for each center using a single finite digraph - * for all auxiliary descriptors + * + * - implemented in Java (Jmol) and JavaScript (JSmol) + * +- * - only a few Java classes; < 1000 lines ++ * - only a few Java classes; < 1000 lines + * + * - efficient, one-pass process for each center using a single finite digraph + * for all auxiliary descriptors @@ -265,10 +265,10 @@ import org.jmol.viewer.JC; - * isotopic mass and, in all other cases, as their element's atomic weight. - * - * Rationale: BB is not self-consistent, including both "mass number" (in the -- * rule) and "atomic mass" in the description, where "79Br < Br < 81Br". And -+ * rule) and "atomic mass" in the description, where "79Br < Br < 81Br". And - * again we have the same Kekule-ambiguous issue as in Rule 1b. The added - * clarification fixes the Kekule issue (not using isotope mass number for -- * duplicate atoms), solves the problem that F < 19F (though 100% nat. -+ * duplicate atoms), solves the problem that F < 19F (though 100% nat. - * abundance), and is easily programmable. - * - * In Jmol the logic is very simple, actually using the isotope mass number, but + * isotopic mass and, in all other cases, as their element's atomic weight. + * + * Rationale: BB is not self-consistent, including both "mass number" (in the +- * rule) and "atomic mass" in the description, where "79Br < Br < 81Br". And ++ * rule) and "atomic mass" in the description, where "79Br < Br < 81Br". And + * again we have the same Kekule-ambiguous issue as in Rule 1b. The added + * clarification fixes the Kekule issue (not using isotope mass number for +- * duplicate atoms), solves the problem that F < 19F (though 100% nat. ++ * duplicate atoms), solves the problem that F < 19F (though 100% nat. + * abundance), and is easily programmable. + * + * In Jmol the logic is very simple, actually using the isotope mass number, but @@ -809,7 +809,7 @@ public class CIPChirality { - * Check if an atom is 1st row. - * - * @param a -- * @return elemno > 2 && elemno <= 10 -+ * @return elemno > 2 && elemno ≤ 10 - */ - static boolean isFirstRow(SimpleNode a) { - int n = a.getElementNumber(); + * Check if an atom is 1st row. + * + * @param a +- * @return elemno > 2 && elemno <= 10 ++ * @return elemno > 2 && elemno ≤ 10 + */ + static boolean isFirstRow(SimpleNode a) { + int n = a.getElementNumber(); @@ -1334,7 +1334,7 @@ public class CIPChirality { - /** - * Rule 2 isotope mass number if identified or average atomic mass if not - * -- * C (12.011) > 12C, O (15.999) < 16O, and F (18.998) < 19F -+ * C (12.011) > 12C, O (15.999) < 16O, and F (18.998) < 19F - * - * Source: - * + /** + * Rule 2 isotope mass number if identified or average atomic mass if not + * +- * C (12.011) > 12C, O (15.999) < 16O, and F (18.998) < 19F ++ * C (12.011) > 12C, O (15.999) < 16O, and F (18.998) < 19F + * + * Source: + * @@ -1491,7 +1491,7 @@ public class CIPChirality { - /** - * auxiliary chirality as determined in createAuxiliaryRule4Data; - * possibilities include R/S, r/s, M/P, m/p, C/T (but not c/t), or ~ (ASCII -- * 126, no stereochemistry); for sorting purposes C=M=R < p=r=s < ~ -+ * 126, no stereochemistry); for sorting purposes C=M=R < p=r=s < ~ - */ - private char auxChirality = '~'; - ---- 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 + /** + * auxiliary chirality as determined in createAuxiliaryRule4Data; + * possibilities include R/S, r/s, M/P, m/p, C/T (but not c/t), or ~ (ASCII +- * 126, no stereochemistry); for sorting purposes C=M=R < p=r=s < ~ ++ * 126, no stereochemistry); for sorting purposes C=M=R < p=r=s < ~ + */ + private char auxChirality = '~'; + +--- src/org/jmol/symmetry/SpaceGroup.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/symmetry/SpaceGroup.java 2021-03-17 09:35:59.179003820 -0600 @@ -162,7 +162,7 @@ class SpaceGroup { /** * @@ -1504,8 +1493,8 @@ * @return a new SpaceGroup if successful or null */ private static SpaceGroup createSGFromList(String name, Lst data) { ---- 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 +--- src/org/jmol/symmetry/Symmetry.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/symmetry/Symmetry.java 2021-03-17 09:35:59.179003820 -0600 @@ -166,8 +166,8 @@ public class Symmetry implements Symmetr * * @param desiredSpaceGroupIndex @@ -1517,88 +1506,88 @@ * @return true if a known space group */ @Override ---- 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 +--- src/org/jmol/symmetry/UnitCellIterator.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/symmetry/UnitCellIterator.java 2021-03-17 09:35:59.179003820 -0600 @@ -44,7 +44,7 @@ public class UnitCellIterator implements - * @param atoms - * @param bsAtoms - * @param distance -- * <= 0 indicates that distance will be set later, probably from a -+ * ≤ 0 indicates that distance will be set later, probably from a - * point - * @return this - */ ---- 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 + * @param atoms + * @param bsAtoms + * @param distance +- * <= 0 indicates that distance will be set later, probably from a ++ * ≤ 0 indicates that distance will be set later, probably from a + * point + * @return this + */ +--- src/org/jmol/thread/SpinThread.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/thread/SpinThread.java 2021-03-17 09:35:59.179003820 -0600 @@ -101,8 +101,8 @@ public class SpinThread extends JmolThre - * - * JavaScript: - * -- * run1(INIT) run1(MAIN) --> setTimeout to run1(CHECK) or run1(FINISH) and -- * return run1(CHECK) --> setTimeout to run1(CHECK) or run1(MAIN) or -+ * run1(INIT) run1(MAIN) → setTimeout to run1(CHECK) or run1(FINISH) and -+ * return run1(CHECK) → setTimeout to run1(CHECK) or run1(MAIN) or - * run1(FINISH) and return - * - */ ---- 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 + * + * JavaScript: + * +- * run1(INIT) run1(MAIN) --> setTimeout to run1(CHECK) or run1(FINISH) and +- * return run1(CHECK) --> setTimeout to run1(CHECK) or run1(MAIN) or ++ * run1(INIT) run1(MAIN) → setTimeout to run1(CHECK) or run1(FINISH) and ++ * return run1(CHECK) → setTimeout to run1(CHECK) or run1(MAIN) or + * run1(FINISH) and return + * + */ +--- src/org/jmol/util/BSUtil.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/util/BSUtil.java 2021-03-17 09:35:59.179003820 -0600 @@ -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 - * -- * Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is -- * a subset of a, then --> a not b if a only intersects with b, then --> a or -+ * Thus, if a equals b → clear all if a is a subset of b, then → b if b is -+ * a subset of a, then → a not b if a only intersects with b, then → a or - * b if a does not intersect with b, then a or b - * - * In "toggle" mode, when you click on any atom of the molecule, you want + * 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 + * +- * Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is +- * a subset of a, then --> a not b if a only intersects with b, then --> a or ++ * Thus, if a equals b → clear all if a is a subset of b, then → b if b is ++ * a subset of a, then → a not b if a only intersects with b, then → a or + * b if a does not intersect with b, then a or b + * + * In "toggle" mode, when you click on any atom of the molecule, you want @@ -145,7 +145,7 @@ final public class BSUtil { - /** - * this one slides deleted bits out of a pattern. - * -- * deleteBits 101011b, 000011b --> 1010b -+ * deleteBits 101011b, 000011b → 1010b - * - * Java 1.4, not 1.3 - * + /** + * this one slides deleted bits out of a pattern. + * +- * deleteBits 101011b, 000011b --> 1010b ++ * deleteBits 101011b, 000011b → 1010b + * + * Java 1.4, not 1.3 + * @@ -174,7 +174,7 @@ final public class BSUtil { - /** - * this one slides bits to higher positions based on a pattern. - * -- * shiftBits 101011b, 000011b --> 10101100b -+ * shiftBits 101011b, 000011b → 10101100b - * - * @param bs - * @param bsAdded ---- 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 + /** + * this one slides bits to higher positions based on a pattern. + * +- * shiftBits 101011b, 000011b --> 10101100b ++ * shiftBits 101011b, 000011b → 10101100b + * + * @param bs + * @param bsAdded +--- src/org/jmol/util/ColorEncoder.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/util/ColorEncoder.java 2021-03-17 09:35:59.179003820 -0600 @@ -172,7 +172,7 @@ import javajs.util.P3; - * @param name - * @param scale if null, then this is a reset. - * @param isOverloaded if TRUE, -- * @return >= 0 for a default color scheme -+ * @return ≥ 0 for a default color scheme - */ - private synchronized int makeColorScheme(String name, int[] scale, - boolean isOverloaded) { ---- 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 + * @param name + * @param scale if null, then this is a reset. + * @param isOverloaded if TRUE, +- * @return >= 0 for a default color scheme ++ * @return ≥ 0 for a default color scheme + */ + private synchronized int makeColorScheme(String name, int[] scale, + boolean isOverloaded) { +--- src/org/jmol/util/CommandHistory.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/util/CommandHistory.java 2021-03-17 09:35:59.180003818 -0600 @@ -169,9 +169,9 @@ final public class CommandHistory { - /** - * Options include: - * all Integer.MAX_VALUE -- * n prev n >= 1 -+ * n prev n ≥ 1 - * next -1 -- * set max to -2 - n n <= -3 -+ * set max to -2 - n n ≤ -3 - * just clear -2 - * clear and turn off; return "" 0 - * clear and turn on; return "" Integer.MIN_VALUE; ---- 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 + /** + * Options include: + * all Integer.MAX_VALUE +- * n prev n >= 1 ++ * n prev n ≥ 1 + * next -1 +- * set max to -2 - n n <= -3 ++ * set max to -2 - n n ≤ -3 + * just clear -2 + * clear and turn off; return "" 0 + * clear and turn on; return "" Integer.MIN_VALUE; +--- src/org/jmol/util/Elements.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/util/Elements.java 2021-03-17 09:35:59.180003818 -0600 @@ -883,7 +883,7 @@ public class Elements { * that contains the atomic number, the charge, and the radius in two * consecutive values, encoded as follows: @@ -1608,39 +1597,39 @@ * * That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius * ---- 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 +--- src/org/jmol/util/MeshCapper.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/util/MeshCapper.java 2021-03-17 09:35:59.180003818 -0600 @@ -37,7 +37,7 @@ import javajs.util.V3; - * - no push/pop stacks - * - * INPUT: stream of [a b] ordered-vertex edges such that triangle a-b-c is -- * interior if (ab.cross.ac).dot.planeNormal > 0 (right-hand rule; -+ * interior if (ab.cross.ac).dot.planeNormal > 0 (right-hand rule; - * counter-clockwise edge flow) - * - * Bob Hanson - Jan 11, 2015 + * - no push/pop stacks + * + * INPUT: stream of [a b] ordered-vertex edges such that triangle a-b-c is +- * interior if (ab.cross.ac).dot.planeNormal > 0 (right-hand rule; ++ * interior if (ab.cross.ac).dot.planeNormal > 0 (right-hand rule; + * counter-clockwise edge flow) + * + * Bob Hanson - Jan 11, 2015 @@ -804,7 +804,7 @@ public class MeshCapper { - * @param v0 - * @param v1 - * @param v2 -- * @return true if properly wound -- (v1-v0).cross.(v2-v0).dot.norm > 0 -+ * @return true if properly wound -- (v1-v0).cross.(v2-v0).dot.norm > 0 - */ - 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 2021-02-05 17:54:50.000000000 -0700 -+++ src/org/jmol/util/Modulation.java 2021-02-22 16:26:47.296461581 -0700 + * @param v0 + * @param v1 + * @param v2 +- * @return true if properly wound -- (v1-v0).cross.(v2-v0).dot.norm > 0 ++ * @return true if properly wound -- (v1-v0).cross.(v2-v0).dot.norm > 0 + */ + 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 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/util/Modulation.java 2021-03-17 09:35:59.180003818 -0600 @@ -305,7 +305,7 @@ public class Modulation { - } - - /** -- * Check that left < x4 < right, but allow for folding -+ * Check that left < x4 < right, but allow for folding - * - * @param x4 - * @return true only if x4 is in the (possibly folded) range of left and right ---- 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 + } + + /** +- * Check that left < x4 < right, but allow for folding ++ * Check that left < x4 < right, but allow for folding + * + * @param x4 + * @return true only if x4 is in the (possibly folded) range of left and right +--- src/org/jmol/util/Node.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/util/Node.java 2021-03-17 09:35:59.180003818 -0600 @@ -73,7 +73,7 @@ public interface Node extends SimpleNode public int getModelIndex(); public int getAtomNumber(); @@ -1650,31 +1639,31 @@ * * @return number of missing H atoms */ ---- 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 +--- src/org/jmol/util/SimpleUnitCell.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/util/SimpleUnitCell.java 2021-03-17 09:35:59.180003818 -0600 @@ -381,16 +381,16 @@ public class SimpleUnitCell { - /** - * Expanded cell notation: - * -- * 111 - 1000 --> center 5,5,5; range 0 to 9 or -5 to +4 -+ * 111 - 1000 → center 5,5,5; range 0 to 9 or -5 to +4 - * -- * 1000000 - 1999999 --> center 50,50,50; range 0 to 99 or -50 to +49 -- * 1000000000 - 1999999999 --> center 500, 500, 500; range 0 to 999 or -500 to -+ * 1000000 - 1999999 → center 50,50,50; range 0 to 99 or -50 to +49 -+ * 1000000000 - 1999999999 → center 500, 500, 500; range 0 to 999 or -500 to - * +499 - * - * @param nnn - * @param cell - * @param offset -- * 0 or 1 typically; < 0 means "apply no offset" -+ * 0 or 1 typically; < 0 means "apply no offset" - * @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 2021-02-05 17:54:50.000000000 -0700 -+++ src/org/jmol/util/Tensor.java 2021-02-22 16:26:47.296461581 -0700 + /** + * Expanded cell notation: + * +- * 111 - 1000 --> center 5,5,5; range 0 to 9 or -5 to +4 ++ * 111 - 1000 → center 5,5,5; range 0 to 9 or -5 to +4 + * +- * 1000000 - 1999999 --> center 50,50,50; range 0 to 99 or -50 to +49 +- * 1000000000 - 1999999999 --> center 500, 500, 500; range 0 to 999 or -500 to ++ * 1000000 - 1999999 → center 50,50,50; range 0 to 99 or -50 to +49 ++ * 1000000000 - 1999999999 → center 500, 500, 500; range 0 to 999 or -500 to + * +499 + * + * @param nnn + * @param cell + * @param offset +- * 0 or 1 typically; < 0 means "apply no offset" ++ * 0 or 1 typically; < 0 means "apply no offset" + * @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 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/util/Tensor.java 2021-03-17 09:35:59.181003817 -0600 @@ -289,7 +289,7 @@ public class Tensor { /** * width of the signal; |e2 - e0| @@ -1700,61 +1689,61 @@ * * which amounts to the same thing and is prettier. (Think about it!) * ---- 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 +--- src/org/jmol/util/Vibration.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/util/Vibration.java 2021-03-17 09:35:59.181003817 -0600 @@ -26,7 +26,7 @@ public class Vibration extends V3 { - // public static final int TYPE_DISPLACEMENT = -3; // not used - - /** -- * modDim will be > 0 for modulation -+ * modDim will be > 0 for modulation - */ - public int modDim = TYPE_VIBRATION; - public float modScale = Float.NaN; // modulation only ---- 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 - * - * @param params -- * include: fileName: starts with ? --> use file dialog; type: PNG, -+ * include: fileName: starts with ? → use file dialog; type: PNG, - * 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 2021-02-05 17:54:50.000000000 -0700 -+++ src/org/jmol/viewer/TransformManager.java 2021-02-22 16:26:47.297461581 -0700 + // public static final int TYPE_DISPLACEMENT = -3; // not used + + /** +- * modDim will be > 0 for modulation ++ * modDim will be > 0 for modulation + */ + public int modDim = TYPE_VIBRATION; + public float modScale = Float.NaN; // modulation only +--- src/org/jmol/viewer/OutputManager.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/viewer/OutputManager.java 2021-03-17 09:35:59.181003817 -0600 +@@ -636,7 +636,7 @@ abstract class OutputManager { + * jmolStatusListener interface + * + * @param params +- * include: fileName: starts with ? --> use file dialog; type: PNG, ++ * include: fileName: starts with ? → use file dialog; type: PNG, + * 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 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/viewer/TransformManager.java 2021-03-17 09:35:59.181003817 -0600 @@ -2190,8 +2190,8 @@ public class TransformManager { - } - - /** -- * sets the period of vibration -- period > 0: sets the period and turns -- * vibration on -- period < 0: sets the period but does not turn vibration on -+ * sets the period of vibration -- period > 0: sets the period and turns -+ * vibration on -- period < 0: sets the period but does not turn vibration on - * -- period = 0: sets the period to zero and turns vibration off -- period - * Float.NaN: uses current setting (frame change) - * + } + + /** +- * sets the period of vibration -- period > 0: sets the period and turns +- * vibration on -- period < 0: sets the period but does not turn vibration on ++ * sets the period of vibration -- period > 0: sets the period and turns ++ * vibration on -- period < 0: sets the period but does not turn vibration on + * -- period = 0: sets the period to zero and turns vibration off -- period + * Float.NaN: uses current setting (frame change) + * @@ -2725,7 +2725,7 @@ public class TransformManager { - - /** - * sets the position of the navigation offset relative to the model (50% -- * center; 0% rear, 100% front; can be <0 or >100) -+ * center; 0% rear, 100% front; can be <0 or >100) - * - * @param percent - */ + + /** + * sets the position of the navigation offset relative to the model (50% +- * center; 0% rear, 100% front; can be <0 or >100) ++ * center; 0% rear, 100% front; can be <0 or >100) + * + * @param percent + */ @@ -2735,7 +2735,7 @@ public class TransformManager { - } - - /** -- * seconds < 0 means "to (x,y)"; >= 0 mean "to (x%, y%)" -+ * seconds < 0 means "to (x,y)"; ≥ 0 mean "to (x%, y%)" - * - * @param seconds - * @param x ---- 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 + } + + /** +- * seconds < 0 means "to (x,y)"; >= 0 mean "to (x%, y%)" ++ * seconds < 0 means "to (x,y)"; ≥ 0 mean "to (x%, y%)" + * + * @param seconds + * @param x +--- src/org/jmol/viewer/Viewer.java.orig 2021-03-07 13:58:32.000000000 -0700 ++++ src/org/jmol/viewer/Viewer.java 2021-03-17 09:35:59.182003816 -0600 @@ -722,9 +722,9 @@ public class Viewer extends JmolViewer i * * disables command threading @@ -1785,7 +1774,7 @@ * * data[3] -- arrayDepth * 0(String),1(float[]),2(float[][]),3(float[][][]) or -1 to indicate -@@ -7895,7 +7895,7 @@ public class Viewer extends JmolViewer i +@@ -7891,7 +7891,7 @@ public class Viewer extends JmolViewer i } /** @@ -1794,7 +1783,7 @@ * 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. * -@@ -8117,8 +8117,8 @@ public class Viewer extends JmolViewer i +@@ -8113,8 +8113,8 @@ public class Viewer extends JmolViewer i } /** @@ -1805,7 +1794,7 @@ * return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE; * * @param howFarBack -@@ -8695,9 +8695,9 @@ public class Viewer extends JmolViewer i +@@ -8691,9 +8691,9 @@ public class Viewer extends JmolViewer i * * @param eval * @param steps @@ -1817,7 +1806,7 @@ * @param bsSelected * @param bsFixed * @param rangeFixed -@@ -9439,10 +9439,10 @@ public class Viewer extends JmolViewer i +@@ -9435,10 +9435,10 @@ public class Viewer extends JmolViewer i * * * @param id @@ -1830,7 +1819,7 @@ * * @param isAssign * from a file reader, not a select query -@@ -9878,7 +9878,7 @@ public class Viewer extends JmolViewer i +@@ -9874,7 +9874,7 @@ 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 @@ -1839,8 +1828,8 @@ */ 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 2021-02-05 17:54:50.000000000 -0700 -+++ src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java 2021-02-22 16:26:47.298461581 -0700 +--- src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java.orig 2021-03-07 13:58:33.000000000 -0700 ++++ src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java 2021-03-17 09:35:59.182003816 -0600 @@ -173,7 +173,7 @@ import naga.packetwriter.RawPacketWriter * * sync 30000 "backgrund blue" diff --git a/jmol.spec b/jmol.spec index d58ab70..ea60101 100644 --- a/jmol.spec +++ b/jmol.spec @@ -6,7 +6,7 @@ # JDK in Fedora is JDK 11, we target that release. Name: jmol -Version: 14.31.31 +Version: 14.31.34 Release: 1%{?dist} Summary: Java viewer for chemical structures in 3D @@ -38,7 +38,6 @@ BuildRequires: docbook-dtds BuildRequires: docbook-style-xsl BuildRequires: gettext BuildRequires: java-devel -BuildRequires: java-javadoc BuildRequires: javapackages-tools BuildRequires: jni-inchi BuildRequires: junit @@ -131,7 +130,7 @@ ln -s %{_jnidir}/jni-inchi/jni-inchi.jar jars sed -i '/netscape\.jar/d' build.xml # Fix EOL encoding -for doc in CHANGES.txt COPYRIGHT.txt LICENSE.txt README.txt; do +for doc in COPYRIGHT.txt LICENSE.txt README.txt; do sed -i.orig "s|\r||g" $doc touch -r $doc.orig $doc rm $doc.orig @@ -223,6 +222,9 @@ cd ../.. %license COPYRIGHT.txt LICENSE.txt %changelog +* Wed Mar 17 2021 Jerry James - 14.31.34-1 +- Version 14.31.34 + * Mon Feb 22 2021 Jerry James - 14.31.31-1 - Version 14.31.31 diff --git a/sources b/sources index d41eeff..6058523 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (Jmol-14.31.31-full.tar.gz) = 2087729d7e1a72313930f83e5e0fb3a7e790e21f430b2587c4c770731b190b6835d93dc4eb400f3c67b1eb00644bd45050d12a171f8108779548e4cbb0993e49 +SHA512 (Jmol-14.31.34-full.tar.gz) = a00a1b226a0fe9bc35c5e386051abb84929e41a6ef9c958ffe9949ddc60accebafc7c0c75020f800fbbddb7c2eda63dbf12e2e307e93bab8fc95f2354efeedd8 SHA512 (Jmol_icon13.svg) = 116b94f19e94e822cae9679d4eab7bab8841144b0cf85ba70de31cf59f3e6c82b478a5a38c4afe6c1c34f684667ce3c51fc0487df63673145060a34934fff785