Revision: 20679
http://sourceforge.net/p/jmol/code/20679
Author: hansonr
Date: 2015-08-07 18:04:07 +0000 (Fri, 07 Aug 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.15_2015.08.07"
bug fix: write property atomno temperature "test.pdb" preserves long residue
names from CIF files
bug fix: load "test.pdb" from write property atomno temperature restores
values for atomno and temperature
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pdb/PqrReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/api/JmolDataManager.java
trunk/Jmol/src/org/jmol/modelset/LabelToken.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/ScriptExpr.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/viewer/DataManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Added Paths:
-----------
trunk/Jmol/src/org/jmol/adapter/readers/pdb/JmolDataReader.java
Added: trunk/Jmol/src/org/jmol/adapter/readers/pdb/JmolDataReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pdb/JmolDataReader.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pdb/JmolDataReader.java
2015-08-07 18:04:07 UTC (rev 20679)
@@ -0,0 +1,169 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2006-10-15 17:34:01 -0500 (Sun, 15 Oct 2006) $
+ * $Revision: 5957 $
+ *
+ * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
+ *
+ * Contact: jmol-develop...@lists.sf.net
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+package org.jmol.adapter.readers.pdb;
+
+import java.util.Hashtable;
+import java.util.Map;
+
+import javajs.util.P3;
+
+import org.jmol.adapter.smarter.Atom;
+import org.jmol.util.Logger;
+import org.jmol.util.Parser;
+
+/**
+ * JmolData file reader, for a modified PDB format
+ *
+ */
+
+public class JmolDataReader extends PdbReader {
+
+
+ private Map<String, float[]> props;
+ private String[] residueNames;
+ private String[] atomNames;
+
+ // REMARK 6 Jmol PDB-encoded data: property atomno temperature;
+ // REMARK 6 Jmol atom names ... ... ...;
+ // REMARK 6 Jmol residue names ... ... ...;
+ // REMARK 6 Jmol data min = {1.0 -41.87 0.0} max = {26.0 66.53 0.0}
unScaledXyz = xyz * {1.0 1.0 0.0} + {0.0 12.33 0.0} plotscale = {100 100 100};
+ // REMARK 6 Jmol property atomno [1.0, 2.0, ...];
+ // REMARK 6 Jmol property temperature [0.0, 23.0, 21.0, ...];
+
+ @Override
+ protected void checkRemark() {
+ // REMARK 6 Jmol
+ while (true) {
+ if (line.length() < 30 || line.indexOf("Jmol") != 11)
+ break;
+ switch ("Ppard".indexOf(line.substring(16, 17))) {
+ case 0: //Jmol PDB-encoded data
+ props = new Hashtable<String, float[]>();
+ asc.setInfo("jmolData", line);
+ if (!line.endsWith("#noautobond"))
+ line += "#noautobond";
+ break;
+ case 1: // Jmol property
+ int pt1 = line.indexOf("[");
+ int pt2 = line.indexOf("]");
+ if (pt1 < 25 || pt2 <= pt1)
+ return;
+ String name = line.substring(25, pt1).trim();
+ line = line.substring(pt1 + 1, pt2).replace(',', ' ');
+ String[] tokens = getTokens();
+ Logger.info("reading " + name + " " + tokens.length);
+ float[] prop = new float[tokens.length];
+ for (int i = prop.length; --i >= 0;)
+ prop[i] = parseFloatStr(tokens[i]);
+ props.put(name, prop);
+ break;
+ case 2: // Jmol atom names
+ // REMARK 6 Jmol atom names ... ... ...;
+ line = line.substring(27);
+ atomNames = getTokens();
+ Logger.info("reading atom names " + atomNames.length);
+ break;
+ case 3: // Jmol residue names
+ // REMARK 6 Jmol residue names ... ... ...;
+ line = line.substring(30);
+ residueNames = getTokens();
+ Logger.info("reading residue names " + residueNames.length);
+ break;
+ case 4: //Jmol data min
+ Logger.info(line);
+ // The idea here is to use a line such as the following:
+ //
+ // REMARK 6 Jmol data min = {-1 -1 -1} max = {1 1 1}
+ // unScaledXyz = xyz / {10 10 10} + {0 0 0}
+ // plotScale = {100 100 100}
+ //
+ // to pass on to Jmol how to graph non-molecular data.
+ // The format allows for the actual data to be linearly transformed
+ // so that it fits into the PDB format for x, y, and z coordinates.
+ // This adapter will then unscale the data and also pass on to
+ // Jmol the unit cell equivalent that takes the actual data (which
+ // will be considered the fractional coordinates) to Jmol coordinates,
+ // which will be a cube centered at {0 0 0} and ranging from {-100
-100 -100}
+ // to {100 100 100}.
+ //
+ // Jmol 12.0.RC23 uses this to pass through the adapter a quaternion,
+ // ramachandran, or other sort of plot.
+
+ float[] data = new float[15];
+ Parser.parseStringInfestedFloatArray(
+ line.substring(10).replace('=', ' ').replace('{', ' ')
+ .replace('}', ' '), null, data);
+ P3 minXYZ = P3.new3(data[0], data[1], data[2]);
+ P3 maxXYZ = P3.new3(data[3], data[4], data[5]);
+ fileScaling = P3.new3(data[6], data[7], data[8]);
+ fileOffset = P3.new3(data[9], data[10], data[11]);
+ P3 plotScale = P3.new3(data[12], data[13], data[14]);
+ if (plotScale.x <= 0)
+ plotScale.x = 100;
+ if (plotScale.y <= 0)
+ plotScale.y = 100;
+ if (plotScale.z <= 0)
+ plotScale.z = 100;
+ if (fileScaling.y == 0)
+ fileScaling.y = 1;
+ if (fileScaling.z == 0)
+ fileScaling.z = 1;
+ setFractionalCoordinates(true);
+ latticeCells = new int[3];
+ asc.xtalSymmetry = null;
+ setUnitCell(plotScale.x * 2 / (maxXYZ.x - minXYZ.x), plotScale.y * 2
+ / (maxXYZ.y - minXYZ.y), plotScale.z * 2
+ / (maxXYZ.z == minXYZ.z ? 1 : maxXYZ.z - minXYZ.z), 90, 90, 90);
+ unitCellOffset = P3.newP(plotScale);
+ unitCellOffset.scale(-1);
+ getSymmetry();
+ symmetry.toFractional(unitCellOffset, false);
+ unitCellOffset.scaleAdd2(-1f, minXYZ, unitCellOffset);
+ symmetry.setOffsetPt(unitCellOffset);
+ asc.setInfo("jmolDataScaling", new P3[] { minXYZ, maxXYZ, plotScale });
+ doApplySymmetry = true;
+ break;
+ }
+ break;
+ }
+ checkCurrentLineForScript();
+ }
+
+ @Override
+ protected void setAdditionalAtomParameters(Atom atom) {
+ if (residueNames != null && atom.index < residueNames.length)
+ atom.group3 = residueNames[atom.index];
+ if (atomNames != null && atom.index < atomNames.length)
+ atom.atomName = atomNames[atom.index];
+ }
+
+ @Override
+ protected void finalizeSubclassReader() throws Exception {
+ asc.setCurrentModelInfo("jmolDataProperties", props);
+ finalizeReaderPDB();
+ }
+
+}
+
Property changes on:
trunk/Jmol/src/org/jmol/adapter/readers/pdb/JmolDataReader.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java 2015-08-06
18:37:56 UTC (rev 20678)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java 2015-08-07
18:04:07 UTC (rev 20679)
@@ -116,8 +116,7 @@
private boolean isConnectStateBug;
private boolean isLegacyModelType;
- private boolean gromacsWideFormat;
- protected boolean isPQR;
+ protected boolean gromacsWideFormat;
private final Map<String, Map<String, Boolean>> htFormul = new
Hashtable<String, Map<String, Boolean>>();
private Map<String, String> htHetero;
@@ -327,14 +326,6 @@
formul();
return true;
case 17:
- if (line.contains("The B-factors in this file hold atomic radii")) {
- isPQR = true;
- return true;
- }
- if (line.contains("This file does not adhere to the PDB standard")) {
- gromacsWideFormat = true;
- return true;
- }
if (line.startsWith("REMARK 350")) {
remark350();
return false;
@@ -343,11 +334,14 @@
remark290();
return false;
}
+ if (line.contains("This file does not adhere to the PDB standard")) {
+ gromacsWideFormat = true;
+ }
if (getTlsGroups) {
if (line.indexOf("TLS DETAILS") > 0)
return remarkTls();
}
- checkCurrentLineForScript();
+ checkRemark();
return true;
case 18:
header();
@@ -368,6 +362,10 @@
return true;
}
+ protected void checkRemark() {
+ checkCurrentLineForScript();
+ }
+
private void checkDSSR() throws Exception {
if (line.trim().startsWith("DSSR:") && asc.ac > 0)
processDSSR(this, htGroup1);
@@ -1020,21 +1018,7 @@
* @param atom
*/
protected void setAdditionalAtomParameters(Atom atom) {
- if (isPQR) {
- if (gromacsWideFormat) {
- atom.partialCharge = parseFloatRange(line, 60, 68);
- atom.radius = fixRadius(parseFloatRange(line, 68, 76));
- } else {
- String[] tokens = getTokens();
- int pt = tokens.length - 2 - (line.length() > 75 ? 1 : 0);
- atom.partialCharge = parseFloatStr(tokens[pt++]);
- atom.radius = fixRadius(parseFloatStr(tokens[pt]));
- }
- return;
- }
-
- float floatOccupancy;
-
+ float floatOccupancy;
if (gromacsWideFormat) {
floatOccupancy = parseFloatRange(line, 60, 68);
atom.bfactor = fixRadius(parseFloatRange(line, 68, 76));
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pdb/PqrReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pdb/PqrReader.java 2015-08-06
18:37:56 UTC (rev 20678)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pdb/PqrReader.java 2015-08-07
18:04:07 UTC (rev 20679)
@@ -25,6 +25,7 @@
package org.jmol.adapter.readers.pdb;
import org.jmol.adapter.readers.pdb.PdbReader;
+import org.jmol.adapter.smarter.Atom;
/**
* PQR file reader.
@@ -60,13 +61,17 @@
public class PqrReader extends PdbReader {
- protected boolean gromacsWideFormat;
-
@Override
- protected void initializeReader() throws Exception {
- isPQR = true;
- super.initializeReader();
+ protected void setAdditionalAtomParameters(Atom atom) {
+ if (gromacsWideFormat) {
+ atom.partialCharge = parseFloatRange(line, 60, 68);
+ atom.radius = fixRadius(parseFloatRange(line, 68, 76));
+ } else {
+ String[] tokens = getTokens();
+ int pt = tokens.length - 2 - (line.length() > 75 ? 1 : 0);
+ atom.partialCharge = parseFloatStr(tokens[pt++]);
+ atom.radius = fixRadius(parseFloatStr(tokens[pt]));
+ }
}
-
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2015-08-06 18:37:56 UTC (rev 20678)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2015-08-07 18:04:07 UTC (rev 20679)
@@ -28,29 +28,26 @@
import java.io.BufferedReader;
import java.util.Map;
-import org.jmol.api.Interface;
-import org.jmol.api.JmolAdapter;
-import org.jmol.api.SymmetryInterface;
-import org.jmol.java.BS;
-import org.jmol.script.SV;
-import org.jmol.symmetry.Symmetry;
-import org.jmol.util.BSUtil;
-import org.jmol.util.Logger;
-import org.jmol.util.Parser;
-
import javajs.api.GenericBinaryDocument;
import javajs.api.GenericLineReader;
+import javajs.util.Lst;
import javajs.util.M3;
+import javajs.util.OC;
import javajs.util.P3;
-
-import javajs.util.OC;
import javajs.util.PT;
import javajs.util.Quat;
+import javajs.util.SB;
import javajs.util.T3;
import javajs.util.V3;
-import javajs.util.Lst;
-import javajs.util.SB;
+import org.jmol.api.Interface;
+import org.jmol.api.JmolAdapter;
+import org.jmol.api.SymmetryInterface;
+import org.jmol.java.BS;
+import org.jmol.script.SV;
+import org.jmol.symmetry.Symmetry;
+import org.jmol.util.BSUtil;
+import org.jmol.util.Logger;
import org.jmol.viewer.Viewer;
@@ -211,7 +208,7 @@
protected float latticeScaling = Float.NaN;
protected P3 fileOffset;
private P3 fileOffsetFractional;
- P3 unitCellOffset;
+ protected P3 unitCellOffset;
private boolean unitCellOffsetFractional;
private Lst<String> moreUnitCellInfo;
@@ -1449,67 +1446,6 @@
}
public void checkCurrentLineForScript() {
- if (line.indexOf("Jmol") >= 0) {
- if (line.indexOf("Jmol PDB-encoded data") >= 0) {
- asc.setInfo("jmolData", line);
- if (!line.endsWith("#noautobond"))
- line += "#noautobond";
- }
- if (line.indexOf("Jmol data min") >= 0) {
- Logger.info(line);
- // The idea here is to use a line such as the following:
- //
- // REMARK 6 Jmol data min = {-1 -1 -1} max = {1 1 1}
- // unScaledXyz = xyz / {10 10 10} + {0 0 0}
- // plotScale = {100 100 100}
- //
- // to pass on to Jmol how to graph non-molecular data.
- // The format allows for the actual data to be linearly transformed
- // so that it fits into the PDB format for x, y, and z coordinates.
- // This adapter will then unscale the data and also pass on to
- // Jmol the unit cell equivalent that takes the actual data (which
- // will be considered the fractional coordinates) to Jmol coordinates,
- // which will be a cube centered at {0 0 0} and ranging from {-100
-100 -100}
- // to {100 100 100}.
- //
- // Jmol 12.0.RC23 uses this to pass through the adapter a quaternion,
- // ramachandran, or other sort of plot.
-
- float[] data = new float[15];
- Parser.parseStringInfestedFloatArray(line.substring(10).replace('=', '
')
- .replace('{', ' ').replace('}', ' '), null, data);
- P3 minXYZ = P3.new3(data[0], data[1], data[2]);
- P3 maxXYZ = P3.new3(data[3], data[4], data[5]);
- fileScaling = P3.new3(data[6], data[7], data[8]);
- fileOffset = P3.new3(data[9], data[10], data[11]);
- P3 plotScale = P3.new3(data[12], data[13], data[14]);
- if (plotScale.x <= 0)
- plotScale.x = 100;
- if (plotScale.y <= 0)
- plotScale.y = 100;
- if (plotScale.z <= 0)
- plotScale.z = 100;
- if (fileScaling.y == 0)
- fileScaling.y = 1;
- if (fileScaling.z == 0)
- fileScaling.z = 1;
- setFractionalCoordinates(true);
- latticeCells = new int[3];
- asc.xtalSymmetry = null;
- setUnitCell(plotScale.x * 2 / (maxXYZ.x - minXYZ.x), plotScale.y * 2
- / (maxXYZ.y - minXYZ.y), plotScale.z * 2
- / (maxXYZ.z == minXYZ.z ? 1 : maxXYZ.z - minXYZ.z), 90, 90, 90);
- unitCellOffset = P3.newP(plotScale);
- unitCellOffset.scale(-1);
- getSymmetry();
- symmetry.toFractional(unitCellOffset, false);
- unitCellOffset.scaleAdd2(-1f, minXYZ, unitCellOffset);
- symmetry.setOffsetPt(unitCellOffset);
- asc.setInfo("jmolDataScaling",
- new P3[] { minXYZ, maxXYZ, plotScale });
- doApplySymmetry = true;
- }
- }
if (line.endsWith("#noautobond")) {
line = line.substring(0, line.lastIndexOf('#')).trim();
asc.setNoAutoBond();
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2015-08-06
18:37:56 UTC (rev 20678)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2015-08-07
18:04:07 UTC (rev 20679)
@@ -50,7 +50,7 @@
"quantum.",
";Adf;Csf;Dgrid;GamessUK;GamessUS;Gaussian;GaussianFchk;GaussianWfn;Jaguar;" +
"Molden;MopacGraphf;GenNBO;NWChem;Odyssey;Psi;Qchem;Spartan;SpartanSmol;" +
"WebMO;",
- "pdb.", ";Pdb;Pqr;P2n;",
+ "pdb.", ";Pdb;Pqr;P2n;JmolData;",
"pymol.", ";PyMOL;",
"simple.",
";Alchemy;Ampac;Cube;FoldingXyz;GhemicalMM;HyperChem;Jme;JSON;Mopac;MopacArchive;Tinker;Input;",
"xtal.",
";Abinit;Aims;Bilbao;Castep;Cgd;Crystal;Dmol;Espresso;Gulp;Jana;Magres;Shelx;Siesta;VaspOutcar;"
+
@@ -347,12 +347,22 @@
private final static String[] jcampdxStartRecords =
{ "Jcampdx", "##TITLE" };
+ private final static String[] jmoldataStartRecords =
+ { "JmolData", "REMARK 6 Jmol" };
+
+ private final static String[] pqrStartRecords =
+ { "Pqr", "REMARK 1 PQR", "REMARK The B-factors" };
+
+ private final static String[] p2nStartRecords =
+ { "P2n", "REMARK 1 P2N" };
+
private final static String[][] fileStartsWithRecords =
{ sptRecords, m3dStartRecords, cubeFileStartRecords,
mol2Records, webmoFileStartRecords,
moldenFileStartRecords, dcdFileStartRecords, tlsDataOnlyFileStartRecords,
inputFileStartRecords, magresFileStartRecords, pymolStartRecords,
- janaStartRecords, jsonStartRecords, jcampdxStartRecords };
+ janaStartRecords, jsonStartRecords, jcampdxStartRecords,
+ jmoldataStartRecords, pqrStartRecords, p2nStartRecords };
////////////////////////////////////////////////////////////////
// Test 3. check first time for special file types
@@ -595,12 +605,6 @@
private final static String[] cifLineStartRecords =
{ "Cif", "data_", "_publ" };
- private final static String[] pqrLineStartRecords =
- { "Pqr", "REMARK 1 PQR" };
-
- private final static String[] p2nLineStartRecords =
- { "P2n", "REMARK 1 P2N" };
-
private final static String[] pdbLineStartRecords = {
"Pdb", "HEADER", "OBSLTE", "TITLE ", "CAVEAT", "COMPND", "SOURCE",
"KEYWDS",
"EXPDTA", "AUTHOR", "REVDAT", "SPRSDE", "JRNL ", "REMARK ",
@@ -641,7 +645,7 @@
{ "VaspOutcar", " vasp.", " INCAR:" };
private final static String[][] lineStartsWithRecords =
- { mmcifLineStartRecords, cifLineStartRecords, pqrLineStartRecords,
p2nLineStartRecords,
+ { mmcifLineStartRecords, cifLineStartRecords,
pdbLineStartRecords, cgdLineStartRecords, shelxLineStartRecords,
ghemicalMMLineStartRecords, jaguarLineStartRecords,
mdlLineStartRecords, spartanSmolLineStartRecords, csfLineStartRecords,
Modified: trunk/Jmol/src/org/jmol/api/JmolDataManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolDataManager.java 2015-08-06 18:37:56 UTC
(rev 20678)
+++ trunk/Jmol/src/org/jmol/api/JmolDataManager.java 2015-08-07 18:04:07 UTC
(rev 20679)
@@ -29,7 +29,7 @@
float getDataFloat(String label, int atomIndex);
- float[] getDataFloatA(String label);
+ float[] getDataFloatA(String label, BS bsSelected);
String getDefaultVdwNameOrData(VDW type, BS bs);
Modified: trunk/Jmol/src/org/jmol/modelset/LabelToken.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/LabelToken.java 2015-08-06 18:37:56 UTC
(rev 20678)
+++ trunk/Jmol/src/org/jmol/modelset/LabelToken.java 2015-08-07 18:04:07 UTC
(rev 20679)
@@ -405,10 +405,10 @@
String propertyName = strFormat.substring(ich, ichClose).toLowerCase();
if (propertyName.startsWith("property_")) {
lt.tok = T.data;
- lt.data = vwr.getDataFloat(propertyName);
+ lt.data = vwr.getDataFloat(propertyName, null);
} else if (propertyName.startsWith("validation.")) {
lt.tok = T.validation;
- lt.data = vwr.getDataFloat("property_" + propertyName.substring(11));
+ lt.data = vwr.getDataFloat("property_" + propertyName.substring(11),
null);
} else {
T token = T.getTokenFromName(propertyName);
if (token != null && isLabelPropertyTok(token.tok))
@@ -427,7 +427,7 @@
break;
}
String s = strFormat.substring(ich, ichCloseBracket);
- lt.data = vwr.getDataFloat(s);
+ lt.data = vwr.getDataFloat(s, null);
// TODO untested j2s issue fix
if (lt.data == null) {
lt.data = vwr.getData(s);
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-08-06 18:37:56 UTC
(rev 20678)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-08-07 18:04:07 UTC
(rev 20679)
@@ -60,6 +60,7 @@
import java.util.Hashtable;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Properties;
/*
@@ -170,7 +171,7 @@
isMutate = ms.getMSInfoB("isMutate");
if (ms.haveBioModels)
jbr = vwr.getJBR().setLoader(this);
- jmolData = (String) ms.getInfoM("jmolData");
+ jmolData = (adapterModelCount == 0 ? (String) ms.getInfoM("jmolData") :
null);
fileHeader = (String) ms.getInfoM("fileHeader");
Lst<P3[]> steps = (Lst<P3[]>) ms.getInfoM("trajectorySteps");
isTrajectory = (steps != null);
@@ -440,6 +441,8 @@
Map<String, Object> atomProperties = (Map<String, Object>) ms.getInfo(i,
"atomProperties");
// list of properties that are to be transfered to H atoms as well.
+ if (jmolData != null)
+ addJmolDataProperties(ms.am[i], (Map<String, float[]>) ms.getInfo(i,
"jmolDataProperties"));
String groupList = (String) ms.getInfo(i,
"groupPropertyList");
if (atomProperties == null)
@@ -615,10 +618,10 @@
if (atomInfo != null)
ms.setInfo(modelIndex, "PDB_CONECT_firstAtom_count_max", atomInfo);
}
+ Model[] models = ms.am;
+ Atom[] atoms = ms.at;
// this next sets the bitset length to avoid
// unnecessary calls to System.arrayCopy
- Model[] models = ms.am;
- Atom[] atoms = ms.at;
models[modelIndex].bsAtoms.set(atoms.length + 1);
models[modelIndex].bsAtoms.clear(atoms.length + 1);
String codes = (String) ms.getInfo(modelIndex, "altLocs");
@@ -836,6 +839,26 @@
Logger.info(nRead + " atoms created");
}
+ private void addJmolDataProperties(Model m, Map<String, float[]>
jmolDataProperties) {
+ if (jmolDataProperties == null)
+ return;
+ BS bs = m.bsAtoms;
+ for (Entry<String, float[]> e : jmolDataProperties.entrySet()) {
+ String key = e.getKey();
+ float[] data = e.getValue();
+ if (key.startsWith("property_")) {
+ vwr.setData(
+ key,
+ new Object[] { key, data, bs,
+ Integer.valueOf(JmolDataManager.DATA_TYPE_AF) }, 0, 0, 0, 0,
0);
+ } else {
+ int tok = T.getTokFromName(key);
+ if (T.tokAttr(tok, T.settable))
+ vwr.setAtomProperty(bs, tok, 0, 0, null, data, null);
+ }
+ }
+ }
+
/**
* Adjust known N and O atom formal charges.
* Note that this does not take care of ligands.
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-08-06 18:37:56 UTC
(rev 20678)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-08-07 18:04:07 UTC
(rev 20679)
@@ -8102,8 +8102,8 @@
if (pal == PAL.PROPERTY) {
if (isColorIndex) {
if (!chk) {
- data = getBitsetPropertyFloat(bsSelected, (isByElement ? T.elemno
- : T.groupid) | T.allfloat, Float.NaN, Float.NaN);
+ data = getCmdExt().getBitsetPropertyFloat(bsSelected,
(isByElement ? T.elemno
+ : T.groupid) | T.allfloat, null, Float.NaN, Float.NaN);
}
} else {
boolean isPropertyExplicit = name.equals("property");
@@ -8112,8 +8112,8 @@
&& T.tokAttr((tok = getToken(++index).tok), T.atomproperty)
&& !T.tokAttr(tok, T.strproperty)) {
if (!chk) {
- data = getBitsetPropertyFloat(bsSelected, getToken(index).tok
- | T.allfloat, Float.NaN, Float.NaN);
+ data = getCmdExt().getBitsetPropertyFloat(bsSelected,
getToken(index).tok
+ | T.allfloat, null, Float.NaN, Float.NaN);
}
index++;
} else if (!isPropertyExplicit && !isIsosurface) {
Modified: trunk/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-08-06 18:37:56 UTC
(rev 20678)
+++ trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-08-07 18:04:07 UTC
(rev 20679)
@@ -28,7 +28,6 @@
import org.jmol.scriptext.MathExt;
import org.jmol.scriptext.ScriptExt;
import org.jmol.scriptext.SmilesExt;
-import org.jmol.shape.Shape;
import org.jmol.util.BSUtil;
import org.jmol.util.Elements;
import org.jmol.util.Escape;
@@ -967,7 +966,7 @@
if (pc + 2 == code.length)
invArg();
if (!chk)
- data = vwr.getDataFloat((String) code[++pc].value);
+ data = vwr.getDataFloat((String) code[++pc].value, null);
}
if (++pc == code.length)
invArg(); // compiler would not let this happen, actually
@@ -1522,21 +1521,6 @@
return SV.newSV(T.propselector, tok, paramAsStr(i));
}
- public float[] getBitsetPropertyFloat(BS bs, int tok, float min, float max)
- throws ScriptException {
- float[] data = (float[]) getBitsetProperty(bs, tok, null, null, null, null,
- false, Integer.MAX_VALUE, false);
- if (!Float.isNaN(min))
- for (int i = 0; i < data.length; i++)
- if (data[i] < min)
- data[i] = Float.NaN;
- if (!Float.isNaN(max))
- for (int i = 0; i < data.length; i++)
- if (data[i] > max)
- data[i] = Float.NaN;
- return data;
- }
-
@SuppressWarnings("unchecked")
public Object getBitsetProperty(BS bs, int tok, P3 ptRef, P4 planeRef,
Object tokenValue, Object opValue,
@@ -1663,7 +1647,7 @@
ptT = new P3();
break;
case T.property:
- data = vwr.getDataFloat((String) opValue);
+ data = vwr.getDataFloat((String) opValue, null);
break;
}
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-08-06 18:37:56 UTC
(rev 20678)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-08-07 18:04:07 UTC
(rev 20679)
@@ -2279,12 +2279,12 @@
if (T.tokAttrOr(tokProp1, T.intproperty, T.floatproperty)
&& T.tokAttrOr(tokProp2, T.intproperty, T.floatproperty)
&& T.tokAttrOr(tokKey, T.intproperty, T.floatproperty)) {
- float[] data1 = eval.getBitsetPropertyFloat(bsFrom, tokProp1
- | T.selectedfloat, Float.NaN, Float.NaN);
- float[] data2 = eval.getBitsetPropertyFloat(bsFrom, tokKey
- | T.selectedfloat, Float.NaN, Float.NaN);
- float[] data3 = eval.getBitsetPropertyFloat(bsTo, tokKey
- | T.selectedfloat, Float.NaN, Float.NaN);
+ float[] data1 = getBitsetPropertyFloat(bsFrom, tokProp1
+ | T.selectedfloat, null, Float.NaN, Float.NaN);
+ float[] data2 = getBitsetPropertyFloat(bsFrom, tokKey
+ | T.selectedfloat, null, Float.NaN, Float.NaN);
+ float[] data3 = getBitsetPropertyFloat(bsTo, tokKey
+ | T.selectedfloat, null, Float.NaN, Float.NaN);
boolean isProperty = (tokProp2 == T.property);
float[] dataOut = new float[isProperty ? vwr.ms.ac
: data3.length];
@@ -2856,6 +2856,7 @@
eval.iToken = st.length;
error(ScriptError.ERROR_endOfStatementUnexpected);
}
+ eval.slen = slen = pt + 1;
break;
}
String qFrame = "";
@@ -2865,7 +2866,9 @@
boolean isDerivative = false;
boolean isSecondDerivative = false;
boolean isRamachandranRelative = false;
- int propertyX = 0, propertyY = 0, propertyZ = 0;
+ String[] props = new String[3];
+ int[] propToks = new int[3];
+
BS bs = BSUtil.copy(vwr.bsA());
String preSelected = "; select " + Escape.eBS(bs) + ";\n ";
String type = eval.optParameterAsString(pt).toLowerCase();
@@ -2887,11 +2890,19 @@
break;
case T.property:
eval.iToken = pt0 + 1;
- propertyX = plotProp();
- if (propertyX == 0)
- invArg();
- propertyY = plotProp();
- propertyZ = plotProp();
+ for (int i = 0; i < 3; i++) {
+ switch (tokAt(eval.iToken)) {
+ case T.format:
+ case T.min:
+ case T.max:
+ i = 2;
+ continue;
+ }
+ if (!T.tokAttr(propToks[i] = tokAt(eval.iToken), T.atomproperty))
+ invArg();
+ props[i] = getToken(eval.iToken).value.toString();
+ eval.iToken++;
+ }
if (tokAt(eval.iToken) == T.format) {
format = stringParameter(++eval.iToken);
pdbFormat = false;
@@ -2905,9 +2916,9 @@
maxXYZ = getPoint3f(++eval.iToken, false);
eval.iToken++;
}
- type = "property " + T.nameOf(propertyX)
- + (propertyY == 0 ? "" : " " + T.nameOf(propertyY))
- + (propertyZ == 0 ? "" : " " + T.nameOf(propertyZ));
+ type = "property " + props[0]
+ + (props[1] == null ? "" : " " + props[1])
+ + (props[2] == null ? "" : " " + props[2]);
if (bs.nextSetBit(0) < 0)
bs = vwr.getModelUndeletedAtomsBitSet(modelIndex);
stateScript = "select " + Escape.eBS(bs) + ";\n ";
@@ -2975,25 +2986,30 @@
float[] dataX = null, dataY = null, dataZ = null;
if (tok == T.property) {
- dataX = eval.getBitsetPropertyFloat(bs, propertyX | T.selectedfloat,
- (minXYZ == null ? Float.NaN : minXYZ.x), (maxXYZ == null ? Float.NaN
+ dataX = getBitsetPropertyFloat(bs, propToks[0] | T.selectedfloat,
+ propToks[0] == T.property? props[0] : null, (minXYZ == null ?
Float.NaN : minXYZ.x), (maxXYZ == null ? Float.NaN
: maxXYZ.x));
- if (propertyY != 0)
- dataY = eval.getBitsetPropertyFloat(bs, propertyY | T.selectedfloat,
- (minXYZ == null ? Float.NaN : minXYZ.y),
+ props[0] = props[0] + " " + Escape.eAF(dataX);
+ if (props[1] != null) {
+ dataY = getBitsetPropertyFloat(bs, propToks[1] | T.selectedfloat,
+ propToks[1] == T.property? props[1] : null, (minXYZ == null ?
Float.NaN : minXYZ.y),
(maxXYZ == null ? Float.NaN : maxXYZ.y));
- if (propertyZ != 0)
- dataZ = eval.getBitsetPropertyFloat(bs, propertyZ | T.selectedfloat,
- (minXYZ == null ? Float.NaN : minXYZ.z),
+ props[1] = props[1] + " " + Escape.eAF(dataY);
+ }
+ if (props[2] != null) {
+ dataZ = getBitsetPropertyFloat(bs, propToks[2] | T.selectedfloat,
+ propToks[2] == T.property? props[2] : null, (minXYZ == null ?
Float.NaN : minXYZ.z),
(maxXYZ == null ? Float.NaN : maxXYZ.z));
+ props[2] = props[2] + " " + Escape.eAF(dataZ);
+ }
if (minXYZ == null)
- minXYZ = P3.new3(getPlotMinMax(dataX, false, propertyX),
- getPlotMinMax(dataY, false, propertyY),
- getPlotMinMax(dataZ, false, propertyZ));
+ minXYZ = P3.new3(getPlotMinMax(dataX, false, propToks[0]),
+ getPlotMinMax(dataY, false, propToks[1]),
+ getPlotMinMax(dataZ, false, propToks[2]));
if (maxXYZ == null)
- maxXYZ = P3.new3(getPlotMinMax(dataX, true, propertyX),
- getPlotMinMax(dataY, true, propertyY),
- getPlotMinMax(dataZ, true, propertyZ));
+ maxXYZ = P3.new3(getPlotMinMax(dataX, true, propToks[0]),
+ getPlotMinMax(dataY, true, propToks[1]),
+ getPlotMinMax(dataZ, true, propToks[2]));
Logger.info("plot min/max: " + minXYZ + " " + maxXYZ);
P3 center = null;
P3 factors = null;
@@ -3004,37 +3020,37 @@
center.ave(maxXYZ, minXYZ);
factors.sub2(maxXYZ, minXYZ);
factors.set(factors.x / 200, factors.y / 200, factors.z / 200);
- if (T.tokAttr(propertyX, T.intproperty)) {
+ if (T.tokAttr(propToks[0], T.intproperty)) {
factors.x = 1;
center.x = 0;
} else if (factors.x > 0.1 && factors.x <= 10) {
factors.x = 1;
}
- if (T.tokAttr(propertyY, T.intproperty)) {
+ if (T.tokAttr(propToks[1], T.intproperty)) {
factors.y = 1;
center.y = 0;
} else if (factors.y > 0.1 && factors.y <= 10) {
factors.y = 1;
}
- if (T.tokAttr(propertyZ, T.intproperty)) {
+ if (T.tokAttr(propToks[2], T.intproperty)) {
factors.z = 1;
center.z = 0;
} else if (factors.z > 0.1 && factors.z <= 10) {
factors.z = 1;
}
- if (propertyZ == 0 || propertyY == 0)
+ if (props[2] == null || props[1] == null)
center.z = minXYZ.z = maxXYZ.z = factors.z = 0;
for (int i = 0; i < dataX.length; i++)
dataX[i] = (dataX[i] - center.x) / factors.x;
- if (propertyY != 0)
+ if (props[1] != null)
for (int i = 0; i < dataY.length; i++)
dataY[i] = (dataY[i] - center.y) / factors.y;
- if (propertyZ != 0)
+ if (props[2] != null)
for (int i = 0; i < dataZ.length; i++)
dataZ[i] = (dataZ[i] - center.z) / factors.z;
}
parameters = new Object[] { bs, dataX, dataY, dataZ, minXYZ, maxXYZ,
- factors, center, format};
+ factors, center, format, props};
}
// all set...
@@ -3090,13 +3106,13 @@
float f = 3;
script = "frame 0.0; frame last; reset;" + "select visible; spacefill "
+ f + "; wireframe 0;" + "draw plotAxisX" + modelCount
- + " {100 -100 -100} {-100 -100 -100} \"" + T.nameOf(propertyX)
+ + " {100 -100 -100} {-100 -100 -100} \"" + props[0]
+ "\";" + "draw plotAxisY" + modelCount
- + " {-100 100 -100} {-100 -100 -100} \"" + T.nameOf(propertyY)
+ + " {-100 100 -100} {-100 -100 -100} \"" + props[1]
+ "\";";
- if (propertyZ != 0)
+ if (props[2] != null)
script += "draw plotAxisZ" + modelCount
- + " {-100 -100 100} {-100 -100 -100} \"" + T.nameOf(propertyZ)
+ + " {-100 -100 100} {-100 -100 -100} \"" + props[2]
+ "\";";
break;
case T.ramachandran:
@@ -3137,21 +3153,6 @@
return "";
}
- private int plotProp() {
- int p = 0;
- switch (tokAt(e.iToken)) {
- case T.format:
- case T.min:
- case T.max:
- break;
- default:
- if (T.tokAttr(p = tokAt(e.iToken), T.atomproperty))
- e.iToken++;
- break;
- }
- return p;
- }
-
private boolean polyhedra() throws ScriptException {
ScriptEval eval = e;
/*
@@ -4987,4 +4988,24 @@
return data;
}
+ public float[] getBitsetPropertyFloat(BS bs, int tok, String property,
+ float min, float max)
+ throws ScriptException {
+
+ float[] data = (property == null ?
+ (float[]) e.getBitsetProperty(bs, tok, null, null, null, null,
+ false, Integer.MAX_VALUE, false)
+ : vwr.getDataFloat(property, bs));
+ if (!Float.isNaN(min))
+ for (int i = 0; i < data.length; i++)
+ if (data[i] < min)
+ data[i] = Float.NaN;
+ if (!Float.isNaN(max))
+ for (int i = 0; i < data.length; i++)
+ if (data[i] > max)
+ data[i] = Float.NaN;
+ return data;
+ }
+
+
}
Modified: trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-08-06 18:37:56 UTC
(rev 20678)
+++ trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-08-07 18:04:07 UTC
(rev 20679)
@@ -1440,7 +1440,7 @@
data = new float[vwr.ms.ac];
if (chk)
continue;
- data = vwr.getDataFloat(str);
+ data = vwr.getDataFloat(str, null);
if (data == null)
invArg();
addShapeProperty(propertyList, propertyName, data);
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-08-06 18:37:56 UTC
(rev 20678)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-08-07 18:04:07 UTC
(rev 20679)
@@ -790,10 +790,10 @@
// parallel mp.addition of float property data sets
if (selected.indexOf("property_") == 0) {
- float[] f1 = vwr.getDataFloat(selected);
+ float[] f1 = vwr.getDataFloat(selected, null);
if (f1 == null)
return mp.addXStr("");
- float[] f2 = (type.indexOf("property_") == 0 ? vwr.getDataFloat(type)
+ float[] f2 = (type.indexOf("property_") == 0 ? vwr.getDataFloat(type,
null)
: null);
if (f2 != null) {
f1 = AU.arrayCopyF(f1, -1);
Modified: trunk/Jmol/src/org/jmol/viewer/DataManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/DataManager.java 2015-08-06 18:37:56 UTC
(rev 20678)
+++ trunk/Jmol/src/org/jmol/viewer/DataManager.java 2015-08-07 18:04:07 UTC
(rev 20679)
@@ -239,14 +239,25 @@
return info;
}
+ /**
+ * When bsSelected is not null, this returns a truncated array
+ *
+ */
@Override
- public float[] getDataFloatA(String label) {
+ public float[] getDataFloatA(String label, BS bsSelected) {
if (dataValues.size() == 0)
return null;
Object[] data = getData(label);
if (data == null || ((Integer)data[DATA_TYPE]).intValue() !=
JmolDataManager.DATA_TYPE_AF)
return null;
- return (float[]) data[DATA_VALUE];
+ float[] f = (float[]) data[DATA_VALUE];
+ if (bsSelected == null)
+ return f;
+ float[] fnew = new float[bsSelected.cardinality()];
+ // load array
+ for (int i = 0, n = f.length, p = bsSelected.nextSetBit(0); p >= 0 && i <
n; p = bsSelected.nextSetBit(p + 1))
+ fnew[i++] = f[p];
+ return fnew;
}
@Override
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-08-06 18:37:56 UTC
(rev 20678)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-08-07 18:04:07 UTC
(rev 20679)
@@ -51,15 +51,20 @@
TODO: curved arrows overextend and with width settings do not truncate shaft
properly
-Jmol.___JmolVersion="14.3.15_2015.08.06"
+Jmol.___JmolVersion="14.3.15_2015.08.07"
+bug fix: write property atomno temperature "test.pdb" preserves long residue
names from CIF files
+bug fix: load "test.pdb" from write property atomno temperature restores
values for atomno and temperature
+
+JmolVersion="14.3.15_2015.08.06"
+
bug fix: stereo setting should not be saved in state.
-- though saved, it was not by default set to normal,
-- thus influencing later loads.
-bug fix: stereo not implemented in JavaScript
+bug fix: STEREO not implemented in JavaScript
-new feature: stereo DTI
+new feature: STEREO DTI
-- left/right dual panel, as just STEREO
-- compresses width by 50% for DTI mode (Dimension Technologies, Inc.)
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-08-06 18:37:56 UTC
(rev 20678)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-08-07 18:04:07 UTC
(rev 20679)
@@ -1999,7 +1999,7 @@
BS bsWritten = new BS();
char ctype = '\0';
LabelToken[] tokens = vwr.ms.getLabeler().compile(vwr,
- "ATOM %-6i%4a%1A%3n %1c%4R%1E ", '\0', null);
+ "ATOM %-6i%4a%1A%3.-3n %1c%4R%1E ", '\0', null);
if (parameters == null) {
ctype = (type.length() > 11 && type.indexOf("quaternion ") >= 0 ? type
.charAt(11) : 'R');
@@ -2019,7 +2019,9 @@
P3 factors = (P3) parameters[6];
P3 center = (P3) parameters[7];
String format = (String) parameters[8];
+ String[] properties = (String[]) parameters[9];
boolean isPDBFormat = (factors != null && format == null);
+ Atom[] atoms = vwr.ms.at;
if (isPDBFormat) {
out.append("REMARK 6 Jmol PDB-encoded data: ").append(type)
.append(";\n");
@@ -2028,10 +2030,42 @@
.append(Escape.eP(maxXYZ)).append(" unScaledXyz = xyz * ")
.append(Escape.eP(factors)).append(" + ").append(Escape.eP(center))
.append(";\n");
+ String atomNames = null;
+ for (int i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms
+ .nextSetBit(i + 1)) {
+ String name = "" + atoms[i].getAtomName();
+ if (atomNames != null || name.length() > 4) {
+ if (atomNames == null) {
+ atomNames = "";
+ i = -1;
+ continue;
+ }
+ atomNames += " " + name;
+ }
+ }
+ if (atomNames != null)
+ out.append("REMARK 6 Jmol atom
names").append(atomNames).append("\n");
+ String resNames = null;
+ for (int i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms
+ .nextSetBit(i + 1)) {
+ String name = "" + atoms[i].getGroup3(true);
+ if (resNames != null || name.length() > 3) {
+ if (resNames == null) {
+ resNames = "";
+ i = -1;
+ continue;
+ }
+ resNames += " " + name;
+ }
+ }
+ if (resNames != null)
+ out.append("REMARK 6 Jmol residue
names").append(resNames).append("\n");
+ for (int i = 0; i < properties.length; i++)
+ if (properties[i] != null)
+ out.append("REMARK 6 Jmol property
").append(properties[i]).append(";\n");
}
String strExtra = "";
Atom atomLast = null;
- Atom[] atoms = vwr.ms.at;
P3 ptTemp = new P3();
if (!isPDBFormat) {
if (format == null)
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-08-06 18:37:56 UTC (rev
20678)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-08-07 18:04:07 UTC (rev
20679)
@@ -2859,7 +2859,7 @@
}
public void setCurrentColorRange(String label) {
- float[] data = getDataFloat(label);
+ float[] data = getDataFloat(label, null);
BS bs = (data == null ? null : (BS) (getDataManager().getData(label))[2]);
if (bs != null && g.rangeSelected)
bs.and(bsA());
@@ -2879,8 +2879,8 @@
return (type == null ? lastData : getDataManager().getData(type));
}
- public float[] getDataFloat(String label) {
- return getDataManager().getDataFloatA(label);
+ public float[] getDataFloat(String label, BS bsSelected) {
+ return getDataManager().getDataFloatA(label, bsSelected);
}
public float[][] getDataFloat2D(String label) {
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
