Revision: 18465
http://sourceforge.net/p/jmol/code/18465
Author: hansonr
Date: 2013-07-18 18:32:28 +0000 (Thu, 18 Jul 2013)
Log Message:
-----------
Modified Paths:
--------------
branches/v13_0/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
branches/v13_0/Jmol/src/org/jmol/shapebio/BioShapeRenderer.java
branches/v13_0/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
branches/v13_0/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v13_0/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-07-18 18:06:27 UTC (rev 18464)
+++ branches/v13_0/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-07-18 18:32:28 UTC (rev 18465)
@@ -46,28 +46,23 @@
/**
* PDB file reader.
- *
+ *
*<p>
- * <a href='http://www.rcsb.org'>
- * http://www.rcsb.org
- * </a>
- *
+ * <a href='http://www.rcsb.org'> http://www.rcsb.org </a>
+ *
* @author Miguel, Egon, and Bob (hans...@stolaf.edu)
*
- * pqr and gromacs pdb_wide_format added by Bob
- * see http://repo.or.cz/w/gromacs.git/blob/HEAD:/src/gmxlib/pdbio.c line 244
- * see http://repo.or.cz/w/gromacs.git/blob/HEAD:/src/gmxlib/pdbio.c line 323
+ * pqr and gromacs pdb_wide_format added by Bob see
+ * http://repo.or.cz/w/gromacs.git/blob/HEAD:/src/gmxlib/pdbio.c line
+ * 244 see
http://repo.or.cz/w/gromacs.git/blob/HEAD:/src/gmxlib/pdbio.c
+ * line 323
*
- * symmetry added by Bob Hanson:
+ * symmetry added by Bob Hanson:
*
- * setFractionalCoordinates()
- * setSpaceGroupName()
- * setUnitCell()
- * initializeCartesianToFractional();
- * setUnitCellItem()
- * setAtomCoord()
- * applySymmetryAndSetTrajectory()
- *
+ * setFractionalCoordinates() setSpaceGroupName() setUnitCell()
+ * initializeCartesianToFractional(); setUnitCellItem() setAtomCoord()
+ * applySymmetryAndSetTrajectory()
+ *
*/
public class PdbReader extends AtomSetCollectionReader {
@@ -78,36 +73,36 @@
private boolean applySymmetry;
private boolean getTlsGroups;
-
- private boolean isMultiModel; // MODEL ...
+
+ private boolean isMultiModel; // MODEL ...
private boolean haveMappedSerials;
private boolean isConnectStateBug;
private boolean isLegacyModelType;
private boolean gromacsWideFormat;
protected boolean isPQR;
-
+
private final Map<String, Map<String, Boolean>> htFormul = new
Hashtable<String, Map<String, Boolean>>();
private Map<String, String> htHetero;
private Map<String, Map<String, Object>> htSites;
private Map<String, Boolean> htElementsInCurrentGroup;
private Map<String, Map<String, String>> htMolIds;
-
+
private List<Map<String, String>> vCompnds;
private List<Matrix4f> vBiomts;
private List<Map<String, Object>> vBiomolecules;
private List<Map<String, Object>> vTlsModels;
private StringBuffer sbTlsErrors;
- private int[] chainAtomCounts;
-
+ private int[] chainAtomCounts;
+
private StringBuffer sbIgnored, sbSelected, sbConect, sb;
private int atomCount;
private int maxSerial;
private int nUNK;
private int nRes;
-
+
private Map<String, String> currentCompnd;
private String currentGroup3;
private String currentKey;
@@ -126,52 +121,47 @@
private int lastTargetSerial = Integer.MIN_VALUE;
private int tlsGroupID;
- final private static String lineOptions =
- "ATOM " + //0
- "HETATM " + //1
- "MODEL " + //2
- "CONECT " + //3
- "HELIX " + //4,5,6
- "SHEET " +
- "TURN " +
- "HET " + //7
- "HETNAM " + //8
- "ANISOU " + //9
- "SITE " + //10
- "CRYST1 " + //11
- "SCALE1 " + //12,13,14
- "SCALE2 " +
- "SCALE3 " +
- "EXPDTA " + //15
- "FORMUL " + //16
- "REMARK " + //17
- "HEADER " + //18
- "COMPND " + //19
- "SOURCE " + //20
- "TITLE "; //21
+ final private static String lineOptions = "ATOM " + //0
+ "HETATM " + //1
+ "MODEL " + //2
+ "CONECT " + //3
+ "HELIX " + //4,5,6
+ "SHEET " + "TURN " + "HET " + //7
+ "HETNAM " + //8
+ "ANISOU " + //9
+ "SITE " + //10
+ "CRYST1 " + //11
+ "SCALE1 " + //12,13,14
+ "SCALE2 " + "SCALE3 " + "EXPDTA " + //15
+ "FORMUL " + //16
+ "REMARK " + //17
+ "HEADER " + //18
+ "COMPND " + //19
+ "SOURCE " + //20
+ "TITLE "; //21
+ @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();
+ sbSelected = new StringBuffer();
+ }
+ isLegacyModelType = (stateScriptVersionInt < 120000);
+ isConnectStateBug = (stateScriptVersionInt >= 120151
+ && stateScriptVersionInt <= 120220 || stateScriptVersionInt >= 120300
+ && stateScriptVersionInt <= 120320);
+ }
- @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();
- sbSelected = new StringBuffer();
- }
- isLegacyModelType = (stateScriptVersionInt < 120000);
- isConnectStateBug = (stateScriptVersionInt >= 120151 &&
stateScriptVersionInt <= 120220
- || stateScriptVersionInt >= 120300 && stateScriptVersionInt <=
120320);
- }
-
@Override
protected boolean checkLine() throws Exception {
int ptOption = ((lineLength = line.length()) < 6 ? -1 : lineOptions
@@ -305,20 +295,24 @@
atomSetCollection.setAtomSetAuxiliaryInfo("biomolecules", vBiomolecules);
setBiomoleculeAtomCounts();
if (vBiomts != null && applySymmetry) {
- atomSetCollection.applySymmetry(vBiomts, notionalUnitCell,
applySymmetryToBonds, filter);
+ atomSetCollection.applySymmetry(vBiomts, notionalUnitCell,
+ applySymmetryToBonds, filter);
vTlsModels = null; // for now, no TLS groups for biomolecules
}
}
if (vTlsModels != null) {
- SymmetryInterface symmetry = (SymmetryInterface)
Interface.getOptionInterface("symmetry.Symmetry");
+ SymmetryInterface symmetry = (SymmetryInterface) Interface
+ .getOptionInterface("symmetry.Symmetry");
int n = atomSetCollection.getAtomSetCount();
if (n == vTlsModels.size()) {
for (int i = n; --i >= 0;)
setTlsGroups(i, i, symmetry);
} else {
- Logger.info(n + " models but " + vTlsModels.size() + " TLS
descriptions");
+ Logger.info(n + " models but " + vTlsModels.size()
+ + " TLS descriptions");
if (vTlsModels.size() == 1) {
- Logger.info(" -- assuming all models have the same TLS description
-- check REMARK 3 for details.");
+ Logger
+ .info(" -- assuming all models have the same TLS description --
check REMARK 3 for details.");
for (int i = n; --i >= 0;)
setTlsGroups(0, i, symmetry);
}
@@ -326,13 +320,15 @@
checkForResidualBFactors(symmetry);
}
if (sbTlsErrors != null) {
- atomSetCollection.setAtomSetCollectionAuxiliaryInfo("tlsErrors",
sbTlsErrors.toString());
+ atomSetCollection.setAtomSetCollectionAuxiliaryInfo("tlsErrors",
+ sbTlsErrors.toString());
appendLoadNote(sbTlsErrors.toString());
}
-
+
super.finalizeReader();
if (vCompnds != null)
- atomSetCollection.setAtomSetCollectionAuxiliaryInfo("compoundSource",
vCompnds);
+ atomSetCollection.setAtomSetCollectionAuxiliaryInfo("compoundSource",
+ vCompnds);
if (htSites != null) { // && atomSetCollection.getAtomSetCount() == 1)
addSites(htSites);
}
@@ -344,43 +340,44 @@
Logger.info(sbIgnored.toString());
}
}
-
+
private void checkForResidualBFactors(SymmetryInterface symmetry) {
Atom[] atoms = atomSetCollection.getAtoms();
boolean isResidual = false;
- for (int i = atomSetCollection.getAtomCount(); --i >= 0;) {
+ for (int i = atomSetCollection.getAtomCount(); --i >= 0;) {
float[] anisou = tlsU.get(atoms[i]);
if (anisou == null)
continue;
- float resid = anisou[7] - (anisou[0] + anisou[1] + anisou[2])/3f;
+ float resid = anisou[7] - (anisou[0] + anisou[1] + anisou[2]) / 3f;
if (resid < 0 || Float.isNaN(resid)) {
isResidual = true; // can't be total
break;
}
- }
-
- Logger.info("TLS analysis suggests Bfactors are " + (isResidual ? "" :
"NOT") + " residuals");
+ }
- for (Map.Entry<Atom, float[]> entry : tlsU.entrySet()) {
- float[] anisou = entry.getValue();
- float resid = anisou[7];
- if (resid == 0)
- continue;
- if (!isResidual)
- resid -= (anisou[0] + anisou[1] + anisou[2])/3f;
- anisou[0] += resid;
- anisou[1] += resid;
- anisou[2] += resid;
- entry.getKey().ellipsoid[1] = symmetry.getEllipsoid(anisou);
-
- // check for equal:
-
- System.out.println("TLS-U: " + Escape.escape(anisou));
- anisou = (entry.getKey().anisoBorU);
- if (anisou != null)
- System.out.println("ANISOU: " + Escape.escape(anisou));
- }
- tlsU = null;
+ Logger.info("TLS analysis suggests Bfactors are "
+ + (isResidual ? "" : "NOT") + " residuals");
+
+ for (Map.Entry<Atom, float[]> entry : tlsU.entrySet()) {
+ float[] anisou = entry.getValue();
+ float resid = anisou[7];
+ if (resid == 0)
+ continue;
+ if (!isResidual)
+ resid -= (anisou[0] + anisou[1] + anisou[2]) / 3f;
+ anisou[0] += resid;
+ anisou[1] += resid;
+ anisou[2] += resid;
+ entry.getKey().ellipsoid[1] = symmetry.getEllipsoid(anisou);
+
+ // check for equal:
+
+ System.out.println("TLS-U: " + Escape.escape(anisou));
+ anisou = (entry.getKey().anisoBorU);
+ if (anisou != null)
+ System.out.println("ANISOU: " + Escape.escape(anisou));
+ }
+ tlsU = null;
}
private void header() {
@@ -390,11 +387,13 @@
String pdbID = (lineLength >= 66 ? line.substring(62, 66).trim() : "");
if (pdbID.length() == 4) {
atomSetCollection.setCollectionName(pdbID);
- atomSetCollection.setAtomSetCollectionAuxiliaryInfo("havePDBHeaderName",
Boolean.TRUE);
+ atomSetCollection.setAtomSetCollectionAuxiliaryInfo("havePDBHeaderName",
+ Boolean.TRUE);
}
if (lineLength > 50)
line = line.substring(0, 50);
- atomSetCollection.setAtomSetCollectionAuxiliaryInfo("CLASSIFICATION",
line.substring(7).trim());
+ atomSetCollection.setAtomSetCollectionAuxiliaryInfo("CLASSIFICATION", line
+ .substring(7).trim());
}
private void title() {
@@ -402,7 +401,7 @@
return;
appendLoadNote(line.substring(10).trim());
}
-
+
private void compnd(boolean isSource) {
if (!isSource) {
if (compnd == null)
@@ -418,8 +417,8 @@
if (vCompnds == null) {
if (isSource)
return;
- vCompnds = new ArrayList<Map<String,String>>();
- htMolIds = new Hashtable<String, Map<String,String>>();
+ vCompnds = new ArrayList<Map<String, String>>();
+ htMolIds = new Hashtable<String, Map<String, String>>();
currentCompnd = new Hashtable<String, String>();
currentCompnd.put("select", "(*)");
currentKey = "MOLECULE";
@@ -482,43 +481,42 @@
}
}
-/*
- REMARK 350 BIOMOLECULE: 1
- REMARK 350 APPLY THE FOLLOWING TO CHAINS: 1, 2, 3, 4, 5, 6,
- REMARK 350 A, B, C
- REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
- REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
- REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
- REMARK 350 BIOMT1 2 0.309017 -0.809017 0.500000 0.00000
- REMARK 350 BIOMT2 2 0.809017 0.500000 0.309017 0.00000
- REMARK 350 BIOMT3 2 -0.500000 0.309017 0.809017 0.00000
-
-
- or, as fount in
http://www.ebi.ac.uk/msd-srv/pqs/pqs-doc/macmol/1k28.mmol
-
-REMARK 350 AN OLIGOMER OF TYPE :HEXAMERIC : CAN BE ASSEMBLED BY
-REMARK 350 APPLYING THE FOLLOWING TO CHAINS:
-REMARK 350 A, D
-REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
-REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
-REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
-REMARK 350 IN ADDITION APPLY THE FOLLOWING TO CHAINS:
-REMARK 350 A, D
-REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000
-REMARK 350 BIOMT2 2 1.000000 -1.000000 0.000000 0.00000
-REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
-REMARK 350 IN ADDITION APPLY THE FOLLOWING TO CHAINS:
-REMARK 350 A, D
-REMARK 350 BIOMT1 3 -1.000000 1.000000 0.000000 0.00000
-REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 0.00000
-REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
+ /*
+ REMARK 350 BIOMOLECULE: 1
+ REMARK 350 APPLY THE FOLLOWING TO CHAINS: 1, 2, 3, 4, 5, 6,
+ REMARK 350 A, B, C
+ REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
+ REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
+ REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
+ REMARK 350 BIOMT1 2 0.309017 -0.809017 0.500000 0.00000
+ REMARK 350 BIOMT2 2 0.809017 0.500000 0.309017 0.00000
+ REMARK 350 BIOMT3 2 -0.500000 0.309017 0.809017 0.00000
+
+
+ or, as fount in
http://www.ebi.ac.uk/msd-srv/pqs/pqs-doc/macmol/1k28.mmol
+
+ REMARK 350 AN OLIGOMER OF TYPE :HEXAMERIC : CAN BE ASSEMBLED BY
+ REMARK 350 APPLYING THE FOLLOWING TO CHAINS:
+ REMARK 350 A, D
+ REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
+ REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
+ REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
+ REMARK 350 IN ADDITION APPLY THE FOLLOWING TO CHAINS:
+ REMARK 350 A, D
+ REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000
+ REMARK 350 BIOMT2 2 1.000000 -1.000000 0.000000 0.00000
+ REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
+ REMARK 350 IN ADDITION APPLY THE FOLLOWING TO CHAINS:
+ REMARK 350 A, D
+ REMARK 350 BIOMT1 3 -1.000000 1.000000 0.000000 0.00000
+ REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 0.00000
+ REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
-*/
-
-
+ */
+
private void remark350() throws Exception {
List<Matrix4f> biomts = null;
- vBiomolecules = new ArrayList<Map<String,Object>>();
+ vBiomolecules = new ArrayList<Map<String, Object>>();
chainAtomCounts = new int[255];
String title = "";
String chainlist = "";
@@ -562,7 +560,8 @@
}
chainlist = ":" + line.substring(41).trim().replace(' ', ':');
needLine = false;
- while (readLine() != null && line.indexOf("BIOMT") < 0 &&
line.indexOf("350") == 7)
+ while (readLine() != null && line.indexOf("BIOMT") < 0
+ && line.indexOf("350") == 7)
chainlist += ":" + line.substring(11).trim().replace(' ', ':');
if (checkFilter("BIOMOLECULE " + iMolecule + ";")) {
setFilter(filter.replace(':', '_') + chainlist);
@@ -611,30 +610,30 @@
}
/*
-REMARK 290
-REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
-REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
-REMARK 290
-REMARK 290 SYMOP SYMMETRY
-REMARK 290 NNNMMM OPERATOR
-REMARK 290 1555 X,Y,Z
-REMARK 290 2555 -X,Y+1/2,-Z
-REMARK 290
-REMARK 290 WHERE NNN -> OPERATOR NUMBER
-REMARK 290 MMM -> TRANSLATION VECTOR
-REMARK 290
-REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
-REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
-REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
-REMARK 290 RELATED MOLECULES.
-REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
-REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
-REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
-REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
-REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 9.32505
-REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
-REMARK 290
-REMARK 290 REMARK: NULL
+ REMARK 290
+ REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
+ REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
+ REMARK 290
+ REMARK 290 SYMOP SYMMETRY
+ REMARK 290 NNNMMM OPERATOR
+ REMARK 290 1555 X,Y,Z
+ REMARK 290 2555 -X,Y+1/2,-Z
+ REMARK 290
+ REMARK 290 WHERE NNN -> OPERATOR NUMBER
+ REMARK 290 MMM -> TRANSLATION VECTOR
+ REMARK 290
+ REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
+ REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
+ REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
+ REMARK 290 RELATED MOLECULES.
+ REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
+ REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
+ REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
+ REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
+ REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 9.32505
+ REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
+ REMARK 290
+ REMARK 290 REMARK: NULL
*/
private void remark290() throws Exception {
@@ -648,14 +647,14 @@
}
}
}
- }
-
+ }
+
// Gromacs pdb_wide_format:
//%-6s%5u %-4.4s %3.3s %c%4d%c %10.5f%10.5f%10.5f%8.4f%8.4f %2s\n")
//0 1 2 3 4 5 6 7
//01234567890123456789012345678901234567890123456789012345678901234567890123456789
//aaaaaauuuuu ssss sss cnnnnc
xxxxxxxxxxyyyyyyyyyyzzzzzzzzzzccccccccrrrrrrrr
-
+
private void atom(int serial) {
Atom atom = new Atom();
atom.atomName = line.substring(12, 16).trim();
@@ -732,15 +731,14 @@
}
}
}
-
-
@Override
protected boolean filterAtom(Atom atom, int iAtom) {
if (!super.filterAtom(atom, iAtom))
return false;
if (configurationPtr > 0) {
- if (atom.sequenceNumber != lastGroup || atom.insertionCode !=
lastInsertion) {
+ if (atom.sequenceNumber != lastGroup
+ || atom.insertionCode != lastInsertion) {
conformationIndex = configurationPtr - 1;
lastGroup = atom.sequenceNumber;
lastInsertion = atom.insertionCode;
@@ -749,12 +747,10 @@
// ignore atoms that have no designation
if (atom.alternateLocationID != '\0') {
// count down until we get the desired index into the list
- String msg = " atom [" + atom.group3 + "]"
- + atom.sequenceNumber
- + (atom.insertionCode == '\0' ? "" : "^" +
atom.insertionCode)
- + (atom.chainID == '\0' ? "" : ":" + atom.chainID)
- + "." + atom.atomName
- + "%" + atom.alternateLocationID + "\n";
+ String msg = " atom [" + atom.group3 + "]" + atom.sequenceNumber
+ + (atom.insertionCode == '\0' ? "" : "^" + atom.insertionCode)
+ + (atom.chainID == '\0' ? "" : ":" + atom.chainID) + "."
+ + atom.atomName + "%" + atom.alternateLocationID + "\n";
if (conformationIndex >= 0 && atom.alternateLocationID != lastAltLoc) {
lastAltLoc = atom.alternateLocationID;
conformationIndex--;
@@ -787,52 +783,51 @@
}
return;
}
-
+
float floatOccupancy;
-
+
if (gromacsWideFormat) {
floatOccupancy = parseFloat(line.substring(60, 68));
atom.bfactor = fixRadius(parseFloat(line.substring(68, 76)));
} else {
/****************************************************************
- * read the occupancy from cols 55-60 (1-based)
- * --should be in the range 0.00 - 1.00
+ * read the occupancy from cols 55-60 (1-based) --should be in the range
+ * 0.00 - 1.00
****************************************************************/
-
+
floatOccupancy = parseFloat(line, 54, 60);
/****************************************************************
* read the bfactor from cols 61-66 (1-based)
****************************************************************/
- atom.bfactor = parseFloat(line, 60, 66);
+ atom.bfactor = parseFloat(line, 60, 66);
}
-
+
atom.occupancy = (Float.isNaN(floatOccupancy) ? 100
: (int) (floatOccupancy * 100));
-
+
}
/**
- * The problem here stems from the fact that developers have not fully
- * understood the PDB specifications -- and that those have changed.
- * The actual rules are as follows (using 1-based numbering:
+ * The problem here stems from the fact that developers have not fully
+ * understood the PDB specifications -- and that those have changed. The
+ * actual rules are as follows (using 1-based numbering:
*
- * 1) Chemical symbols may be in columns 77 and 78 for total disambiguity.
- * 2) Only valid chemical symbols should be in columns 13 and 14
- * These are the first two characters of a four-character field.
- * 3) Four-character atom names for hydrogen necessarily start in
- * column 13, so when that is the case, if the four-letter
- * name starts with "H" then it is hydrogen regardless of what
- * letter comes next. For example, "HG3 " is mercury (and should
- * be in a HETATM record, not an ATOM record, anyway), but "HG33"
- * is hydrogen, presumably.
- *
- * This leave open the ambiguity of a four-letter H name in a
- * heteroatom set where the symbol is really H, not Hg or Ha, or Ho or
Hf, etc.
- *
+ * 1) Chemical symbols may be in columns 77 and 78 for total disambiguity. 2)
+ * Only valid chemical symbols should be in columns 13 and 14 These are the
+ * first two characters of a four-character field. 3) Four-character atom
+ * names for hydrogen necessarily start in column 13, so when that is the
+ * case, if the four-letter name starts with "H" then it is hydrogen
+ * regardless of what letter comes next. For example, "HG3 " is mercury (and
+ * should be in a HETATM record, not an ATOM record, anyway), but "HG33" is
+ * hydrogen, presumably.
*
+ * This leave open the ambiguity of a four-letter H name in a heteroatom set
+ * where the symbol is really H, not Hg or Ha, or Ho or Hf, etc.
+ *
+ *
* @param isHetero
- * @return an atom symbol
+ * @return an atom symbol
*/
protected String deduceElementSymbol(boolean isHetero) {
if (lineLength >= 78) {
@@ -847,36 +842,38 @@
char ch13 = line.charAt(13);
// PDB atom symbols are supposed to be in these two characters
// But they could be right-aligned or left-aligned
- if ((htElementsInCurrentGroup == null ||
- htElementsInCurrentGroup.get(line.substring(12, 14)) != null) &&
- Atom.isValidElementSymbolNoCaseSecondChar(ch12, ch13))
+ if ((htElementsInCurrentGroup == null || htElementsInCurrentGroup.get(line
+ .substring(12, 14)) != null)
+ && Atom.isValidElementSymbolNoCaseSecondChar(ch12, ch13))
return (isHetero || ch12 != 'H' ? "" + ch12 + ch13 : "H");
// not a known two-letter code
if (ch12 == 'H') // added check for PQR files "HD22" for example
return "H";
// check for " NZ" for example
- if ((htElementsInCurrentGroup == null ||
- htElementsInCurrentGroup.get("" + ch13) != null) &&
- Atom.isValidElementSymbol(ch13))
+ if ((htElementsInCurrentGroup == null || htElementsInCurrentGroup.get(""
+ + ch13) != null)
+ && Atom.isValidElementSymbol(ch13))
return "" + ch13;
// check for misplaced "O " for example
- if (ch12 != ' ' && (htElementsInCurrentGroup == null ||
- htElementsInCurrentGroup.get("" + ch12) != null) &&
- Atom.isValidElementSymbol(ch12))
+ if (ch12 != ' '
+ && (htElementsInCurrentGroup == null || htElementsInCurrentGroup.get(""
+ + ch12) != null) && Atom.isValidElementSymbol(ch12))
return "" + ch12;
// could be GLX or ASX;
// probably a bad file. But we will make ONE MORE ATTEMPT
// and read columns 14/15 instead of 12/13. What the heck!
char ch14 = line.charAt(14);
- if (ch12 == ' ' && ch13 != 'X' && (htElementsInCurrentGroup == null ||
- htElementsInCurrentGroup.get(line.substring(13, 15)) != null) &&
- Atom.isValidElementSymbolNoCaseSecondChar(ch13, ch14))
- return "" + ch13 + ch14;
+ if (ch12 == ' '
+ && ch13 != 'X'
+ && (htElementsInCurrentGroup == null || htElementsInCurrentGroup
+ .get(line.substring(13, 15)) != null)
+ && Atom.isValidElementSymbolNoCaseSecondChar(ch13, ch14))
+ return "" + ch13 + ch14;
return "Xx";
}
-
+
private boolean haveDoubleBonds;
-
+
private void conect() {
// adapted for improper non-crossreferenced files such as 1W7R
if (sbConect == null) {
@@ -951,21 +948,21 @@
SHEET 3 A 6 ARG A 22 ILE A 26 1 N VAL A 23 O GLU A 47
-TYPE OF HELIX CLASS NUMBER (COLUMNS 39 - 40)
---------------------------------------------------------------
-Right-handed alpha (default) 1
-Right-handed omega 2
-Right-handed pi 3
-Right-handed gamma 4
-Right-handed 310 5
-Left-handed alpha 6
-Left-handed omega 7
-Left-handed gamma 8
-27 ribbon/helix 9
-Polyproline 10
+ TYPE OF HELIX CLASS NUMBER (COLUMNS 39 - 40)
+ --------------------------------------------------------------
+ Right-handed alpha (default) 1
+ Right-handed omega 2
+ Right-handed pi 3
+ Right-handed gamma 4
+ Right-handed 310 5
+ Left-handed alpha 6
+ Left-handed omega 7
+ Left-handed gamma 8
+ 27 ribbon/helix 9
+ Polyproline 10
*/
-
+
private void structure() {
EnumStructure structureType = EnumStructure.NONE;
EnumStructure substructureType = EnumStructure.NONE;
@@ -981,7 +978,8 @@
endChainIDIndex = 31;
endIndex = 33;
if (line.length() >= 40)
- substructureType = Structure.getHelixType(parseInt(line.substring(38,
40)));
+ substructureType = Structure.getHelixType(parseInt(line.substring(38,
+ 40)));
} else if (line.startsWith("SHEET ")) {
structureType = EnumStructure.SHEET;
startChainIDIndex = 21;
@@ -1035,18 +1033,16 @@
return 0;
}
}
-
+
private void model(int modelNumber) {
/****************************************************************
- * mth 2004 02 28
- * note that the pdb spec says:
- * COLUMNS DATA TYPE FIELD DEFINITION
- * ----------------------------------------------------------------------
- * 1 - 6 Record name "MODEL "
- * 11 - 14 Integer serial Model serial number.
- *
- * but I received a file with the serial
- * number right after the word MODEL :-(
+ * mth 2004 02 28 note that the pdb spec says: COLUMNS DATA TYPE FIELD
+ * DEFINITION
+ * ---------------------------------------------------------------------- 1
+ * - 6 Record name "MODEL " 11 - 14 Integer serial Model serial number.
+ *
+ * but I received a file with the serial number right after the word MODEL
+ * :-(
****************************************************************/
checkNotPDB();
haveMappedSerials = false;
@@ -1063,7 +1059,8 @@
// be no center of symmetry, no rotation-inversions,
// no atom-centered rotation axes, and no mirror or glide planes.
atomSetCollection.setCheckSpecial(!isPDB);
- atomSetCollection.setAtomSetAuxiliaryInfo("isPDB", isPDB ? Boolean.TRUE :
Boolean.FALSE);
+ atomSetCollection.setAtomSetAuxiliaryInfo("isPDB", isPDB ? Boolean.TRUE
+ : Boolean.FALSE);
nUNK = nRes = 0;
currentGroup3 = null;
}
@@ -1072,21 +1069,21 @@
float a = getFloat(6, 9);
if (a == 1)
a = Float.NaN; // 1 for a means no unit cell
- setUnitCell(a, getFloat(15, 9), getFloat(24, 9), getFloat(33,
- 7), getFloat(40, 7), getFloat(47, 7));
+ setUnitCell(a, getFloat(15, 9), getFloat(24, 9), getFloat(33, 7), getFloat(
+ 40, 7), getFloat(47, 7));
setSpaceGroupName(parseTrimmed(line, 55, 66));
}
private float getFloat(int ich, int cch) throws Exception {
- return parseFloat(line, ich, ich+cch);
+ return parseFloat(line, ich, ich + cch);
}
private void scale(int n) throws Exception {
int pt = n * 4 + 2;
- setUnitCellItem(pt++,getFloat(10, 10));
- setUnitCellItem(pt++,getFloat(20, 10));
- setUnitCellItem(pt++,getFloat(30, 10));
- setUnitCellItem(pt++,getFloat(45, 10));
+ setUnitCellItem(pt++, getFloat(10, 10));
+ setUnitCellItem(pt++, getFloat(20, 10));
+ setUnitCellItem(pt++, getFloat(30, 10));
+ setUnitCellItem(pt++, getFloat(45, 10));
}
private void expdta() {
@@ -1100,14 +1097,15 @@
int ichLeftParen = formula.indexOf('(');
if (ichLeftParen >= 0) {
int ichRightParen = formula.indexOf(')');
- if (ichRightParen < 0 || ichLeftParen >= ichRightParen ||
- ichLeftParen + 1 == ichRightParen ) // pick up () case in 1SOM.pdb
+ if (ichRightParen < 0 || ichLeftParen >= ichRightParen
+ || ichLeftParen + 1 == ichRightParen) // pick up () case in 1SOM.pdb
return; // invalid formula;
formula = parseTrimmed(formula, ichLeftParen + 1, ichRightParen);
}
Map<String, Boolean> htElementsInGroup = htFormul.get(groupName);
if (htElementsInGroup == null)
- htFormul.put(groupName, htElementsInGroup = new Hashtable<String,
Boolean>());
+ htFormul.put(groupName,
+ htElementsInGroup = new Hashtable<String, Boolean>());
// now, look for atom names in the formula
next[0] = 0;
String elementWithCount;
@@ -1122,7 +1120,7 @@
htElementsInGroup.put("" + chFirst, Boolean.TRUE);
}
}
-
+
private void het() {
if (line.length() < 30) {
return;
@@ -1137,7 +1135,7 @@
String hetName = parseTrimmed(line, 30, 70);
htHetero.put(groupName, hetName);
}
-
+
private void hetnam() {
if (htHetero == null) {
htHetero = new Hashtable<String, String>();
@@ -1145,7 +1143,8 @@
String groupName = parseToken(line, 11, 14);
String hetName = parseTrimmed(line, 15, 70);
if (groupName == null) {
- Logger.error("ERROR: HETNAM record does not contain a group name: " +
line);
+ Logger.error("ERROR: HETNAM record does not contain a group name: "
+ + line);
return;
}
String htName = htHetero.get(groupName);
@@ -1155,57 +1154,57 @@
htHetero.put(groupName, hetName);
//Logger.debug("hetero: "+groupName+" "+hetName);
}
-
+
/*
- The ANISOU records present the anisotropic temperature factors.
+ The ANISOU records present the anisotropic temperature factors.
-Record Format
+ Record Format
-COLUMNS DATA TYPE FIELD DEFINITION
-----------------------------------------------------------------------
- 1 - 6 Record name "ANISOU"
+ COLUMNS DATA TYPE FIELD DEFINITION
+ ----------------------------------------------------------------------
+ 1 - 6 Record name "ANISOU"
- 7 - 11 Integer serial Atom serial number.
+ 7 - 11 Integer serial Atom serial number.
-13 - 16 Atom name Atom name.
+ 13 - 16 Atom name Atom name.
-17 Character altLoc Alternate location indicator.
+ 17 Character altLoc Alternate location indicator.
-18 - 20 Residue name resName Residue name.
+ 18 - 20 Residue name resName Residue name.
-22 Character chainID Chain identifier.
+ 22 Character chainID Chain identifier.
-23 - 26 Integer resSeq Residue sequence number.
+ 23 - 26 Integer resSeq Residue sequence number.
-27 AChar iCode Insertion code.
+ 27 AChar iCode Insertion code.
-29 - 35 Integer u[0][0] U(1,1)
+ 29 - 35 Integer u[0][0] U(1,1)
-36 - 42 Integer u[1][1] U(2,2)
+ 36 - 42 Integer u[1][1] U(2,2)
-43 - 49 Integer u[2][2] U(3,3)
+ 43 - 49 Integer u[2][2] U(3,3)
-50 - 56 Integer u[0][1] U(1,2)
+ 50 - 56 Integer u[0][1] U(1,2)
-57 - 63 Integer u[0][2] U(1,3)
+ 57 - 63 Integer u[0][2] U(1,3)
-64 - 70 Integer u[1][2] U(2,3)
+ 64 - 70 Integer u[1][2] U(2,3)
-73 - 76 LString(4) segID Segment identifier,
left-justified.
+ 73 - 76 LString(4) segID Segment identifier,
left-justified.
-77 - 78 LString(2) element Element symbol, right-justified.
+ 77 - 78 LString(2) element Element symbol, right-justified.
-79 - 80 LString(2) charge Charge on the atom.
+ 79 - 80 LString(2) charge Charge on the atom.
-Details
+ Details
-* Columns 7 - 27 and 73 - 80 are identical to the corresponding ATOM/HETATM
record.
+ * Columns 7 - 27 and 73 - 80 are identical to the corresponding ATOM/HETATM
record.
-* The anisotropic temperature factors (columns 29 - 70) are scaled by a factor
of 10**4 (Angstroms**2) and are presented as integers.
+ * The anisotropic temperature factors (columns 29 - 70) are scaled by a
factor of 10**4 (Angstroms**2) and are presented as integers.
-* The anisotropic temperature factors are stored in the same coordinate frame
as the atomic coordinate records.
+ * The anisotropic temperature factors are stored in the same coordinate
frame as the atomic coordinate records.
*/
-
+
private void anisou() {
float[] data = new float[8];
data[6] = 1; //U not B
@@ -1229,8 +1228,8 @@
data[pt] = parseFloat(line, i, i + 7);
for (int i = 0; i < 6; i++) {
if (Float.isNaN(data[i])) {
- Logger.error("Bad ANISOU record: " + line);
- return;
+ Logger.error("Bad ANISOU record: " + line);
+ return;
}
data[i] /= 10000f;
}
@@ -1240,35 +1239,36 @@
// Ortep Type 8: D = 2pi^2, C = 2, a*b*
// Ortep Type 10: D = 2pi^2, C = 2, Cartesian
}
+
/*
* http://www.wwpdb.org/documentation/format23/sect7.html
*
- Record Format
+ Record Format
-COLUMNS DATA TYPE FIELD DEFINITION
-------------------------------------------------------------------------
- 1 - 6 Record name "SITE "
- 8 - 10 Integer seqNum Sequence number.
-12 - 14 LString(3) siteID Site name.
-16 - 17 Integer numRes Number of residues comprising
+ COLUMNS DATA TYPE FIELD DEFINITION
+ ------------------------------------------------------------------------
+ 1 - 6 Record name "SITE "
+ 8 - 10 Integer seqNum Sequence number.
+ 12 - 14 LString(3) siteID Site name.
+ 16 - 17 Integer numRes Number of residues comprising
site.
-19 - 21 Residue name resName1 Residue name for first residue
+ 19 - 21 Residue name resName1 Residue name for first residue
comprising site.
-23 Character chainID1 Chain identifier for first residue
+ 23 Character chainID1 Chain identifier for first
residue
comprising site.
-24 - 27 Integer seq1 Residue sequence number for first
+ 24 - 27 Integer seq1 Residue sequence number for first
residue comprising site.
-28 AChar iCode1 Insertion code for first residue
+ 28 AChar iCode1 Insertion code for first residue
comprising site.
-30 - 32 Residue name resName2 Residue name for second residue
-...
-41 - 43 Residue name resName3 Residue name for third residue
-...
-52 - 54 Residue name resName4 Residue name for fourth residue
-
+ 30 - 32 Residue name resName2 Residue name for second residue
+ ...
+ 41 - 43 Residue name resName3 Residue name for third residue
+ ...
+ 52 - 54 Residue name resName4 Residue name for fourth residue
+
*/
-
+
private void site() {
if (htSites == null) {
htSites = new Hashtable<String, Map<String, Object>>();
@@ -1284,7 +1284,7 @@
htSite.put("groups", "");
htSites.put(siteID, htSite);
}
- String groups = (String)htSite.get("groups");
+ String groups = (String) htSite.get("groups");
for (int i = 0; i < 4; i++) {
int pt = 18 + i * 11;
String resName = parseTrimmed(line, pt, pt + 3);
@@ -1399,10 +1399,10 @@
range.put("residues", new int[] { res1, res2 });
ranges.add(range);
} else {
- tlsAddError(" TLS group residues are not in order (range
ignored)");
+ tlsAddError(" TLS group residues are not in order (range
ignored)");
}
} else {
- tlsAddError(" TLS group chains are different (range ignored)");
+ tlsAddError(" TLS group chains are different (range ignored)");
}
} else if (tokens[0].equalsIgnoreCase("SELECTION")) {
/*
@@ -1444,7 +1444,8 @@
parseFloat(line.substring(n - 18, n - 9)), parseFloat(line
.substring(n - 9, n)));
}
- if (Float.isNaN(origin.x) || Float.isNaN(origin.y) ||
Float.isNaN(origin.z)) {
+ 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);
}
@@ -1456,9 +1457,8 @@
* REMARK 3 T13: -0.0070 T23: 0.0011
*/
char tensorType = tokens[0].charAt(0);
- String s = (readLine().substring(10)
- + readLine().substring(10) + readLine().substring(10)).replace(
- tensorType, ' ').replace(':', ' ');
+ String s = (readLine().substring(10) + readLine().substring(10) +
readLine()
+ .substring(10)).replace(tensorType, ' ').replace(':', ' ');
//System.out.println("Tensor data = " + s);
tokens = getTokens(s);
float[][] tensor = new float[3][3];
@@ -1512,7 +1512,7 @@
*
* @param iGroup
* @param iModel
- * @param symmetry
+ * @param symmetry
*/
@SuppressWarnings("unchecked")
private void setTlsGroups(int iGroup, int iModel, SymmetryInterface
symmetry) {
@@ -1546,18 +1546,18 @@
}
Logger.info("TLS ID=" + tlsGroupID + " model atom index range "
+ index1 + "-" + index2);
- boolean isSameChain = (chain0 == chain1); // will be true
+ boolean isSameChain = (chain0 == chain1); // will be true
// could demand a contiguous section here for each range.
for (int iAtom = index0; iAtom < indexMax; iAtom++) {
Atom atom = atoms[iAtom];
- if (isSameChain ? atom.sequenceNumber >= res0 && atom.sequenceNumber
<= res1
- : atom.chainID > chain0 && atom.chainID < chain1
- || atom.chainID == chain0 && atom.sequenceNumber >= res0
- || atom.chainID == chain1 && atom.sequenceNumber <= res1
- ) {
- data[iAtom - index0] = tlsGroupID;
- setTlsEllipsoid(atom, group, symmetry);
- }
+ if (isSameChain ? atom.sequenceNumber >= res0
+ && atom.sequenceNumber <= res1 : atom.chainID > chain0
+ && atom.chainID < chain1 || atom.chainID == chain0
+ && atom.sequenceNumber >= res0 || atom.chainID == chain1
+ && atom.sequenceNumber <= res1) {
+ data[iAtom - index0] = tlsGroupID;
+ setTlsEllipsoid(atom, group, symmetry);
+ }
}
}
}
@@ -1571,20 +1571,23 @@
}
private int findAtomForRange(int atom1, int atom2, char chain, int resno,
- boolean isLast) {
+ boolean isLast) {
int iAtom = findAtom(atom1, atom2, chain, resno, true);
- return (isLast && iAtom >= 0 ? findAtom(iAtom, atom2, chain, resno, false)
: iAtom);
+ return (isLast && iAtom >= 0 ? findAtom(iAtom, atom2, chain, resno, false)
+ : iAtom);
}
- private int findAtom(int atom1, int atom2, char chain, int resno, boolean
isTrue) {
+ private int findAtom(int atom1, int atom2, char chain, int resno,
+ boolean isTrue) {
Atom[] atoms = atomSetCollection.getAtoms();
for (int i = atom1; i < atom2; i++) {
- Atom atom = atoms[i];
- if ((atom.chainID == chain && atom.sequenceNumber == resno) == isTrue)
- return i;
+ Atom atom = atoms[i];
+ if ((atom.chainID == chain && atom.sequenceNumber == resno) == isTrue)
+ return i;
}
if (isTrue) {
- Logger.warn("PdbReader findAtom chain=" + chain + " resno=" + resno + "
not found");
+ Logger.warn("PdbReader findAtom chain=" + chain + " resno=" + resno
+ + " not found");
tlsAddError("atom not found: chain=" + chain + " resno=" + resno);
}
return (isTrue ? -1 : atom2);
@@ -1594,13 +1597,14 @@
private static final float RAD_PER_DEG = (float) (Math.PI / 180);
private static final float _8PI2_ = (float) (8 * Math.PI * Math.PI);
- private Map<Atom, float[]>tlsU;
-
- private void setTlsEllipsoid(Atom atom, Map<String, Object> group,
SymmetryInterface symmetry) {
+ private Map<Atom, float[]> tlsU;
+
+ private void setTlsEllipsoid(Atom atom, Map<String, Object> group,
+ SymmetryInterface symmetry) {
Point3f origin = (Point3f) group.get("origin");
if (Float.isNaN(origin.x))
return;
-
+
float[][] T = (float[][]) group.get("tT");
float[][] L = (float[][]) group.get("tL");
float[][] S = (float[][]) group.get("tS");
@@ -1656,16 +1660,16 @@
anisou[7] = bresidual;
if (Float.isNaN(bresidual))
System.out.println("hmm");
-
+
if (tlsU == null)
tlsU = new Hashtable<Atom, float[]>();
- tlsU.put(atom, anisou);
+ tlsU.put(atom, anisou);
// symmetry is set to [1 1 1 90 90 90] -- Cartesians, not actual unit cell
atom.ellipsoid = new Quadric[] { null, null, symmetry.getEllipsoid(dataT)
};
//if (atom.atomIndex == 0)
- //System.out.println("pdbreader ellip 0 = " + atom.ellipsoid[1]);
+ //System.out.println("pdbreader ellip 0 = " + atom.ellipsoid[1]);
}
private void tlsAddError(String error) {
@@ -1675,7 +1679,7 @@
tlsGroupID).append('\t').append(error).append('\n');
}
- protected static float fixRadius(float r) {
+ protected static float fixRadius(float r) {
return (r < 0.9f ? 1 : r);
// based on parameters in
http://pdb2pqr.svn.sourceforge.net/viewvc/pdb2pqr/trunk/pdb2pqr/dat/
// AMBER forcefield, H atoms may be given 0 (on O) or 0.6 (on N) for radius
@@ -1686,4 +1690,3 @@
}
}
-
Modified: branches/v13_0/Jmol/src/org/jmol/shapebio/BioShapeRenderer.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/shapebio/BioShapeRenderer.java
2013-07-18 18:06:27 UTC (rev 18464)
+++ branches/v13_0/Jmol/src/org/jmol/shapebio/BioShapeRenderer.java
2013-07-18 18:32:28 UTC (rev 18465)
@@ -334,9 +334,12 @@
//e.printStackTrace();
}
}
- g3d.fillHermite(isNucleic ? 4 : 7, diameterBeg, diameterMid,
- diameterEnd, controlPointScreens[iPrev], controlPointScreens[i],
- controlPointScreens[iNext], controlPointScreens[iNext2]);
+ if (diameterBeg == 0 && diameterEnd == 0)
+ g3d.drawLine(controlPointScreens[i], controlPointScreens[iNext]);
+ else
+ g3d.fillHermite(isNucleic ? 4 : 7, diameterBeg, diameterMid, diameterEnd,
+ controlPointScreens[iPrev], controlPointScreens[i],
+ controlPointScreens[iNext], controlPointScreens[iNext2]);
}
//// cardinal hermite box or flat ribbon or twin strand (cartoons,
meshRibbon, ribbon)
Modified: branches/v13_0/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
2013-07-18 18:06:27 UTC (rev 18464)
+++ branches/v13_0/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
2013-07-18 18:32:28 UTC (rev 18465)
@@ -242,6 +242,7 @@
if (ellipsoid.axes == null || ellipsoid.lengths == null)
return;
Matrix3f mat = new Matrix3f();
+ mat.setIdentity();
Matrix3f mTemp = new Matrix3f();
Vector3f v1 = new Vector3f();
ellipsoid.coef = new double[10];
Modified: branches/v13_0/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
2013-07-18 18:06:27 UTC (rev 18464)
+++ branches/v13_0/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
2013-07-18 18:32:28 UTC (rev 18465)
@@ -1040,7 +1040,7 @@
// returns triangles and lines
for (int i = v.size(); --i >= 0;) {
Point3f[] pts = (Point3f[]) v.get(i);
- draw1.append(drawid).append("planep").append(i).append(
+ draw1.append(drawid).append("planep").append(i).append(" ").append(
Escape.escape(pts[0])).append(Escape.escape(pts[1]));
if (pts.length == 3)
draw1.append(Escape.escape(pts[2]));
Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-18
18:06:27 UTC (rev 18464)
+++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-18
18:32:28 UTC (rev 18465)
@@ -9,8 +9,12 @@
# Don't use ___ in your text, as that is the key for stripping out
# the information saved in the JAR version of this file.
-___version=13.0.18
+___version=13.0.19
+bug fix: cartoons with too small nonzero size will not render anything
+
+version=13.0.18
+
bug fix NOT: pdbAddHydrogens may miss O3' or O5' H atoms at end of DNA strands
bug fix NOT: pdbAddHydrogens may miss H in first group of a chain
bug fix: "ligand" should include all _g=0 (nonPDB atoms)
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