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[Jmol-commits] SF.net SVN: jmol:[16471] trunk/Jmol/src/org/jmol
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From: <ha...@us...> - 2011-11-15 03:52:44
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Revision: 16471
http://jmol.svn.sourceforge.net/jmol/?rev=16471&view=rev
Author: hansonr
Date: 2011-11-15 03:52:37 +0000 (Tue, 15 Nov 2011)
Log Message:
-----------
version=12.3.6_dev
# new feature: load files "xxx.tlsout" "xxxx.pdb"
# -- loads REFMAC-style TLS data into xxxx.pdb
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/shapespecial/EllipsoidsRenderer.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Added Paths:
-----------
trunk/Jmol/src/org/jmol/adapter/readers/more/TlsDataOnlyReader.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2011-11-15 03:23:26 UTC (rev 16470)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2011-11-15 03:52:37 UTC (rev 16471)
@@ -140,13 +140,17 @@
"TITLE "; //21
- @Override
+ @SuppressWarnings("unchecked")
+@Override
protected void initializeReader() throws Exception {
setIsPDB();
pdbHeader = (getHeader ? new StringBuffer() : null);
applySymmetry = !checkFilter("NOSYMMETRY");
getTlsGroups = checkFilter("TLS");
-
+ if (htParams.containsKey("vTlsModels")) {
+ // from load files "tls.out" "xxxx.pdb"
+ vTlsModels = (List<Map<String, Object>>) htParams.remove("vTlsModels");
+ }
if (checkFilter("CONF ")) {
configurationPtr = parseInt(filter, filter.indexOf("CONF ") + 5);
sbIgnored = new StringBuffer();
Added: trunk/Jmol/src/org/jmol/adapter/readers/more/TlsDataOnlyReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/TlsDataOnlyReader.java (rev 0)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/TlsDataOnlyReader.java 2011-11-15 03:52:37 UTC (rev 16471)
@@ -0,0 +1,157 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2006-03-15 07:52:29 -0600 (Wed, 15 Mar 2006) $
+ * $Revision: 4614 $
+ *
+ * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
+ *
+ * Contact: jmo...@li...
+ *
+ * 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.more;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
+import javax.vecmath.Point3f;
+
+import org.jmol.adapter.smarter.AtomSetCollectionReader;
+import org.jmol.util.Escape;
+import org.jmol.util.Logger;
+import org.jmol.util.Parser;
+
+/*
+ * TLS output reader -- data only; no atoms
+ *
+ */
+
+public class TlsDataOnlyReader extends AtomSetCollectionReader {
+
+ private List<Map<String, Object>> vTlsModels;
+ private StringBuffer sbTlsErrors;
+ private int tlsGroupID;
+
+ @Override
+ protected void initializeReader() throws Exception {
+ readTlsData();
+ continuing = false;
+ }
+
+ // ## REFMAC ORDER: t11 t22 t33 t12 t13 t23
+ // ## REFMAC ORDER: l11 l22 l33 l12 l13 l23
+ // ## REFMAC ORDER: <S22 - S11> <S11 - S33> <S12> <S13> <S23> <S21> <S31> <S32>
+
+ private final static String[] TLnn = new String[] { "11", "22", "33", "12", "13", "23" };
+ private final static String[] Snn = new String[] { "22", "11", "12", "13", "23", "21", "31", "32" };
+
+ private void readTlsData() throws Exception {
+ vTlsModels = new ArrayList<Map<String, Object>>();
+ List<Map<String, Object>> tlsGroups;
+ Map<String, Object> tlsGroup = null;
+ List<Map<String, Object>> ranges = null;
+ Map<String, Object> range = null;
+ tlsGroups = new ArrayList<Map<String, Object>>();
+ while (readLine() != null) {
+ String[] tokens = getTokens(line.replace('\'', ' '));
+ if (tokens.length == 0)
+ continue;
+ if (tokens[0].equals("TLS")) {
+ tlsGroup = new Hashtable<String, Object>();
+ ranges = new ArrayList<Map<String, Object>>();
+ tlsGroup.put("ranges", ranges);
+ tlsGroups.add(tlsGroup);
+ tlsGroup.put("id", Integer.valueOf(++tlsGroupID));
+ } else if (tokens[0].equals("RANGE")) {
+ /*
+ RANGE 'A 1.' 'A 7.' ALL
+ */
+ range = new Hashtable<String, Object>();
+ char chain1 = tokens[1].charAt(0);
+ char chain2 = tokens[3].charAt(0);
+ int res1 = Parser.parseInt(tokens[2]);
+ int res2 = Parser.parseInt(tokens[4]);
+ // ALL ?
+ if (chain1 == chain2) {
+ range.put("chains", "" + chain1 + chain2);
+ if (res1 <= res2) {
+ range.put("residues", new int[] { res1, res2 });
+ ranges.add(range);
+ } else {
+ tlsAddError(" TLS group residues are not in order (range ignored)");
+ }
+ } else {
+ tlsAddError(" TLS group chains are different (range ignored)");
+ }
+ } else if (tokens[0].equals("ORIGIN")) {
+ /*
+ ORIGIN 11.6283 8.2746 10.6813
+ */
+ Point3f origin = new Point3f();
+ tlsGroup.put("origin", origin);
+ origin.set(parseFloat(tokens[1]), parseFloat(tokens[2]),
+ parseFloat(tokens[3]));
+ if (Float.isNaN(origin.x) || Float.isNaN(origin.y)
+ || Float.isNaN(origin.z)) {
+ origin.set(Float.NaN, Float.NaN, Float.NaN);
+ tlsAddError("invalid origin: " + line);
+ }
+ } else if (tokens[0].equals("T") || tokens[0].equals("L")
+ || tokens[0].equals("S")) {
+ /*
+ T 0.0631 0.0710 0.0706 0.0097 -0.0103 -0.0070
+ L 3.3102 4.0562 3.5219 1.4620 -1.0250 -1.1798
+ S 0.0297 -0.0733 0.0732 0.0069 -0.1241 -0.1282 0.0034 0.0501
+ */
+ char tensorType = tokens[0].charAt(0);
+ String[] nn = (tensorType == 'S' ? Snn : TLnn);
+ float[][] tensor = new float[3][3];
+ tlsGroup.put("t" + tensorType, tensor);
+
+ for (int i = 1; i < tokens.length; i++) {
+ int ti = nn[i].charAt(0) - '1';
+ int tj = nn[i].charAt(1) - '1';
+ tensor[ti][tj] = parseFloat(tokens[++i]);
+ if (ti < tj)
+ tensor[tj][ti] = tensor[ti][tj];
+ }
+ if (tensorType == 'S')
+ tensor[0][0] = -tensor[0][0];
+ for (int i = 0; i < 3; i++)
+ for (int j = 0; j < 3; j++)
+ if (Float.isNaN(tensor[i][j])) {
+ tlsAddError("invalid tensor: " + Escape.escapeArray(tensor));
+ }
+ }
+ }
+ Logger.info(tlsGroupID + " TLS groups read");
+ Hashtable<String, Object> groups = new Hashtable<String, Object>();
+ groups.put("groupCount", Integer.valueOf(tlsGroupID));
+ groups.put("groups", tlsGroups);
+ vTlsModels.add(groups);
+ htParams.put("vTlsModels", vTlsModels);
+ }
+
+ private void tlsAddError(String error) {
+ if (sbTlsErrors == null)
+ sbTlsErrors = new StringBuffer();
+ sbTlsErrors.append(fileName).append('\t').append("TLS group ").append(
+ tlsGroupID).append('\t').append(error).append('\n');
+ }
+
+}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2011-11-15 03:23:26 UTC (rev 16470)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2011-11-15 03:52:37 UTC (rev 16471)
@@ -199,10 +199,12 @@
public AtomSetCollection(AtomSetCollection[] array) {
this("Array", null);
- setAtomSetCollectionAuxiliaryInfo("isMultiFile", Boolean.TRUE);
- for (int i = 0; i < array.length; i++) {
- appendAtomSetCollection(i, array[i]);
- }
+ int n = 0;
+ for (int i = 0; i < array.length; i++)
+ if (array[i].atomCount > 0)
+ appendAtomSetCollection(n++, array[i]);
+ if (n > 1)
+ setAtomSetCollectionAuxiliaryInfo("isMultiFile", Boolean.TRUE);
}
/**
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2011-11-15 03:23:26 UTC (rev 16470)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2011-11-15 03:52:37 UTC (rev 16471)
@@ -355,7 +355,7 @@
if (atomSetCollection.errorMessage != null)
return atomSetCollection.errorMessage + "\nfor file " + filePath
+ "\ntype " + name;
- if (atomSetCollection.getAtomCount() == 0)
+ if (atomSetCollection.getAtomCount() == 0 && fileType.indexOf("DataOnly") < 0)
return "No atoms found\nfor file " + filePath + "\ntype " + name;
return atomSetCollection;
}
@@ -373,8 +373,7 @@
@SuppressWarnings("unchecked")
private void initialize() {
initializeSymmetry();
- viewer = (JmolViewer) htParams.get("viewer");
- htParams.remove("viewer"); // don't pass this on to user
+ viewer = (JmolViewer) htParams.remove("viewer"); // don't pass this on to user
if (htParams.containsKey("stateScriptVersionInt"))
stateScriptVersionInt = ((Integer) htParams.get("stateScriptVersionInt"))
.intValue();
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2011-11-15 03:23:26 UTC (rev 16470)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2011-11-15 03:52:37 UTC (rev 16471)
@@ -45,7 +45,7 @@
private final static String[] readerSets = new String[] {
"cifpdb.", ";Cif;Pdb;",
"molxyz.", ";Mol3D;Mol;Xyz;",
- "more.", ";BinaryDcd;Gromacs;MdCrd;MdTop;Mol2;Pqr;P2n;",
+ "more.", ";BinaryDcd;Gromacs;MdCrd;MdTop;Mol2;Pqr;P2n;TlsDataOnly;",
"quantum.", ";Adf;Csf;Dgrid;GamessUK;GamessUS;Gaussian;GausianWfn;Jaguar;" +
"Molden;MopacGraphf;GenNBO;NWChem;Odyssey;Psi;Qchem;Spartan;SpartanSmol;" +
"WebMO;",
@@ -270,7 +270,7 @@
atomSetCollectionReader = (AtomSetCollectionReader) atomSetCollectionReaderClass
.newInstance();
} catch (Exception e) {
- err = "File reader was not found:" + readerName;
+ err = "File reader was not found:" + className;
Logger.error(err);
return err;
}
@@ -911,8 +911,12 @@
private final static String[] dcdFileStartRecords =
{"BinaryDcd", "T\0\0\0CORD", "\0\0\0TCORD"};
+ private final static String[] tlsDataOnlyFileStartRecords =
+ {"TlsDataOnly", "REFMAC\n\nTL", "REFMAC\r\n\r\n", "REFMAC\r\rTL"};
+
private final static String[][] fileStartsWithRecords =
- { cubeFileStartRecords, mol2Records, webmoFileStartRecords, moldenFileStartRecords, dcdFileStartRecords };
+ { cubeFileStartRecords, mol2Records, webmoFileStartRecords,
+ moldenFileStartRecords, dcdFileStartRecords, tlsDataOnlyFileStartRecords };
////////////////////////////////////////////////////////////////
// these test lines that startWith one of these strings
Modified: trunk/Jmol/src/org/jmol/shapespecial/EllipsoidsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/EllipsoidsRenderer.java 2011-11-15 03:23:26 UTC (rev 16470)
+++ trunk/Jmol/src/org/jmol/shapespecial/EllipsoidsRenderer.java 2011-11-15 03:52:37 UTC (rev 16471)
@@ -203,6 +203,9 @@
factoredLengths[i] = ellipsoid.lengths[i] * ellipsoid.scale;
if (Float.isNaN(factoredLengths[i]))
isOK = false;
+ else if (factoredLengths[i] < 0.05f)
+ factoredLengths[i] = 0.05f; // for extremely flat ellipsoids, we need at least some length
+
}
axes = ellipsoid.vectors;
if (axes == null) { //isotropic
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-11-15 03:23:26 UTC (rev 16470)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-11-15 03:52:37 UTC (rev 16471)
@@ -3,6 +3,9 @@
version=12.3.6_dev
+# new feature: load files "xxx.tlsout" "xxxx.pdb"
+# -- loads REFMAC-style TLS data into xxxx.pdb
+
# =============================================================================
#version=12.3.5
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