--- src/org/jmol/adapter/readers/cif/CifReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/cif/CifReader.java 2021-11-29 14:03:35.562101209 -0700
@@ -762,7 +762,7 @@ public class CifReader extends AtomSetCo
/**
*
- * the PDB transformation matrix cartesian --> fractional
+ * the PDB transformation matrix cartesian → fractional
*
* @throws Exception
*/
@@ -1991,7 +1991,7 @@ 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/cif/MMCifReader.java 2021-11-29 14:03:35.562101209 -0700
@@ -463,7 +463,7 @@ public class MMCifReader extends CifRead
};
/**
- * get canonical 1-letter DNA/RNA sequence code from 3-letter code. For example, "2MG" --> "G"
+ * get canonical 1-letter DNA/RNA sequence code from 3-letter code. For example, "2MG" → "G"
* @return true
* @throws Exception
*/
--- src/org/jmol/adapter/readers/cif/MSRdr.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/cif/MSRdr.java 2021-11-29 14:03:35.562101209 -0700
@@ -340,7 +340,7 @@ public class MSRdr implements MSInterfac
/**
* Create a script that will run to turn modulation on and to display only
- * atoms with modulated occupancy >= 0.5.
+ * atoms with modulated occupancy ≥ 0.5.
*
*/
@Override
--- src/org/jmol/adapter/readers/molxyz/MolReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/molxyz/MolReader.java 2021-11-29 14:03:35.563101209 -0700
@@ -49,7 +49,7 @@ import org.jmol.util.Logger;
*
* setAtomCoord(atom, x, y, z) applySymmetryAndSetTrajectory()
*
- * simple 2D-->3D conversion using
+ * simple 2D→3D conversion using
*
* load "xxx.mol" FILTER "2D"
*
--- src/org/jmol/adapter/readers/molxyz/V3000Rdr.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/molxyz/V3000Rdr.java 2021-11-29 14:03:35.563101209 -0700
@@ -37,7 +37,7 @@ import org.jmol.adapter.smarter.AtomSetC
* <p>
* <a href='http://www.mdli.com/downloads/public/ctfile/ctfile.jsp'>
* http://www.mdli.com/downloads/public/ctfile/ctfile.jsp </a>
- * <p>
+ * </p>
*/
public class V3000Rdr {
private MolReader mr;
--- src/org/jmol/adapter/readers/more/AFLOWReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/more/AFLOWReader.java 2021-11-29 14:03:35.563101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/more/JcampdxReader.java 2021-11-29 14:03:35.563101209 -0700
@@ -49,34 +49,33 @@ import org.jmol.viewer.JC;
*
* specifications (by example here):
*
- * ##$MODELS= <Models> <ModelData id="acetophenone" type="MOL"> acetophenone
+ * ##$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 </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>
+ * 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 <ModelData> 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)
*
- * ##$PEAKS= <Peaks type="IR" xUnits="1/cm" yUnits="TRANSMITTANCE" > <PeakData
+ * ##$PEAKS= <Peaks type="IR" xUnits="1/cm" yUnits="TRANSMITTANCE" > <PeakData
* id="1" title="asymm stretch of aromatic CH group (~3100 cm-1)"
* peakShape="broad" model="irvibs.1" xMax="3121" xMin="3081" yMax="1" yMin="0"
- * /> <PeakData id="2" title="symm stretch of aromatic CH group (~3085 cm-1)"
+ * /> <PeakData id="2" title="symm stretch of aromatic CH group (~3085 cm-1)"
* peakShape="broad" model="irvibs.2" xMax="3101" xMin="3071" yMax="1" yMin="0"
- * /> ... </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.
*
*
- * <p>
*/
public class JcampdxReader extends MolReader implements JmolJDXMOLReader {
@@ -309,7 +308,7 @@ public class JcampdxReader extends MolRe
}
/**
- * integrate the <PeakAssignment> 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/more/MdTopReader.java 2021-11-29 14:03:35.563101209 -0700
@@ -34,10 +34,6 @@ import org.jmol.util.Logger;
* requires subsequent COORD "xxxx.mdcrd" file
*
*<p>
- * <a href=''>
- *
- * </a>
- *
* 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.
*
*
- *<p>
+ *</p>
*/
public class MdTopReader extends ForceFieldReader {
--- src/org/jmol/adapter/readers/more/Mol2Reader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/more/Mol2Reader.java 2021-11-29 14:03:35.564101209 -0700
@@ -34,7 +34,7 @@ import org.jmol.api.JmolAdapter;
/**
* A minimal multi-file reader for TRIPOS SYBYL mol2 files.
*<p>
- * <a href='http://www.tripos.com/data/support/mol2.pdf '>
+ * <a href='http://www.tripos.com/data/support/mol2.pdf'>
* http://www.tripos.com/data/support/mol2.pdf
* </a>
*
@@ -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
*
- *<p>
+ *</p>
*/
public class Mol2Reader extends ForceFieldReader {
--- src/org/jmol/adapter/readers/pdb/PdbReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/pdb/PdbReader.java 2021-11-29 14:03:35.564101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/pymol/PickleReader.java 2021-11-29 14:03:35.564101209 -0700
@@ -21,7 +21,7 @@ import javajs.util.Lst;
* 2013.04.06 -- added memo functions. PyMOL pickling is using LONG_BINPUT way too often.
* This results in a huge unnecessary memory overhead. My only solution is to only
* cache Strings in memo, and then only selectively -- not parts of movie; not when
- * markCount > 5 (residues). This seems to work, but it is still way overkill, since each
+ * markCount > 5 (residues). This seems to work, but it is still way overkill, since each
* atom generates several items.
*
* see http://www.picklingtools.com/
--- src/org/jmol/adapter/readers/pymol/PyMOL.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/pymol/PyMOL.java 2021-11-29 14:03:35.565101209 -0700
@@ -22,7 +22,7 @@ import org.jmol.util.Logger;
* with note therein:
*
* for i in cmd.get_color_indices(1):
- * print>>fp, (
+ * print>>fp, (
* ( 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/pymol/PyMOLReader.java 2021-11-29 14:03:35.565101209 -0700
@@ -55,12 +55,12 @@ import javajs.util.V3;
* development started Feb 2013 Jmol 13.1.13
* reasonably full implementation May 2013 Jmol 13.1.16
*
- * PyMOL state --> Jmol model
- * PyMOL object --> Jmol named atom set, isosurface, CGO, or measurement
- * PyMOL group --> Jmol named atom set (TODO: add isosurfaces and measures to these?)
+ * PyMOL state → Jmol model
+ * PyMOL object → Jmol named atom set, isosurface, CGO, or measurement
+ * PyMOL group → Jmol named atom set (TODO: add isosurfaces and measures to these?)
* PyMOL movie: an initial view and a set of N "frames"
* PyMOL frame: references (a) a state, (b) a script, and (c) a view
- * PyMOL scene --> Jmol scene, including view, frame, visibilities, colors
+ * PyMOL scene → Jmol scene, including view, frame, visibilities, colors
*
* using set LOGFILE, we can dump this to a readable form.
*
--- src/org/jmol/adapter/readers/pymol/PyMOLScene.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/pymol/PyMOLScene.java 2021-11-29 14:03:35.566101209 -0700
@@ -846,7 +846,7 @@ class PyMOLScene implements JmolSceneGen
* create all objects for a given molecule or scene
* @param reps
* @param allowSurface
- * @param ac0 > 0 for a molecule; -1 for a scene
+ * @param ac0 > 0 for a molecule; -1 for a scene
* @param ac
*/
void createShapeObjects(BS[] reps, boolean allowSurface, int ac0,
--- src/org/jmol/adapter/readers/quantum/AdfReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/quantum/AdfReader.java 2021-11-29 14:03:35.566101209 -0700
@@ -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/).
*
* <p> 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.</p>
*
* <p> 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.</p>
*
*<p> 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.</p>
*
*
* @author Bradley A. Smith (yeldar@home.com)
--- src/org/jmol/adapter/readers/quantum/BasisFunctionReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/quantum/BasisFunctionReader.java 2021-11-29 14:03:35.566101209 -0700
@@ -40,7 +40,7 @@ import java.util.Map;
/**
*
- * @author hansonr <hansonr@stolaf.edu>
+ * @author hansonr <hansonr@stolaf.edu>
*/
public abstract class BasisFunctionReader extends AtomSetCollectionReader {
--- src/org/jmol/adapter/readers/quantum/CsfReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/quantum/CsfReader.java 2021-11-29 14:03:35.566101209 -0700
@@ -47,7 +47,7 @@ import org.jmol.util.Logger;
* streamlined CSF dataset reading capabilities 2007/04/09
*
*
- * @author hansonr <hansonr@stolaf.edu>
+ * @author hansonr <hansonr@stolaf.edu>
*/
public class CsfReader extends MopacSlaterReader {
--- src/org/jmol/adapter/readers/quantum/MoldenReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/quantum/MoldenReader.java 2021-11-29 14:03:35.567101209 -0700
@@ -20,7 +20,7 @@ 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 <hansonr@stolaf.edu> 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
*
@@ -28,7 +28,7 @@ import org.jmol.util.Logger;
* -- optional zeta in ANGS
* -- optional mopac scaling
*
- * @author Matthew Zwier <mczwier@gmail.com>
+ * @author Matthew Zwier <mczwier@gmail.com>
*/
public class MoldenReader extends MopacSlaterReader {
--- src/org/jmol/adapter/readers/quantum/MopacGraphfReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/quantum/MopacGraphfReader.java 2021-11-29 14:03:35.567101209 -0700
@@ -34,7 +34,7 @@ import org.jmol.adapter.smarter.Atom;
/**
* Reads Mopac 2007 GRAPHF output files
*
- * @author Bob Hanson <hansonr@stolaf.edu>
+ * @author Bob Hanson <hansonr@stolaf.edu>
*
*/
public class MopacGraphfReader extends MopacSlaterReader {
--- src/org/jmol/adapter/readers/quantum/MopacSlaterReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/quantum/MopacSlaterReader.java 2021-11-29 14:03:35.567101209 -0700
@@ -30,7 +30,7 @@ import org.jmol.adapter.smarter.Atom;
/**
*
- * @author hansonr <hansonr@stolaf.edu>
+ * @author hansonr <hansonr@stolaf.edu>
*/
abstract class MopacSlaterReader extends SlaterReader {
--- src/org/jmol/adapter/readers/quantum/QCJSONReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/quantum/QCJSONReader.java 2021-11-29 14:03:35.567101209 -0700
@@ -18,11 +18,11 @@ import org.qcschema.QCSchemaUnits;
* A molecular structure and orbital reader for MolDen files.
* See http://www.cmbi.ru.nl/molden/molden_format.html
*
- * updated by Bob Hanson <hansonr@stolaf.edu> 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 <mczwier@gmail.com>
+ * @author Matthew Zwier <mczwier@gmail.com>
*/
public class QCJSONReader extends MoldenReader {
--- src/org/jmol/adapter/readers/quantum/SlaterReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/quantum/SlaterReader.java 2021-11-29 14:03:35.568101209 -0700
@@ -35,7 +35,7 @@ import java.util.Map;
/**
*
- * @author hansonr <hansonr@stolaf.edu>
+ * @author hansonr <hansonr@stolaf.edu>
*/
abstract class SlaterReader extends MOReader {
@@ -59,8 +59,8 @@ abstract class SlaterReader extends MORe
*
* 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/quantum/WebMOReader.java 2021-11-29 14:03:35.568101209 -0700
@@ -46,7 +46,7 @@ import org.jmol.util.Logger;
* </a>
*
* right now WebMO files don't allow for multiple MOS, but we will assume here that that may change.
- *<p>
+ *</p>
*/
public class WebMOReader extends MopacSlaterReader {
--- src/org/jmol/adapter/readers/simple/GhemicalMMReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/simple/GhemicalMMReader.java 2021-11-29 14:03:35.568101209 -0700
@@ -67,7 +67,7 @@ import org.jmol.api.JmolAdapter;
* !End
* </code>
*
- * @author Egon Willighagen <egonw@sci.kun.nl>
+ * @author Egon Willighagen <egonw@sci.kun.nl>
*/
public class GhemicalMMReader extends AtomSetCollectionReader {
--- src/org/jmol/adapter/readers/simple/HyperChemReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/simple/HyperChemReader.java 2021-11-29 14:03:35.568101209 -0700
@@ -32,7 +32,7 @@ import org.jmol.api.JmolAdapter;
/**
* Support for .hin, HyperChem's native file format.
* http://www.hyper.com
- * <p />
+ * <p>
* Record format is:
* <code>
* 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
* </code>
- * interesting fields are partialCharge, x, y, z, bondCount<br />
- * bonds are atom number and s/d/t/a for single/double/triple/aromatic
+ * interesting fields are partialCharge, x, y, z, bondCount<br>
+ * bonds are atom number and s/d/t/a for single/double/triple/aromatic</p>
*/
public class HyperChemReader extends AtomSetCollectionReader {
--- src/org/jmol/adapter/readers/simple/MopacReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/simple/MopacReader.java 2021-11-29 14:03:35.568101209 -0700
@@ -34,7 +34,7 @@ import org.jmol.util.Logger;
/**
* Reads Mopac 93, 6, 7, 2002, or 2009 output files
*
- * @author Egon Willighagen <egonw@jmol.org>
+ * @author Egon Willighagen <egonw@jmol.org>
*/
public class MopacReader extends AtomSetCollectionReader {
--- src/org/jmol/adapter/readers/xtal/CrystalReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/adapter/readers/xtal/CrystalReader.java 2021-11-29 14:03:35.569101209 -0700
@@ -73,7 +73,7 @@ import org.jmol.util.Tensor;
* mat4CrystalToPrimitive M4 convenience inverse of
* mat4PrimitiveToCrystal
*
- * fileSymmetryOperations List<String> 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
*
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/api/JmolViewer.java 2021-11-29 14:03:35.569101209 -0700
@@ -414,7 +414,7 @@ abstract public class JmolViewer {
* NOTE: THIS METHOD DOES NOT PRESERVE THE STATE
*
* @param arrayData a Vector of models, where each model is either a String
- * or a String[] or a Vector<String>
+ * 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/awt/FileDropper.java 2021-11-29 14:03:35.569101209 -0700
@@ -55,7 +55,7 @@ import javajs.util.SB;
* <p>
* Note that multiple drops ARE thread safe.
*
- * @author Billy <simon.tyrrell@virgin.net>
+ * @author Billy <simon.tyrrell@virgin.net>
*/
public class FileDropper implements DropTargetListener {
private String fd_oldFileName;
--- src/org/jmol/awtjs2d/Platform.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/awtjs2d/Platform.java 2021-11-29 14:03:35.569101209 -0700
@@ -28,11 +28,11 @@ import javajs.util.SB;
/**
* JavaScript 2D canvas version requires Ajax-based URL stream processing.
*
- * Jmol "display" --> HTML5 "canvas"
- * Jmol "image" --> HTML5 "canvas" (because we need width and height)
- * Jmol "graphics" --> HTML5 "context(2d)" (one for display, one off-screen for fonts)
- * Jmol "font" --> JmolFont
- * Jmol "fontMetrics" --> HTML5 "context(2d)"
+ * Jmol "display" → HTML5 "canvas"
+ * Jmol "image" → HTML5 "canvas" (because we need width and height)
+ * Jmol "graphics" → HTML5 "context(2d)" (one for display, one off-screen for fonts)
+ * Jmol "font" → JmolFont
+ * Jmol "fontMetrics" → HTML5 "context(2d)"
* (Not fully implemented)
*
* @author Bob Hanson
--- src/org/jmol/awtjs/swing/SwingController.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/awtjs/swing/SwingController.java 2021-11-29 14:03:35.570101209 -0700
@@ -26,7 +26,7 @@ public interface SwingController {
* var component = Jmol.Swing.htDialogs[element.id];
* var info = component.toString();
*
- * if (info.indexOf("JCheck") >= 0)
+ * if (info.indexOf("JCheck") ≥ 0)
* 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/bspt/Bspt.java 2021-11-29 14:03:35.570101209 -0700
@@ -46,13 +46,15 @@ import javajs.util.T3;
* We are working with three dimensions. For the purposes of the Bspt code these
* dimensions are stored as 0, 1, or 2. Each node of the tree splits along the
* next dimension, wrapping around to 0.
+ * </p>
*
* <pre>
* mySplitDimension = (parentSplitDimension + 1) % 3;
* </pre>
*
- * 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
+ * <p>
+ * 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.
*</p>
--- src/org/jmol/bspt/PointIterator.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/bspt/PointIterator.java 2021-11-29 14:03:35.570101209 -0700
@@ -39,7 +39,7 @@ public class PointIterator {
* @param pt if not null and pt.x == Float.NaN, this is an internal comparison, to return a "cleaned" list of points
* @param ap3 the list of points, required
* @param ap31 a second list of points, optional
- * @param ret null, "", int[], Lst<T3>, 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/dssx/AnnotationParser.java 2021-11-29 14:03:35.570101209 -0700
@@ -309,7 +309,7 @@ public class AnnotationParser implements
}
/**
- * Returns a Lst<Object> 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/dssx/DSSP.java 2021-11-29 14:03:35.570101209 -0700
@@ -363,9 +363,9 @@ public class DSSP {
* the interatomic distance from A to B. In chemical units, r is in angstroms,
* the dimensional factor f = 332, and E is in kcal/mol. We ... assign an H
* 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/i18n/Language.java 2021-11-29 14:03:35.571101209 -0700
@@ -135,7 +135,7 @@ public class Language {
* @param nativeLanguage Language name in its own language (see ISO 639-1 for the values)
* @param display True if this language has a good percentage of translations done
*
- * {@link "http://en.wikipedia.org/wiki/List_of_ISO_639-1_codes"}
+ * See <a href="http://en.wikipedia.org/wiki/List_of_ISO_639-1_codes">the list of ISO-639-1 codes</a>.
*/
private Language(String code, String language, String nativeLanguage, boolean display) {
this.code = code;
--- src/org/jmol/jvxl/api/VertexDataServer.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/jvxl/api/VertexDataServer.java 2021-11-29 14:03:35.571101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/jvxl/data/JvxlCoder.java 2021-11-29 14:03:35.571101209 -0700
@@ -447,12 +447,14 @@ public class JvxlCoder {
/**
* contour data are appended to a string buffer in the form of a
- * <jmolContourData count="[nContours]">
- * <jmolContour index="0" value="-0.033" color="[xff0000]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>
- * <jmolContour index="1" value=" 0.000" color="[xffff00]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>
- * <jmolContour index="2" value=" 0.033" color="[x00ffff]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>
+ * <pre>
+ * <jmolContourData count="[nContours]">
+ * <jmolContour index="0" value="-0.033" color="[xff0000]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>
+ * <jmolContour index="1" value=" 0.000" color="[xffff00]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>
+ * <jmolContour index="2" value=" 0.033" color="[x00ffff]" encoding="base90iff1" data="fractional data">triangle bitset data</jmolContour>
* ...
- * </jmolContourData>
+ * </jmolContourData>
+ * </pre>
*
* One presumes an ordered set of triangles.
* The contour intersects these triangles along two edges or at two vertices.
@@ -688,7 +690,7 @@ public class JvxlCoder {
*
* ASCII:
* -30 -20 -10 0 +10 +20 +30
- * <=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|
+ * <=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|
*
* So the above sequence would simply be:
*
@@ -796,8 +798,8 @@ public class JvxlCoder {
*
* The tag will indicate the minimum and maximum values:
*
- * <jvxlVertexData count="150" min="(15.218472, -28.304049, 34.71112)"
- * max="(97.8228, 54.011948, 109.95208)" data="...."> </jvxlVertexData>
+ * <jvxlVertexData count="150" min="(15.218472, -28.304049, 34.71112)"
+ * max="(97.8228, 54.011948, 109.95208)" data="...."> </jvxlVertexData>
*
* 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/jvxl/data/VolumeData.java 2021-11-29 14:03:35.571101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/jvxl/readers/BCifDensityReader.java 2021-11-29 14:03:35.571101209 -0700
@@ -43,7 +43,7 @@ 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/jvxl/readers/CifDensityReader.java 2021-11-29 14:03:35.571101209 -0700
@@ -36,7 +36,7 @@ import javajs.util.PT;
* CIF density reader. See https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box,
* for example:
*
- * 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/jvxl/readers/JvxlXmlReader.java 2021-11-29 14:03:35.572101209 -0700
@@ -748,7 +748,7 @@ public class JvxlXmlReader extends Volum
/**
* retrieve Jvxl 2.0 format vertex/triangle/edge/color data found
- * within <jvxlSurfaceData> element
+ * within <jvxlSurfaceData> element
*
* @throws Exception
*/
@@ -790,7 +790,7 @@ public class JvxlXmlReader extends Volum
}
/**
- * decode vertex data found within <jvxlVertexData> element as created by
+ * decode vertex data found within <jvxlVertexData> element as created by
* jvxlEncodeVertexData (see above)
*
* @param data
@@ -855,7 +855,7 @@ public class JvxlXmlReader extends Volum
}
/**
- * decode triangle data found within <jvxlTriangleData> element as created
+ * decode triangle data found within <jvxlTriangleData> element as created
* with jvxlEncodeTriangleData (see above)
*
* @param tdata
--- src/org/jmol/jvxl/readers/KinemageReader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/jvxl/readers/KinemageReader.java 2021-11-29 14:03:35.572101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/minimize/forcefield/ForceFieldMMFF.java 2021-11-29 14:03:35.572101209 -0700
@@ -64,7 +64,7 @@ import javajs.util.PT;
*
* 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 javajs.util.PT;
* 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/minimize/Util.java 2021-11-29 14:03:35.572101209 -0700
@@ -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/modelsetbio/AlphaPolymer.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/modelsetbio/AlphaPolymer.java 2021-11-29 14:03:35.572101209 -0700
@@ -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.
*<p>
- * Levitt and Greer <br />
- * Automatic Identification of Secondary Structure in Globular Proteins <br />
- * J.Mol.Biol.(1977) 114, 181-293 <br />
+ * Levitt and Greer <br>
+ * Automatic Identification of Secondary Structure in Globular Proteins <br>
+ * J.Mol.Biol.(1977) 114, 181-293
+ *</p>
*<p>
* <a
* href='http://csb.stanford.edu/levitt/Levitt_JMB77_Secondary_structure.pdf'>
--- src/org/jmol/modelsetbio/AminoPolymer.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/modelsetbio/AminoPolymer.java 2021-11-29 14:03:35.573101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/modelsetbio/BioResolver.java 2021-11-29 14:03:35.573101209 -0700
@@ -1538,7 +1538,7 @@ 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/modelsetbio/Monomer.java 2021-11-29 14:03:35.573101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/modelset/Group.java 2021-11-29 14:03:35.573101209 -0700
@@ -92,7 +92,7 @@ public class Group implements Structure
/**
- * @j2sIngore
+ * @j2sIgnore
*/
public Group() {}
--- src/org/jmol/modelset/ModelLoader.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/modelset/ModelLoader.java 2021-11-29 14:03:35.574101209 -0700
@@ -675,7 +675,7 @@ 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/modelset/ModelSet.java 2021-11-29 14:03:35.574101209 -0700
@@ -3800,7 +3800,7 @@ 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/multitouch/sparshui/TwoPointGesture.java 2021-11-29 14:03:35.574101209 -0700
@@ -29,8 +29,8 @@ import com.sparshui.server.TouchPoint;
*
* v00 from pt(1,0) to pt(2,0)
*
- * ZOOM IN: <---- x -----> (at any angle)
- * ZOOM OUT: ----> x <----- (at any angle)
+ * ZOOM IN: <---- x -----> (at any angle)
+ * ZOOM OUT: ----> x <----- (at any angle)
*
* ROTATE CW: ^ |
* | x | (at any angle, not implemented)
@@ -42,9 +42,9 @@ import com.sparshui.server.TouchPoint;
*
* 2-point drag:
*
- * --------->
+ * --------->
* x (any direction)
- * --------->
+ * --------->
*
* Bob Hanson 12/13/2009
*
--- src/org/jmol/popup/JmolPopup.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/popup/JmolPopup.java 2021-11-29 14:03:35.575101209 -0700
@@ -268,7 +268,7 @@ 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/quantum/NciCalculation.java 2021-11-29 14:03:35.575101209 -0700
@@ -361,7 +361,7 @@ 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/quantum/NMRCalculation.java 2021-11-29 14:03:35.575101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/quantum/NMRNoeMatrix.java 2021-11-29 14:03:35.575101209 -0700
@@ -83,7 +83,7 @@ import org.jmol.viewer.Viewer;
* if the atoms have not been set up properly.
*
* @author YE91009
- * @created 28 February 2007
+ * @since 28 February 2007
*/
public class NMRNoeMatrix {
--- src/org/jmol/scriptext/MathExt.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/scriptext/MathExt.java 2021-11-29 14:03:35.576101209 -0700
@@ -1912,7 +1912,7 @@ public class MathExt {
* _(key) prepends "auxiliaryInfo.models", delivering a modelCount-length
* array of information
*
- * $ print _("aflowInfo[SELECT auid WHERE H__eV___VASP_ < 0]")
+ * $ print _("aflowInfo[SELECT auid WHERE H__eV___VASP_ < 0]")
*
*
* {atomset}._(key) selects for model Auxiliary info related to models of the
@@ -1923,9 +1923,9 @@ public class MathExt {
*
* Examples:
*
- * print _("aflowInfo[select sg where volume_cell > 70]")
+ * print _("aflowInfo[select sg where volume_cell > 70]")
*
- * print {model>10}._("aflowInfo[select sg where volume_cell > 70]")
+ * print {model>10}._("aflowInfo[select sg where volume_cell > 70]")
*
* @param mp
* @param args
@@ -2146,7 +2146,7 @@ public class MathExt {
}
/**
- * [ {...},{...}... ] ==> [[...],[...]]
+ * [ {...},{...}... ] → [[...],[...]]
*
* @param listIn
* @param formatList
--- src/org/jmol/script/ScriptCompiler.java.orig 2021-11-29 14:03:35.576101209 -0700
+++ src/org/jmol/script/ScriptCompiler.java 2021-11-29 14:05:28.032096723 -0700
@@ -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
@@ -2514,7 +2514,7 @@ 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 for (var i=0;i < 10; i++)
*
* @param ch
* @return true if end of line
@@ -2689,7 +2689,7 @@ 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/ScriptParam.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/script/ScriptParam.java 2021-11-29 14:03:35.577101209 -0700
@@ -1078,7 +1078,7 @@ abstract public class ScriptParam extend
}
/**
- * reads standard n.m float-as-integer n*1000000 + m and returns (n % 7) << 5
+ * reads standard n.m float-as-integer n*1000000 + m and returns (n % 7) << 5
* + (m % 0x1F)
*
* @param bondOrderInteger
--- src/org/jmol/shapebio/BioShape.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/shapebio/BioShape.java 2021-11-29 14:03:35.577101209 -0700
@@ -120,32 +120,32 @@ public class BioShape extends AtomShape
* <a href='http://www.rcsb.org/pdb/lists/pdb-l/200303/000609.html'>
* http://www.rcsb.org/pdb/lists/pdb-l/200303/000609.html
* </a>
- * <code>
- * > -----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
- * >
+ * <pre><code>
+ * > -----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<u**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
- *</code>
+ *</code></pre>
*
* @param bFactor100
* @return ?
--- src/org/jmol/shapespecial/Polyhedra.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/shapespecial/Polyhedra.java 2021-11-29 14:03:35.577101209 -0700
@@ -654,7 +654,7 @@ public class Polyhedra extends AtomShape
/**
*
* @param id may be null
- * @param iatom may be < 0 to (along with id==null) to get matching polyhedron
+ * @param iatom may be < 0 to (along with id==null) to get matching polyhedron
* @param allowCollapsed
* @return Polyhedron or null
*/
@@ -1393,7 +1393,7 @@ public class Polyhedra extends AtomShape
* Objective is to find all triangles with *essentially* the same normal and to
* then group them into a face. But we have to be careful here; not everything is
* perfect. We can have be so slightly off in a 4- or 6-face, and we still want it
- * to be called a face. We allow a normal dot product (i.e. cos(theta)) to be < 0.05.
+ * to be called a face. We allow a normal dot product (i.e. cos(theta)) to be < 0.05.
* This empirically seems to work.
*
* @param triangles
--- src/org/jmol/shapesurface/IsosurfaceMesh.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/shapesurface/IsosurfaceMesh.java 2021-11-29 14:03:35.577101209 -0700
@@ -77,7 +77,6 @@ public class IsosurfaceMesh extends Mesh
/**
* @param vwr
- * @XXXXj2sIgnoreSuperConstructor
*
* @param thisID
* @param colix
@@ -376,9 +375,9 @@ public class IsosurfaceMesh extends Mesh
}
/**
- * two values -- v1, and v2, which need not be ordered v1 < v2. v == v1 --> 0
- * v == v2 --> 1 v1 < v < v2 --> f in (0,1) v2 < v < v1 --> f in (0,1) i.e.
- * (v1 < v) == (v < v2)
+ * two values -- v1, and v2, which need not be ordered v1 < v2. v == v1 → 0
+ * v == v2 → 1 v1 < v < v2 → f in (0,1) v2 < v < v1 → f in (0,1) i.e.
+ * (v1 < v) == (v < v2)
*
* We check AB, then (usually) BC, then (sometimes) CA.
*
@@ -388,14 +387,14 @@ public class IsosurfaceMesh extends Mesh
* A 1.0 0.5 1.0 1.0 / \ / \ / \ / \ / \ / \ / \ / \ / \ / \ C-----B 1.0--0.5
* 1.0--1.0 0.5--1.0 1.0---1.0 case I case II case III case IV
*
- * case I: AB[0] and BC[1], type == 3 --> CA not tested. case II: AB[1] and
- * CA[0]; f1 == 1.0 --> BC not tested. case III: AB[0] and BC[0], type == 3
- * --> CA not tested. case IV: AB[0] and BC[0], type == 3 --> CA not tested.
+ * case I: AB[0] and BC[1], type == 3 → CA not tested. case II: AB[1] and
+ * CA[0]; f1 == 1.0 → BC not tested. case III: AB[0] and BC[0], type == 3
+ * → CA not tested. case IV: AB[0] and BC[0], type == 3 → CA not tested.
*
* what if v = 0.5?
*
- * case I: AB[1]; BC not tested --> type == 1, invalid. case II: AB[0]; type
- * == 1, f1 == 0.0 --> CA not tested. case III: BC[1]; f2 == 1.0 --> CA not
+ * case I: AB[1]; BC not tested → type == 1, invalid. case II: AB[0]; type
+ * == 1, f1 == 0.0 → CA not tested. case III: BC[1]; f2 == 1.0 → CA not
* tested.
*
* @param vertexValues
--- src/org/jmol/smiles/package.html.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/smiles/package.html 2021-11-29 14:03:35.578101209 -0700
@@ -63,7 +63,7 @@ the term <a href="#aromaticity">aromatic
<br><br>
- <h3>Comparision to <a target="_blank" href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">Daylight SMILES</a></h3>
+ <h2>Comparison to <a target="_blank" href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">Daylight SMILES</a></h2>
All single-component aspects of Daylight SMILES are implemented, including
aromaticity and atom- and bond-based stereochemistry ("chirality").
<br><br>
@@ -83,7 +83,8 @@ and may dramatically increase processing
Jmol SMILES adds the following two aspects to Daylight SMILES:
<br>
<br>
-<table border="1" cellpadding="5" width="500">
+<table border="1">
+<caption>Daylight SMILES aspects</caption>
<tr><td valign="top"><b>%(n)</b></td><td>Jmol SMILES adds unlimited branching. Daylight SMILES
allows indication of "rings" using the digits 1-9, for example, <b>C1CCCC1</b>. Actually, these numbers
do not necessarily indicate rings. Rather, in association with "." component notation,
@@ -136,7 +137,8 @@ the Jmol version used for its creation a
Jmol bioSMILES adds the following to Jmol SMILES:
<br>
<br>
-<table border="1" cellpadding="5" width="500">
+<table border="1">
+<caption>bioSMILES additions</caption>
<tr><td valign=top>~X~</td><td>
Jmol bioSMILES separates all protein, nucleic, and carbohydrate polymers into separate SMILES components,
separated by ".".
@@ -196,7 +198,7 @@ indicating a branched manose hexamer. No
<br>
- <h3>Comparision to <a target="_blank" href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">Daylight SMARTS</a></h3>
+ <h2>Comparison to <a target="_blank" href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">Daylight SMARTS</a></h2>
<ul>
<li>[H1] interpreted as [*H1] -- "an atom with one connected H atom".
@@ -227,7 +229,6 @@ Note that these variables are any string
</pre>
Note that $(...) need not be within [...], and
wherever it is, it always means "just the first atom".
-</li>
</li><li>All primitives that are not element names, <b>*</b>, <b>A</b>, or <b>a</b> must be
enclosed in brackets. In addition, the following elements must be enclosed in brackets
@@ -236,10 +237,10 @@ Note that these variables are any string
</li><li>Allows any order of bracketed primitives: [H2C13] same as [13CH2].
-</li><li>All atom and bond logic implemented: [X,!X,X&X,X&X&X;X&X]-,=X
+</li><li>All atom and bond logic implemented: [X,!X,X&X,X&X&X;X&X]-,=X
-</li><li>"&" is optional: [13CH2] same as [13&C&H2]
- except in cases of ambiguity with element symbols: [Rh] is rhodium, not [R&h].
+</li><li>"&" is optional: [13CH2] same as [13&C&H2]
+ except in cases of ambiguity with element symbols: [Rh] is rhodium, not [R&h].
</li><li>Jmol SMARTS does NOT implement:
<ul><li> "zero-level parentheses", since the match is
@@ -259,7 +260,8 @@ Note that these variables are any string
<br><br>
All Daylight SMARTS primitives are implemented. These include:
<br>
-<table border="1" cellpadding="5" width="500">
+<table border="1">
+<caption>Daylight SMARTS primitives</caption>
<tr><td>[Element]</td><td>capitalized - standard notation Na, Si, etc. -- specific non-aromatic atom</td></tr>
<tr><td>[element]</td><td>uncapitalized - specific aromatic atom (as for standard notation, no limitations)</td></tr>
<tr><td>*</td><td>any atom</td></tr>
@@ -282,20 +284,21 @@ All Daylight SMARTS primitives are imple
Jmol SMARTS adds the following primitives:
<br>
<br>
-<table border="1" cellpadding="5" width="800">
+<table border="1">
+<caption>SMARTS primitives</caption>
<tr><td>d</td><td>non-hydrogen degree -- number of non-hydrogen connections</td></tr>
<tr><td>=</td><td>Jmol atom index, for example: [=23]</td></tr>
<tr><td>"xxx"</td><td>atom type, in double quotes, for example: ["39"r5] (After <b>calculate partialcharge</b> this will be the MMFF94 atom type. [Jmol 12.3.24]</td></tr>
-<tr><td>$(select xxx)"</td><td>external selection method. For Jmol, this is an atom expression. For example: [c$(select temperature>10)] [Jmol 12.3.26]</td></tr>
+<tr><td>$(select xxx)"</td><td>external selection method. For Jmol, this is an atom expression. For example: [c$(select temperature>10)] [Jmol 12.3.26]</td></tr>
<tr><td>r500</td><td>a specifically aromatic 5-membered ring [Jmol 12.3.24]</td></tr>
<tr><td>r600</td><td>a specifically aromatic 6-membered ring [Jmol 12.3.24]</td></tr>
<tr><td>number?</td><td>mass number or undefined (so, for example, [C12?] means any carbon that isn't explicitly C13 or C14</td></tr>
<tr><td>$n(pattern)</td><td>A specific number of occurances of <b>pattern</b>. For example, <b>C[$3(C=C)]C</b> is synonymous with <b>CC=CC=CC=CC</b>.</td></tr>
<tr><td>$min-max(pattern)</td><td>A variable number of occurances of <b>pattern</b>.
For example: <b>A[$0-2(C:G)]A</b> is synonymous with <b>AA</b> or <b>AC(:G)A</b> or <b>AC(:G)C(:G)A</b>.</td></tr>
-<tr><td>residueName#resno^insCode.atomName#atomicNumber</b> </td><td>
+<tr><td><b>residueName#resno^insCode.atomName#atomicNumber</b> </td><td>
All five fields are optional; only the period itself is required.
-This primitive may appear with other primitives provided (a) it is first, and (b) it is followed by an operator ("," ,"&", or ";").
+This primitive may appear with other primitives provided (a) it is first, and (b) it is followed by an operator ("," ,"&", or ";").
This allows searching a bioSMILES string using SMARTS patterns that only involve standard atom types. In the above example,
notice that the connecting atoms to protein chains within the non-bioSEQUENCE component indicates the
connections to the protein using this extended notation. Thus, both the actual 3D model and the bioSMARTS string for 1d66
@@ -312,7 +315,8 @@ the phosphorus atom in nucleic acids, or
Jmol SMARTS adds the following in-line options:
<br>
<br>
-<table border="1" cellpadding="5" width="500">
+<table border="1">
+<caption>SMARTS in-line options</caption>
<tr><td valign=top>
/..../</td><td>
<b>processing directives</b> Jmol recognizes <b>/..../</b> at the beginning of a pattern as processing directives.
@@ -322,7 +326,7 @@ These directives can be introduced indiv
<b>invertStereo</b> reverses the sense of chirality (R-, S- stereochemistry). Double-bond stereochemistry is not reverse.
<b>noStereo</b> turns off all stereochemical checking.
</li><li><b>aromaticDouble</b> allows for using "=" between two aromatic atoms to indicate an explicitly double aromatic bond.
-To specify an explicitly single aromatic bond, use <b>@&!=</b>.
+ To specify an explicitly single aromatic bond, use <b>{@literal @}&!=</b>.
<b>aromaticStrict</b> uses a 6-electron Hueckel model for specifying aromaticity.
</li><li><b>noAromatic</b> turns off all aromaticity checks.It may be desirable when no distinction between
aromatic and nonaromatic atoms is desired. For large biomolecules /noAromatic/ can
@@ -419,7 +423,8 @@ in this case being equivalent to (and sl
Jmol bioSMARTS adds the following pattern options to Jmol SMARTS:
<br>
<br>
-<table border="1" cellpadding="5" width="500">
+<table border="1">
+<caption>bioSMARTS pattern options</caption>
<tr><td>
<b>"~"</b>
</td><td>Any biopolymer.
@@ -497,7 +502,7 @@ includes:
<br><br>
-<a name="smilesspecs"><h3>Detailed Jmol SMILES/bioSMILES Specification</h3></a>
+<h2><a id="smilesspecs">Detailed Jmol SMILES/bioSMILES Specification</a></h2>
<br><br>
<pre>
# note: prior to parsing, all white space is removed
@@ -521,7 +526,7 @@ includes:
| "[" [bracketedExpression] "]" }
[unbracketedAtomType] == [atomType]
- & ! { "Ac" | "Ba" | "Ca" | "Na" | "Pa" | "Sc"
+ & ! { "Ac" | "Ba" | "Ca" | "Na" | "Pa" | "Sc"
| "ac" | "ba" | "ca" | "na" | "pa" | "sc" }
# note: Brackets are required for these elements: [Na], [Ca], etc.
# These elements Xy are instead interpreted as "X" "y", a single-letter
@@ -558,7 +563,7 @@ includes:
# and must be preceded by an atomExpression for the
# first occurance and either an atomExpression or a bond
# for the second occurance
- # note: Jmol bioSMARTS extends the possible number of rings to > 100 by
+ # note: Jmol bioSMARTS extends the possible number of rings to > 100 by
# allowing %(n)
[connections] == [connection] | NULL }
@@ -590,7 +595,7 @@ includes:
</pre>
<br><br>
-<a name="specs"><h3>Detailed Jmol SMARTS/Jmol bioSMARTS Specification</h3></a>
+<h2><a id="specs">Detailed Jmol SMARTS/Jmol bioSMARTS Specification</a></h2>
<br><br>
<pre>
@@ -638,7 +643,7 @@ includes:
[unbracketedAtomType] == [atomType]
- & ! { "Ac" | "Ba" | "Ca" | "Na" | "Pa" | "Sc"
+ & ! { "Ac" | "Ba" | "Ca" | "Na" | "Pa" | "Sc"
| "ac" | "ba" | "ca" | "na" | "pa" | "sc" }
# note: Brackets are required for these elements: [Na], [Ca], etc.
# These elements Xy are instead interpreted as "X" "y", a single-letter
@@ -653,21 +658,21 @@ includes:
[bracketedExpression] == "[" { [atomOrSet] | [atomOrSet] ";" [atomAndSet] } "]"
[atomOrSet] == { [atomAndSet] | [atomAndSet] "," [atomAndSet] }
- [atomAndSet] == { [atomPrimitives] | [atomPrimitives] "&" [atomAndSet]
+ [atomAndSet] == { [atomPrimitives] | [atomPrimitives] "&" [atomAndSet]
| "!" [atomPrimitive]
- | "!" [atomPrimitive] "&" [atomAndSet] }
+ | "!" [atomPrimitive] "&" [atomAndSet] }
######## ATOM PRIMITIVES ########
[atomPrimitives] == { [atomPrimitive] | [atomPrimitive] [atomPrimitives] }
- # note -- if & is not used, certain combinations of primitiveDescritors
+ # note -- if & is not used, certain combinations of primitiveDescriptors
# are not allowed. Specifically, combinations that together
# form the symbol for an element will be read as the element (Ar, Rh, etc.)
# when NOT followed by a digit and no element has already been defined
- # So, for example, [Ar] is argon, [Ar3] is [A&r3], [ORh] is [O&R&h],
- # but [Ard2] is [Ar&d2] -- "argon with two non-hydrogen connections"
- # Also, "!" may not be use with implied "&".
- # Thus, [!a], [!a&!h2], and [h2&!a] are all valid, but [!ah2] is invalid.
+ # So, for example, [Ar] is argon, [Ar3] is [A&r3], [ORh] is [O&R&h],
+ # but [Ard2] is [Ar&d2] -- "argon with two non-hydrogen connections"
+ # Also, "!" may not be use with implied "&".
+ # Thus, [!a], [!a&!h2], and [h2&!a] are all valid, but [!ah2] is invalid.
[atomPrimitive] == { [isotope] | [atomType] | [charge] | [stereochemistry]
| [a_Prop] | [A_Prop] | [D_Prop] | [H_Prop] | [h_Prop]
| [R_Prop] | [r_Prop] | [v_Prop] | [X_Prop]
@@ -786,9 +791,9 @@ includes:
[bondExpression] == { [bondOrSet] | [bondOrSet] ";" [bondAndSet] }
[bondOrSet] == { [bondAndSet] | [bondAndSet] "," [bondAndSet] }
- [bondAndSet] == { [bondPrimitives] | [bondPrimitives] "&" [bondAndSet]
+ [bondAndSet] == { [bondPrimitives] | [bondPrimitives] "&" [bondAndSet]
| "!" [bondPrimitive]
- | "!" [bondPrimitive] "&" [bondAndSet] }
+ | "!" [bondPrimitive] "&" [bondAndSet] }
######## BOND PRIMITIVES ########
@@ -797,9 +802,9 @@ includes:
# note: All bondExpressions are not valid. Stereochemistry should not
# be mixed with the others, as it represents a single bond always.
# In addition, "." ("no bond") cannot be mixed with any bond type.
- # Nothing would be retrieved by "-&=", as a bond cannot be both single
+ # Nothing would be retrieved by "-&=", as a bond cannot be both single
# and double. However, "-@" is potentially very useful -- "ring single-bonds"
- # or "=&!@" -- "doubly-bonded atoms where the double bond is not in a ring"
+ # or "=&!@" -- "doubly-bonded atoms where the double bond is not in a ring"
# note: Jmol will not match two totally independent molecular pieces. For example,
# Jmol will not math [Na+].[Cl-]
# note: "+" indicates "adjacent biomolecular groups in a chain"
@@ -822,7 +827,7 @@ includes:
</pre>
<br><br>
-<a name="aromaticity"><h3>Jmol SMILES and Jmol SMARTS Definition of "aromatic"</h3></a>
+<h2><a id="aromaticity">Jmol SMILES and Jmol SMARTS Definition of "aromatic"</a></h2>
<br><br>
@@ -878,7 +883,7 @@ assume a bonding scheme (PDB, GAUSSIAN,
<br>updated 8/26/2015: switch to HTML5; added measure option for multiple ranges
<br>updated 5/21/2012: added $(select...)
<br>updated 5/13/2012: added /aromaticStrict/ and /aromaticDouble/
- <br>updated 5/13/2012: added [<atomType>]
+ <br>updated 5/13/2012: added [<atomType>]
<br>updated 4/10/2012: fix for [$(...)n] and [$(...)min-max]
<br>original5/19/2010
<br><br>
--- src/org/jmol/smiles/SmilesAromatic.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/smiles/SmilesAromatic.java 2021-11-29 14:03:35.578101209 -0700
@@ -336,7 +336,7 @@ public class SmilesAromatic {
* @param vMean
* @param n
* @param cutoff
- * @return true if stddev < cutoff
+ * @return true if stddev < cutoff
*/
private final static boolean checkStandardDeviation(V3[] vNorms, V3 vMean,
int n, float cutoff) {
--- src/org/jmol/smiles/SmilesMatcher.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/smiles/SmilesMatcher.java 2021-11-29 14:03:35.578101209 -0700
@@ -57,13 +57,13 @@ import javajs.util.PT;
*
* Specification for this implementation can be found in package.html.
*
- * <p>
+ * </p>
*
* <pre>
* <code>
* public methods:
*
- * int areEqual -- checks a SMILES string against a reference (-1 for error; 0 for no finds; >0 for number of finds)
+ * int areEqual -- checks a SMILES string against a reference (-1 for error; 0 for no finds; >0 for number of finds)
*
* BitSet[] find -- finds one or more occurances of a SMILES or SMARTS string within a SMILES string
*
--- src/org/jmol/smiles/SmilesParser.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/smiles/SmilesParser.java 2021-11-29 14:03:35.579101209 -0700
@@ -119,7 +119,7 @@ public class SmilesParser {
*
* @param pattern
* SMILES String
- * @return Molecule corresponding <ctode>pattern</code>
+ * @return Molecule corresponding <code>pattern</code>
* @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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/symmetry/CIPChirality.java 2021-11-29 14:03:35.579101209 -0700
@@ -67,7 +67,7 @@ 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
@@ -264,10 +264,10 @@ 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
@@ -808,7 +808,7 @@ 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();
@@ -1333,7 +1333,7 @@ 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:
*
@@ -1490,7 +1490,7 @@ 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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/symmetry/SpaceGroup.java 2021-11-29 14:03:35.579101209 -0700
@@ -162,7 +162,7 @@ class SpaceGroup {
/**
*
* @param name
- * @param data Lst<SymmetryOperation> or Lst<M4>
+ * @param data Lst<SymmetryOperation> or Lst<M4>
* @return a new SpaceGroup if successful or null
*/
private static SpaceGroup createSGFromList(String name, Lst<?> data) {
--- src/org/jmol/symmetry/Symmetry.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/symmetry/Symmetry.java 2021-11-29 14:03:35.580101209 -0700
@@ -164,7 +164,7 @@ public class Symmetry implements Symmetr
*
* @param desiredSpaceGroupIndex
* @param name
- * @param data a Lst<SymmetryOperation> or Lst<M4>
+ * @param data a Lst<SymmetryOperation> or Lst<M4>
* @param modDim in [3+d] modulation dimension
* @return true if a known space group
*/
--- src/org/jmol/symmetry/UnitCellIterator.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/symmetry/UnitCellIterator.java 2021-11-29 14:03:35.580101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/thread/SpinThread.java 2021-11-29 14:03:35.580101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/util/BSUtil.java 2021-11-29 14:03:35.580101209 -0700
@@ -110,8 +110,8 @@ final public class BSUtil {
* For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if
* a is not set, then add to a all set bits of b
*
- * 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
*
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/util/ColorEncoder.java 2021-11-29 14:03:35.581101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/util/CommandHistory.java 2021-11-29 14:03:35.581101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/util/Elements.java 2021-11-29 14:03:35.581101209 -0700
@@ -884,7 +884,7 @@ public class Elements {
* that contains the atomic number, the charge, and the radius in two
* consecutive values, encoded as follows:
*
- * (atomicNumber << 4) + (charge + 4), radiusAngstroms*1000
+ * (atomicNumber << 4) + (charge + 4), radiusAngstroms*1000
*
* That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius
*
--- src/org/jmol/util/MeshCapper.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/util/MeshCapper.java 2021-11-29 14:03:35.581101209 -0700
@@ -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
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/util/Modulation.java 2021-11-29 14:03:35.581101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/util/Node.java 2021-11-29 14:03:35.582101209 -0700
@@ -73,7 +73,7 @@ public interface Node extends SimpleNode
public int getModelIndex();
public int getAtomNumber();
/**
- * can be > 0 for PDB model with no H atoms or for SMILES string CCC
+ * can be > 0 for PDB model with no H atoms or for SMILES string CCC
*
* @return number of missing H atoms
*/
--- src/org/jmol/util/SimpleUnitCell.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/util/SimpleUnitCell.java 2021-11-29 14:03:35.582101209 -0700
@@ -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 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/util/Tensor.java 2021-11-29 14:03:35.582101209 -0700
@@ -289,7 +289,7 @@ public class Tensor {
/**
* width of the signal; |e2 - e0|
*
- * @return unitless; >= 0
+ * @return unitless; ≥ 0
*/
public float span() {
return Math.abs(eigenValues[2] - eigenValues[0]);
@@ -654,13 +654,13 @@ public class Tensor {
/**
* The expression:
*
- * |sigma_3 - sigma_iso| >= |sigma_1 - sigma_iso| >= |sigma_2 - sigma_iso|
+ * |sigma_3 - sigma_iso| ≥ |sigma_1 - sigma_iso| ≥ |sigma_2 - sigma_iso|
*
* simply sorts the values from largest to smallest or smallest to largest,
* depending upon the direction of the asymmetry, always setting the last
* value to be the farthest from the mean. We use a simpler form here:
*
- * |sigma_3 - sigma_1| >= |sigma_3 - sigma_2| >= |sigma_2 - sigma_1|
+ * |sigma_3 - sigma_1| ≥ |sigma_3 - sigma_2| ≥ |sigma_2 - sigma_1|
*
* which amounts to the same thing and is prettier. (Think about it!)
*
--- src/org/jmol/util/Vibration.java.orig 2021-11-27 22:53:30.000000000 -0700
+++ src/org/jmol/util/Vibration.java 2021-11-29 14:03:35.582101209 -0700
@@ -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 2021-11-27 22:53:31.000000000 -0700
+++ src/org/jmol/viewer/OutputManager.java 2021-11-29 14:03:35.582101209 -0700
@@ -650,7 +650,7 @@ 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 2021-11-27 22:53:31.000000000 -0700
+++ src/org/jmol/viewer/TransformManager.java 2021-11-29 14:03:35.583101209 -0700
@@ -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)
*
@@ -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
*/
@@ -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 2021-11-27 22:53:31.000000000 -0700
+++ src/org/jmol/viewer/Viewer.java 2021-11-29 14:03:35.583101209 -0700
@@ -1680,9 +1680,9 @@ public class Viewer extends JmolViewer
*
* disables command threading
*
- * disables DELAY, TIMEOUT, PAUSE, LOOP, GOTO, SPIN <rate>, ANIMATION ON
+ * disables DELAY, TIMEOUT, PAUSE, LOOP, GOTO, SPIN <rate>, ANIMATION ON
*
- * turns SPIN <rate> <end> into just ROTATE <end>
+ * turns SPIN <rate> <end> into just ROTATE <end>
*/
public boolean headless;
@@ -4065,7 +4065,7 @@ public class Viewer extends JmolViewer
*
* data[1] -- string or float[] or float[][] or float[][][]
*
- * data[2] -- selection bitset or int[] atomMap when field > 0
+ * data[2] -- selection bitset or int[] atomMap when field > 0
*
* data[3] -- arrayDepth
* 0(String),1(float[]),2(float[][]),3(float[][][]) or -1 to indidate
@@ -4130,7 +4130,7 @@ public class Viewer extends JmolViewer
*
* data[1] -- string or float[] or float[][] or float[][][]
*
- * data[2] -- selection bitset or int[] atomMap when field > 0
+ * data[2] -- selection bitset or int[] atomMap when field > 0
*
* data[3] -- arrayDepth
* 0(String),1(float[]),2(float[][]),3(float[][][]) or -1 to indicate
@@ -8161,7 +8161,7 @@ public class Viewer extends JmolViewer
}
/**
- * fills an array with data -- if nX < 0 and this would involve JavaScript,
+ * fills an array with data -- if nX < 0 and this would involve JavaScript,
* 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.
*
@@ -8379,8 +8379,8 @@ public class Viewer extends JmolViewer
}
/**
- * Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n ==
- * -1 ; set max to -2 - n n <= -3 ; just clear n == -2 ; clear and turn off;
+ * Options include: ; all n == Integer.MAX_VALUE ; n prev n ≥ 1 ; next n ==
+ * -1 ; set max to -2 - n n ≤ -3 ; just clear n == -2 ; clear and turn off;
* return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;
*
* @param howFarBack
@@ -8960,9 +8960,9 @@ public class Viewer extends JmolViewer
*
* @param eval
* @param steps
- * Integer.MAX_VALUE --> use defaults
+ * Integer.MAX_VALUE → use defaults
* @param crit
- * -1 --> use defaults
+ * -1 → use defaults
* @param bsSelected
* @param bsFixed
* @param rangeFixed
@@ -9776,10 +9776,10 @@ public class Viewer extends JmolViewer
*
*
* @param id
- * < 256 is just the character of a single-character upper-case chain
+ * < 256 is just the character of a single-character upper-case chain
* id, upper or lower case query;
*
- * >= 256 < 300 is lower case found in structure
+ * ≥ 256 < 300 is lower case found in structure
*
* @param isAssign
* from a file reader, not a select query
@@ -10227,7 +10227,7 @@ public class Viewer extends JmolViewer
* @param options
* if nonzero, a option, currently just T.offset, indicating that pt1
* is an {i j k} offset from cell 555
- * @return string, Object[], or Lst<Object[]>
+ * @return string, Object[], or Lst<Object[]>
*/
public Object getSymmetryInfo(int iatom, String xyz, int iOp, P3 translation, P3 pt1,
P3 pt2, int type, String desc,
--- src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java.orig 2021-11-27 22:53:31.000000000 -0700
+++ src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java 2021-11-29 14:03:35.584101209 -0700
@@ -173,7 +173,7 @@ import naga.packetwriter.RawPacketWriter
*
* sync 30000 "backgrund blue"
*
- * {"type":"reply","reply":"SCRIPT:script compiler ERROR: command expected\n----\n >>>> backgrund blue <<<<"}
+ * {"type":"reply","reply":"SCRIPT:script compiler ERROR: command expected\n----\n >>>> background blue <<<<"}
*
* Note that the ERROR callback does not fire for compile errors,
* only for errors found while running a parsed script:
@@ -192,7 +192,7 @@ import naga.packetwriter.RawPacketWriter
*
* gives the simple reply:
*
- * {"type":"reply","reply":"LOADSTRUCT:https://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=true"}
+ * {"type":"reply","reply":"LOADSTRUCT:https://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=true"}
*
* but after
*
@@ -201,8 +201,8 @@ import naga.packetwriter.RawPacketWriter
* we get additional details, and array of data with nine elements:
*
* {"type":"reply","reply":["LOADSTRUCT",
- * "https://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=true",
- * "file?format=sdf&get3d=true",
+ * "https://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=true",
+ * "file?format=sdf&get3d=true",
* "C8H10N4O2", null, 3, "1.1", "1.1", null]}
*
* Exact specifications for these callbacks are not well documented.
@@ -243,22 +243,22 @@ import naga.packetwriter.RawPacketWriter
* Note that all of the move and sync commands utilize the Jmol sync functionality originally
* intended for applets. So any valid sync command may be used with the "sync" style. These include
* essentially all the actions that a user can make with a mouse, including the
- * following, where the notation <....> represents a number of a given type. These
+ * following, where the notation <....> represents a number of a given type. These
* events interrupt any currently running script, just as with typical mouse actions.
*
- * "centerAt <int:x> <int:y> <float:ptx> <float:pty> <float:ptz>"
+ * "centerAt <int:x> <int:y> <float:ptx> <float:pty> <float:ptz>"
* -- set {ptx,pty,ptz} at screen (x,y)
- * "rotateMolecule <float:deltaX> <float:deltaY>"
- * "rotateXYBy <float:deltaX> <float:deltaY>"
- * "rotateZBy <int:degrees>"
- * "rotateZBy <int:degrees> <int:x> <int:y>" (with center reset)
- * "rotateArcBall <int:x> <int:y> <float:factor>"
- * "spinXYBy <int:x> <int:y> <float:speed>"
+ * "rotateMolecule <float:deltaX> <float:deltaY>"
+ * "rotateXYBy <float:deltaX> <float:deltaY>"
+ * "rotateZBy <int:degrees>"
+ * "rotateZBy <int:degrees> <int:x> <int:y>" (with center reset)
+ * "rotateArcBall <int:x> <int:y> <float:factor>"
+ * "spinXYBy <int:x> <int:y> <float:speed>"
* -- a "flick" gesture
- * "translateXYBy <float:deltaX, float:deltaY>"
- * "zoomBy <int:pixels>"
- * "zoomByFactor <float:factor>"
- * "zoomByFactor <float:factor> <int:x> <int:y>" (with center reset)
+ * "translateXYBy <float:deltaX, float:deltaY>"
+ * "zoomBy <int:pixels>"
+ * "zoomByFactor <float:factor>"
+ * "zoomByFactor <float:factor> <int:x> <int:y>" (with center reset)
*
* In addition, a Jmol client send "raw" JSON strings over the socket via the SYNC command:
*