Revision: 20305
http://sourceforge.net/p/jmol/code/20305
Author: hansonr
Date: 2015-02-18 22:56:05 +0000 (Wed, 18 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.02.18b"
bug fix: POV-Ray renderer does not show proper backbone
bug fix: POV-Ray renderer with a translucent surface shows bonds that should be
hidden
bug fix: CML reader does not show proper atom names for crystal structures
bug fix: unitcell info for PDB file biomolecule does not show "biomolecule 1"
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/popup/JmolGenericPopup.java
trunk/Jmol/src/org/jmol/render/SticksRenderer.java
trunk/Jmol/src/org/jmol/renderbio/BackboneRenderer.java
trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java
trunk/Jmol/src/org/jmol/symmetry/SymmetryInfo.java
trunk/Jmol/src/org/jmol/symmetry/UnitCell.java
trunk/Jmol/src/org/jmol/util/ModulationSet.java
trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-02-18
22:39:06 UTC (rev 20304)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-02-18
22:56:05 UTC (rev 20305)
@@ -241,7 +241,7 @@
if (htAudit != null && auditBlockCode.contains("_MOD_")) {
String key = PT.rep(auditBlockCode, "_MOD_", "_REFRNCE_");
if (asc.setSymmetry((SymmetryInterface) htAudit.get(key)) != null) {
- notionalUnitCell = asc.getSymmetry().getNotionalUnitCell();
+ unitCellParams = asc.getSymmetry().getUnitCellParams();
iHaveUnitCell = true;
}
} else if (htAudit != null) {
@@ -630,7 +630,7 @@
float v = parseFloatStr(data);
if (Float.isNaN(v))
return;
- //could enable EM box: notionalUnitCell[0] = 1;
+ //could enable EM box: unitCellParams[0] = 1;
for (int i = 0; i < TransformFields.length; i++) {
if (key.indexOf(TransformFields[i]) >= 0) {
setUnitCellItem(6 + i, v);
@@ -1720,7 +1720,7 @@
Logger.debug(molecularType + " removing " + i + " "
+ atoms[i].atomName + " " + atoms[i]);
}
- asc.setCurrentModelInfo("notionalUnitcell", null);
+ asc.setCurrentModelInfo("unitCellParams", null);
if (nMolecular++ == asc.iSet) {
asc.clearGlobalBoolean(AtomSetCollection.GLOBAL_FRACTCOORD);
asc.clearGlobalBoolean(AtomSetCollection.GLOBAL_SYMMETRY);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-02-18 22:39:06 UTC (rev 20304)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-02-18 22:56:05 UTC (rev 20305)
@@ -129,7 +129,7 @@
setBiomolecules(ht);
if (thisBiomolecule != null) {
asc.getXSymmetry().applySymmetryBio(thisBiomolecule,
- notionalUnitCell, applySymmetryToBonds, filter);
+ unitCellParams, applySymmetryToBonds, filter);
asc.xtalSymmetry = null;
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java 2015-02-18
22:39:06 UTC (rev 20304)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java 2015-02-18
22:56:05 UTC (rev 20305)
@@ -428,7 +428,7 @@
asc.setCurrentModelInfo("biomolecules", vBiomolecules);
setBiomoleculeAtomCounts();
if (thisBiomolecule != null && applySymmetry) {
- asc.getXSymmetry().applySymmetryBio(thisBiomolecule, notionalUnitCell,
applySymmetryToBonds, filter);
+ asc.getXSymmetry().applySymmetryBio(thisBiomolecule, unitCellParams,
applySymmetryToBonds, filter);
vTlsModels = null; // for now, no TLS groups for biomolecules
asc.xtalSymmetry = null;
}
@@ -1343,14 +1343,14 @@
}
private void scale(int n) throws Exception {
- if (notionalUnitCell == null)
+ if (unitCellParams == null)
return;
// Could be an EM image
// this information will only be processed
// if a lattice is requested.
int pt = n * 4 + 2;
- notionalUnitCell[0] = cryst1;
+ unitCellParams[0] = cryst1;
setUnitCellItem(pt++,getFloat(10, 10));
setUnitCellItem(pt++,getFloat(20, 10));
setUnitCellItem(pt++,getFloat(30, 10));
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
2015-02-18 22:39:06 UTC (rev 20304)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
2015-02-18 22:56:05 UTC (rev 20305)
@@ -97,7 +97,7 @@
// the same atom array gets reused
// it will grow to the maximum length;
// ac holds the current number of atoms
- private int ac;
+ private int aaLen;
private Atom[] atomArray = new Atom[100];
private int bondCount;
@@ -138,6 +138,7 @@
* the current state
*/
protected int state = START;
+ private int atomIndex0;
/*
* added 2/2007 Bob Hanson:
@@ -279,7 +280,7 @@
}
if (name.equalsIgnoreCase("atomArray")) {
state = MOLECULE_ATOM_ARRAY;
- ac = 0;
+ aaLen = 0;
boolean coords3D = false;
if (atts.containsKey("atomID")) {
breakOutAtomTokens(atts.get("atomID"));
@@ -317,7 +318,7 @@
for (int i = tokenCount; --i >= 0;)
atomArray[i].elementSymbol = tokens[i];
}
- for (int i = ac; --i >= 0;) {
+ for (int i = aaLen; --i >= 0;) {
Atom atom = atomArray[i];
if (!coords3D)
atom.z = 0;
@@ -421,7 +422,7 @@
}
}
- final private static String[] notionalUnitcellTags = { "a", "b", "c",
"alpha",
+ final private static String[] unitCellParamTags = { "a", "b", "c", "alpha",
"beta", "gamma" };
@Override
@@ -476,7 +477,7 @@
if (name.equals("scalar")) {
state = CRYSTAL;
if (scalarTitle != null)
- checkUnitCellItem(notionalUnitcellTags, scalarTitle);
+ checkUnitCellItem(unitCellParamTags, scalarTitle);
else if (scalarDictRef != null)
checkUnitCellItem(JmolAdapter.cellParamNames, (scalarDictValue
.startsWith("_") ? scalarDictValue : "_" + scalarDictValue));
@@ -533,7 +534,7 @@
case MOLECULE_ATOM_ARRAY:
if (name.equalsIgnoreCase("atomArray")) {
state = MOLECULE;
- for (int i = 0; i < ac; ++i)
+ for (int i = 0; i < aaLen; ++i)
addAtom(atomArray[i]);
}
break;
@@ -603,10 +604,11 @@
return;
String s;
Atom[] atoms = asc.atoms;
- for (int i = 0; i < ac; i++)
+ for (int i = atomIndex0; i < asc.ac; i++)
if ((s = atomIdNames.getProperty(atoms[i].atomName)) != null)
atoms[i].atomName = s;
atomIdNames = null;
+ atomIndex0 = asc.ac;
}
private void addNewBond(String a1, String a2, int order) {
@@ -694,13 +696,13 @@
}
void checkAtomArrayLength(int newAtomCount) {
- if (ac == 0) {
+ if (aaLen == 0) {
if (newAtomCount > atomArray.length)
atomArray = new Atom[newAtomCount];
for (int i = newAtomCount; --i >= 0;)
atomArray[i] = new Atom();
- ac = newAtomCount;
- } else if (newAtomCount != ac) {
+ aaLen = newAtomCount;
+ } else if (newAtomCount != aaLen) {
throw new IndexOutOfBoundsException("bad atom attribute length");
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2015-02-18 22:39:06 UTC (rev 20304)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2015-02-18 22:56:05 UTC (rev 20305)
@@ -183,7 +183,7 @@
protected String sgName;
protected boolean ignoreFileUnitCell;
protected boolean ignoreFileSpaceGroupName;
- public float[] notionalUnitCell; //0-5 a b c alpha beta gamma; 6-21 matrix
c->f
+ public float[] unitCellParams; //0-5 a b c alpha beta gamma; 6-21 matrix c->f
protected int desiredModelNumber = Integer.MIN_VALUE;
public SymmetryInterface symmetry;
protected OC out;
@@ -688,15 +688,15 @@
protected void initializeSymmetry() {
previousSpaceGroup = sgName;
- previousUnitCell = notionalUnitCell;
+ previousUnitCell = unitCellParams;
iHaveUnitCell = ignoreFileUnitCell;
if (!ignoreFileUnitCell) {
- notionalUnitCell = new float[25];
+ unitCellParams = new float[25];
//0-5 a b c alpha beta gamma
//6-21 m00 m01... m33 cartesian-->fractional
//22-24 supercell.x supercell.y supercell.z
for (int i = 25; --i >= 0;)
- notionalUnitCell[i] = Float.NaN;
+ unitCellParams[i] = Float.NaN;
symmetry = null;
}
if (!ignoreFileSpaceGroupName)
@@ -722,7 +722,7 @@
iHaveUnitCell = true;
doCheckUnitCell = true;
sgName = previousSpaceGroup;
- notionalUnitCell = previousUnitCell;
+ unitCellParams = previousUnitCell;
}
return lastAtomCount;
}
@@ -748,10 +748,10 @@
private void initializeCartesianToFractional() {
for (int i = 0; i < 16; i++)
- if (!Float.isNaN(notionalUnitCell[6 + i]))
+ if (!Float.isNaN(unitCellParams[6 + i]))
return; //just do this once
for (int i = 0; i < 16; i++)
- notionalUnitCell[6 + i] = ((i % 5 == 0 ? 1 : 0));
+ unitCellParams[6 + i] = ((i % 5 == 0 ? 1 : 0));
nMatrixElements = 0;
}
@@ -759,7 +759,7 @@
if (ignoreFileUnitCell)
return;
for (int i = 6; i < 22; i++)
- notionalUnitCell[i] = Float.NaN;
+ unitCellParams[i] = Float.NaN;
checkUnitCell(6);
}
@@ -768,9 +768,9 @@
return;
if (i == 0 && x == 1 || i == 3 && x == 0)
return;
- if (!Float.isNaN(x) && i >= 6 && Float.isNaN(notionalUnitCell[6]))
+ if (!Float.isNaN(x) && i >= 6 && Float.isNaN(unitCellParams[6]))
initializeCartesianToFractional();
- notionalUnitCell[i] = x;
+ unitCellParams[i] = x;
if (Logger.debugging) {
Logger.debug("setunitcellitem " + i + " " + x);
}
@@ -787,15 +787,15 @@
if (ignoreFileUnitCell)
return;
clearUnitCell();
- notionalUnitCell[0] = a;
- notionalUnitCell[1] = b;
- notionalUnitCell[2] = c;
+ unitCellParams[0] = a;
+ unitCellParams[1] = b;
+ unitCellParams[2] = c;
if (alpha != 0)
- notionalUnitCell[3] = alpha;
+ unitCellParams[3] = alpha;
if (beta != 0)
- notionalUnitCell[4] = beta;
+ unitCellParams[4] = beta;
if (gamma != 0)
- notionalUnitCell[5] = gamma;
+ unitCellParams[5] = gamma;
iHaveUnitCell = checkUnitCell(6);
}
@@ -804,28 +804,28 @@
return;
if (i == 0)
for (int j = 0; j < 6; j++)
- notionalUnitCell[j] = 0;
+ unitCellParams[j] = 0;
i = 6 + i * 3;
- notionalUnitCell[i++] = xyz[i0++];
- notionalUnitCell[i++] = xyz[i0++];
- notionalUnitCell[i] = xyz[i0];
- if (Float.isNaN(notionalUnitCell[0])) {
+ unitCellParams[i++] = xyz[i0++];
+ unitCellParams[i++] = xyz[i0++];
+ unitCellParams[i] = xyz[i0];
+ if (Float.isNaN(unitCellParams[0])) {
for (i = 0; i < 6; i++)
- notionalUnitCell[i] = -1;
+ unitCellParams[i] = -1;
}
iHaveUnitCell = checkUnitCell(15);
}
private boolean checkUnitCell(int n) {
for (int i = 0; i < n; i++)
- if (Float.isNaN(notionalUnitCell[i]))
+ if (Float.isNaN(unitCellParams[i]))
return false;
- if (n == 22 && notionalUnitCell[0] == 1) {
- if (notionalUnitCell[1] == 1
- && notionalUnitCell[2] == 1
- && notionalUnitCell[6] == 1
- && notionalUnitCell[11] == 1
- && notionalUnitCell[16] == 1
+ if (n == 22 && unitCellParams[0] == 1) {
+ if (unitCellParams[1] == 1
+ && unitCellParams[2] == 1
+ && unitCellParams[6] == 1
+ && unitCellParams[11] == 1
+ && unitCellParams[16] == 1
)
return false;
// this is an mmCIF or PDB case for NMR models having
@@ -850,7 +850,7 @@
if (!iHaveUnitCell)
return null;
if (symmetry == null) {
- getNewSymmetry().setUnitCell(notionalUnitCell, false);
+ getNewSymmetry().setUnitCell(unitCellParams, false);
checkUnitCellOffset();
}
return symmetry;
@@ -1161,7 +1161,7 @@
}
if (doConvertToFractional && !fileCoordinatesAreFractional &&
getSymmetry() != null) {
if (!symmetry.haveUnitCell())
- symmetry.setUnitCell(notionalUnitCell, false);
+ symmetry.setUnitCell(unitCellParams, false);
symmetry.toFractional(atom, false);
iHaveFractionalCoordinates = true;
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java 2015-02-18
22:39:06 UTC (rev 20304)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java 2015-02-18
22:56:05 UTC (rev 20305)
@@ -81,7 +81,7 @@
return (this.symmetry = symmetry);
}
- private float[] notionalUnitCell = new float[6];
+ private float[] unitCellParams = new float[6];
private float[] baseUnitCell;
// expands to 26 for cartesianToFractional matrix as array (PDB) and
supercell
@@ -151,23 +151,23 @@
private Lst<float[]> trajectoryUnitCells;
- private void setNotionalUnitCell(float[] info, M3 matUnitCellOrientation,
+ private void setUnitCell(float[] info, M3 matUnitCellOrientation,
P3 unitCellOffset) {
- notionalUnitCell = new float[info.length];
+ unitCellParams = new float[info.length];
this.unitCellOffset = unitCellOffset;
for (int i = 0; i < info.length; i++)
- notionalUnitCell[i] = info[i];
+ unitCellParams[i] = info[i];
asc.haveUnitCell = true;
- asc.setCurrentModelInfo("notionalUnitcell", notionalUnitCell);
+ asc.setCurrentModelInfo("unitCellParams", unitCellParams);
if (asc.isTrajectory) {
if (trajectoryUnitCells == null) {
trajectoryUnitCells = new Lst<float[]>();
asc.setInfo("unitCells", trajectoryUnitCells);
}
- trajectoryUnitCells.addLast(notionalUnitCell);
+ trajectoryUnitCells.addLast(unitCellParams);
}
asc.setGlobalBoolean(AtomSetCollection.GLOBAL_UNITCELLS);
- getSymmetry().setUnitCell(notionalUnitCell, false);
+ getSymmetry().setUnitCell(unitCellParams, false);
// we need to set the auxiliary info as well, because
// ModelLoader creates a new symmetry object.
if (unitCellOffset != null) {
@@ -201,7 +201,7 @@
SymmetryInterface applySymmetryFromReader(SymmetryInterface readerSymmetry)
throws Exception {
asc.setCoordinatesAreFractional(acr.iHaveFractionalCoordinates);
- setNotionalUnitCell(acr.notionalUnitCell, acr.matUnitCellOrientation,
+ setUnitCell(acr.unitCellParams, acr.matUnitCellOrientation,
acr.unitCellOffset);
setAtomSetSpaceGroupName(acr.sgName);
setSymmetryRange(acr.symmetryRange);
@@ -213,7 +213,7 @@
readerSymmetry = acr.getNewSymmetry();
doApplySymmetry = readerSymmetry.createSpaceGroup(
acr.desiredSpaceGroupIndex, (acr.sgName.indexOf("!") >= 0 ? "P1"
- : acr.sgName), acr.notionalUnitCell);
+ : acr.sgName), acr.unitCellParams);
} else {
acr.doPreSymmetry();
readerSymmetry = null;
@@ -392,7 +392,7 @@
symmetry = null;
symmetry = getSymmetry();
- setNotionalUnitCell(new float[] { 0, 0, 0, 0, 0, 0, va.x, va.y, va.z,
+ setUnitCell(new float[] { 0, 0, 0, 0, 0, 0, va.x, va.y, va.z,
vb.x, vb.y, vb.z, vc.x, vc.y, vc.z }, null, offset);
setAtomSetSpaceGroupName(oabc == null ? "P1" : "cell=" + supercell);
symmetry.setSpaceGroup(doNormalize);
@@ -720,8 +720,8 @@
symmetry.getLatticeDesignation());
asc.setCurrentModelInfo("unitCellRange", unitCells);
asc.setCurrentModelInfo("unitCellTranslations", unitCellTranslations);
- baseUnitCell = notionalUnitCell;
- notionalUnitCell = new float[6];
+ baseUnitCell = unitCellParams;
+ unitCellParams = new float[6];
reset();
}
@@ -972,7 +972,7 @@
@SuppressWarnings("unchecked")
public void applySymmetryBio(Map<String, Object> thisBiomolecule,
- float[] notionalUnitCell,
+ float[] unitCellParams,
boolean applySymmetryToBonds, String filter) {
if (latticeCells != null && latticeCells[0] != 0) {
Logger.error("Cannot apply biomolecule when lattice cells are
indicated");
@@ -987,13 +987,13 @@
return;
symmetry = null;
// it's not clear to me why you would do this:
- if (!Float.isNaN(notionalUnitCell[0])) // PDB can do this;
- setNotionalUnitCell(notionalUnitCell, null, unitCellOffset);
+ if (!Float.isNaN(unitCellParams[0])) // PDB can do this;
+ setUnitCell(unitCellParams, null, unitCellOffset);
getSymmetry().setSpaceGroup(doNormalize);
//symmetry.setUnitCell(null);
addSpaceGroupOperation("x,y,z", false);
String name = (String) thisBiomolecule.get("name");
- setAtomSetSpaceGroupName(name);
+ setAtomSetSpaceGroupName(acr.sgName = name);
int len = biomts.size();
this.applySymmetryToBonds = applySymmetryToBonds;
bondCount0 = asc.bondCount;
@@ -1095,11 +1095,6 @@
asc.errorMessage = "appendAtomCollection error: " + e;
}
}
- // mat.m03 /= notionalUnitCell[0]; // PDB could have set this to
Float.NaN
- // if (Float.isNaN(mat.m03))
- // mat.m03 = 1;
- // mat.m13 /= notionalUnitCell[1];
- // mat.m23 /= notionalUnitCell[2];
if (i > 0)
symmetry.addBioMoleculeOperation(mat, false);
}
@@ -1199,28 +1194,12 @@
*
*/
public void scaleFractionalVibs() {
- float[] params = getBaseSymmetry().getNotionalUnitCell();
+ float[] params = getBaseSymmetry().getUnitCellParams();
P3 ptScale = P3.new3(1 / params[0], 1 / params[1], 1 / params[2]);
-// P3 pt = new P3();
int i0 = asc.getAtomSetAtomIndex(asc.iSet);
for (int i = asc.ac; --i >= i0;) {
Vibration v = (Vibration) asc.atoms[i].vib;
if (v != null) {
-// pt = ptScale;
-// if (mod != null) {
- // this is not relevant, because this has to be done in
doPreSymmetry()
- // before subsystems are set, I think.
-// // if there are modulations, then a fractional vib would be
-// // a vib within a modulation set.
-// v = mod.getVibration(false);
-// if (v == null)
-// continue;
-// SymmetryInterface subsym = mod.getSubSystemUnitCell();
-// if (subsym != null) {
-// params = subsym.getNotionalUnitCell();
-// pt.set(1 / params[0], 1 / params[1], 1 / params[2]);
-// }
-// }
v.scaleT(ptScale);
}
}
Modified: trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2015-02-18 22:39:06 UTC
(rev 20304)
+++ trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2015-02-18 22:56:05 UTC
(rev 20305)
@@ -60,7 +60,7 @@
Lst<String> getMoreInfo();
- public float[] getNotionalUnitCell();
+ public float[] getUnitCellParams();
public Matrix getOperationRsVs(int op);
@@ -172,7 +172,7 @@
public void setTimeReversal(int op, int val);
- public void setUnitCell(float[] notionalUnitCell, boolean setRelative);
+ public void setUnitCell(float[] params, boolean setRelative);
public void initializeOrientation(M3 matUnitCellOrientation);
Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2015-02-18 22:39:06 UTC (rev
20304)
+++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2015-02-18 22:56:05 UTC (rev
20305)
@@ -396,10 +396,8 @@
downsampleFullSceneAntialiasing(false);
}
platform.setBackgroundColor(bgcolor);
-
platform.notifyEndOfRendering();
- //setWidthHeight(antialiasEnabled);
- currentlyRendering = false;
+ currentlyRendering = isPass2 = false;
}
public static void mergeBufferPixel(int[] pbuf, int offset, int argbB,
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-02-18 22:39:06 UTC
(rev 20304)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-02-18 22:56:05 UTC
(rev 20305)
@@ -1005,9 +1005,9 @@
* @return just the first unit cell
*
*/
- public float[] getNotionalUnitcell() {
+ public float[] getUnitCellParams() {
SymmetryInterface c = getUnitCell(0);
- return (c == null ? null : c.getNotionalUnitCell());
+ return (c == null ? null : c.getUnitCellParams());
}
public boolean setCrystallographicDefaults() {
Modified: trunk/Jmol/src/org/jmol/popup/JmolGenericPopup.java
===================================================================
--- trunk/Jmol/src/org/jmol/popup/JmolGenericPopup.java 2015-02-18 22:39:06 UTC
(rev 20304)
+++ trunk/Jmol/src/org/jmol/popup/JmolGenericPopup.java 2015-02-18 22:56:05 UTC
(rev 20305)
@@ -378,7 +378,7 @@
isPDB = checkBoolean("isPDB");
isMultiFrame = (modelCount > 1);
isSymmetry = checkBoolean("hasSymmetry");
- isUnitCell = modelInfo.containsKey("notionalUnitcell");
+ isUnitCell = modelInfo.containsKey("unitCellParams");
fileHasUnitCell = (isPDB && isUnitCell || checkBoolean("fileHasUnitCell"));
isLastFrame = (modelIndex == modelCount - 1);
altlocs = vwr.ms.getAltLocListInModel(modelIndex);
Modified: trunk/Jmol/src/org/jmol/render/SticksRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/SticksRenderer.java 2015-02-18 22:39:06 UTC
(rev 20304)
+++ trunk/Jmol/src/org/jmol/render/SticksRenderer.java 2015-02-18 22:56:05 UTC
(rev 20305)
@@ -94,21 +94,22 @@
hbondsSolid = vwr.getBoolean(T.hbondssolid);
isAntialiased = g3d.isAntialiased();
boolean needTranslucent = false;
- if (!isExport && isPass2)
- for (int i = bsForPass2.nextSetBit(0); i >= 0; i = bsForPass2
- .nextSetBit(i + 1)) {
- bond = bonds[i];
- renderBond();
- }
- else
+ if (isPass2) {
+ if (!isExport)
+ for (int i = bsForPass2.nextSetBit(0); i >= 0; i = bsForPass2
+ .nextSetBit(i + 1)) {
+ bond = bonds[i];
+ renderBond();
+ }
+ } else {
for (int i = ms.bondCount; --i >= 0;) {
bond = bonds[i];
- if ((bond.shapeVisibilityFlags & myVisibilityFlag) != 0
- && renderBond()) {
+ if ((bond.shapeVisibilityFlags & myVisibilityFlag) != 0 &&
renderBond()) {
needTranslucent = true;
bsForPass2.set(i);
}
}
+ }
return needTranslucent;
}
@@ -249,6 +250,7 @@
}
}
+
// set the diameter
xA = a.sX;
Modified: trunk/Jmol/src/org/jmol/renderbio/BackboneRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/BackboneRenderer.java 2015-02-18
22:39:06 UTC (rev 20304)
+++ trunk/Jmol/src/org/jmol/renderbio/BackboneRenderer.java 2015-02-18
22:56:05 UTC (rev 20305)
@@ -41,6 +41,7 @@
@Override
protected void renderBioShape(BioShape bioShape) {
+ boolean checkPass2 = (!isExport && !vwr.gdata.isPass2);
boolean showSteps = vwr.getBoolean(T.backbonesteps)
&& bioShape.bioPolymer.isNucleic();
isDataFrame = vwr.ms.isJmolDataFrameForModel(bioShape.modelIndex);
@@ -49,7 +50,7 @@
Atom atomA = ms.at[leadAtomIndices[i]];
short cA = colixes[i];
mad = mads[i];
- drawSegment(atomA, ms.at[leadAtomIndices[i + 1]], cA, colixes[i + 1],
100);
+ drawSegment(atomA, ms.at[leadAtomIndices[i + 1]], cA, colixes[i + 1],
100, checkPass2);
if (showSteps) {
NucleicMonomer g = (NucleicMonomer) monomers[i];
Lst<BasePair> bps = g.getBasePairs();
@@ -57,22 +58,22 @@
for (int j = bps.size(); --j >= 0;) {
int iAtom = bps.get(j).getPartnerAtom(g);
if (iAtom > i)
- drawSegment(atomA, ms.at[iAtom], cA, cA, 1000);
+ drawSegment(atomA, ms.at[iAtom], cA, cA, 1000, checkPass2);
}
}
}
}
}
- private void drawSegment(Atom atomA, Atom atomB, short colixA, short colixB,
float max) {
- if (atomA.nBackbonesDisplayed == 0
- || atomB.nBackbonesDisplayed == 0
- || ms.isAtomHidden(atomB.i)
- || !isDataFrame && atomA.distanceSquared(atomB) > max)
+ private void drawSegment(Atom atomA, Atom atomB, short colixA, short colixB,
+ float max, boolean checkPass2) {
+ if (atomA.nBackbonesDisplayed == 0 || atomB.nBackbonesDisplayed == 0
+ || ms.isAtomHidden(atomB.i) || !isDataFrame
+ && atomA.distanceSquared(atomB) > max)
return;
colixA = C.getColixInherited(colixA, atomA.colixAtom);
colixB = C.getColixInherited(colixB, atomB.colixAtom);
- if (!isExport && !isPass2 && !setBioColix(colixA) && !setBioColix(colixB))
+ if (checkPass2 && !setBioColix(colixA) && !setBioColix(colixB))
return;
int xA = atomA.sX, yA = atomA.sY, zA = atomA.sZ;
int xB = atomB.sX, yB = atomB.sY, zB = atomB.sZ;
@@ -82,8 +83,8 @@
if (mad < 0) {
g3d.drawLine(colixA, colixB, xA, yA, zA, xB, yB, zB);
} else {
- int width = (int) (exportType == GData.EXPORT_CARTESIAN ? mad : vwr
- .tm.scaleToScreen((zA + zB) / 2, mad));
+ int width = (int) (isExport ? mad : vwr.tm.scaleToScreen((zA + zB) / 2,
+ mad));
g3d.fillCylinderXYZ(colixA, colixB, GData.ENDCAPS_SPHERICAL, width, xA,
yA, zA, xB, yB, zB);
}
Modified: trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java 2015-02-18
22:39:06 UTC (rev 20304)
+++ trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java 2015-02-18
22:56:05 UTC (rev 20305)
@@ -88,7 +88,6 @@
protected short[] colixesBack;
protected STR[] structureTypes;
- protected boolean isPass2;
protected boolean wireframeOnly;
protected abstract void renderBioShape(BioShape bioShape);
@@ -103,7 +102,6 @@
}
private void setGlobals() {
- isPass2 = vwr.gdata.isPass2;
invalidateMesh = false;
needTranslucent = false;
g3d.addRenderer(T.hermitelevel);
Modified: trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2015-02-18 22:39:06 UTC
(rev 20304)
+++ trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2015-02-18 22:56:05 UTC
(rev 20305)
@@ -256,7 +256,7 @@
spaceGroup = spaceGroup.substring(0, spaceGroup.indexOf("[")).trim();
if (spaceGroup.equals("unspecified!"))
return "no space group identified in file";
- sg = SpaceGroup.determineSpaceGroupNA(spaceGroup,
cellInfo.getNotionalUnitCell());
+ sg = SpaceGroup.determineSpaceGroupNA(spaceGroup,
cellInfo.getUnitCellParams());
} else if (spaceGroup.equalsIgnoreCase("ALL")) {
return SpaceGroup.dumpAll();
} else if (spaceGroup.equalsIgnoreCase("ALLSEITZ")) {
@@ -575,11 +575,11 @@
}
private final static SpaceGroup determineSpaceGroupNA(String name,
- float[] notionalUnitcell)
{
- return (notionalUnitcell == null ? determineSpaceGroup(name, 0f, 0f, 0f,
0f, 0f, 0f, -1)
- : determineSpaceGroup(name, notionalUnitcell[0], notionalUnitcell[1],
- notionalUnitcell[2], notionalUnitcell[3], notionalUnitcell[4],
- notionalUnitcell[5], -1));
+ float[] unitCellParams) {
+ return (unitCellParams == null ? determineSpaceGroup(name, 0f, 0f, 0f, 0f,
0f, 0f, -1)
+ : determineSpaceGroup(name, unitCellParams[0], unitCellParams[1],
+ unitCellParams[2], unitCellParams[3], unitCellParams[4],
+ unitCellParams[5], -1));
}
private final static SpaceGroup determineSpaceGroup(String name, float a,
float b,
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-02-18 22:39:06 UTC
(rev 20304)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-02-18 22:56:05 UTC
(rev 20305)
@@ -331,12 +331,12 @@
@SuppressWarnings("unchecked")
@Override
public void setSymmetryInfo(int modelIndex,
- Map<String, Object> modelAuxiliaryInfo, float[]
notionalCell) {
+ Map<String, Object> modelAuxiliaryInfo, float[]
unitCellParams) {
symmetryInfo = new SymmetryInfo();
- float[] notionalUnitcell =
symmetryInfo.setSymmetryInfo(modelAuxiliaryInfo, notionalCell);
- if (notionalUnitcell == null)
+ float[] params = symmetryInfo.setSymmetryInfo(modelAuxiliaryInfo,
unitCellParams);
+ if (params == null)
return;
- setUnitCell(notionalUnitcell, modelAuxiliaryInfo.containsKey("jmolData"));
+ setUnitCell(params, modelAuxiliaryInfo.containsKey("jmolData"));
unitCell.moreInfo = (Lst<String>)
modelAuxiliaryInfo.get("moreUnitCellInfo");
modelAuxiliaryInfo.put("infoUnitCell", getUnitCellAsArray(false));
setOffsetPt((P3) modelAuxiliaryInfo.get("unitCellOffset"));
@@ -368,8 +368,8 @@
}
@Override
- public void setUnitCell(float[] notionalUnitCell, boolean setRelative) {
- unitCell = UnitCell.newA(notionalUnitCell, setRelative);
+ public void setUnitCell(float[] unitCellParams, boolean setRelative) {
+ unitCell = UnitCell.newA(unitCellParams, setRelative);
}
@Override
@@ -424,8 +424,8 @@
}
@Override
- public float[] getNotionalUnitCell() {
- return unitCell.getNotionalUnitCell();
+ public float[] getUnitCellParams() {
+ return unitCell.getUnitCellParams();
}
@Override
Modified: trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java 2015-02-18 22:39:06 UTC
(rev 20304)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java 2015-02-18 22:56:05 UTC
(rev 20305)
@@ -871,7 +871,7 @@
if (type == T.point) {
if (isBio)
return "";
- symTemp.setUnitCell(uc.getNotionalUnitCell(), false);
+ symTemp.setUnitCell(uc.getUnitCellParams(), false);
uc.toFractional(pt, false);
if (Float.isNaN(pt.x))
return "";
Modified: trunk/Jmol/src/org/jmol/symmetry/SymmetryInfo.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryInfo.java 2015-02-18 22:39:06 UTC
(rev 20304)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryInfo.java 2015-02-18 22:56:05 UTC
(rev 20305)
@@ -53,7 +53,14 @@
SymmetryInfo() {
}
- float[] setSymmetryInfo(Map<String, Object> info, float[] notionalUnitCell) {
+
+ /**
+ *
+ * @param info
+ * @param unitCellParams an array of parameters could be from model, but
also could be from a trajectory listing
+ * @return actual unit cell parameters
+ */
+ float[] setSymmetryInfo(Map<String, Object> info, float[] unitCellParams) {
cellRange = (int[]) info.get("unitCellRange");
periodicOriginXyz = (P3) info.get("periodicOriginXyz");
sgName = (String) info.get("spaceGroup");
@@ -86,15 +93,15 @@
infoStr += s;
}
infoStr += "\n";
- if (notionalUnitCell == null)
- notionalUnitCell = (float[]) info.get("notionalUnitcell");
- if (!SimpleUnitCell.isValid(notionalUnitCell))
+ if (unitCellParams == null)
+ unitCellParams = (float[]) info.get("unitCellParams");
+ if (!SimpleUnitCell.isValid(unitCellParams))
return null;
coordinatesAreFractional = info.containsKey("coordinatesAreFractional") ?
((Boolean) info.get("coordinatesAreFractional")).booleanValue()
: false;
isMultiCell = (coordinatesAreFractional && symmetryOperations != null);
- return notionalUnitCell;
+ return unitCellParams;
}
}
Modified: trunk/Jmol/src/org/jmol/symmetry/UnitCell.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/UnitCell.java 2015-02-18 22:39:06 UTC
(rev 20304)
+++ trunk/Jmol/src/org/jmol/symmetry/UnitCell.java 2015-02-18 22:56:05 UTC
(rev 20305)
@@ -86,9 +86,9 @@
return c;
}
- public static UnitCell newA(float[] notionalUnitcell, boolean setRelative) {
+ public static UnitCell newA(float[] params, boolean setRelative) {
UnitCell c = new UnitCell();
- c.init(notionalUnitcell);
+ c.init(params);
c.initUnitcellVertices();
c.allFractionalRelative = setRelative;
return c;
@@ -488,12 +488,12 @@
}
public boolean isSameAs(UnitCell uc) {
- if (uc.notionalUnitcell.length != notionalUnitcell.length)
+ if (uc.unitCellParams.length != unitCellParams.length)
return false;
- for (int i = notionalUnitcell.length; --i >= 0;)
- if (notionalUnitcell[i] != uc.notionalUnitcell[i]
- && !(Float.isNaN(notionalUnitcell[i]) && Float
- .isNaN(uc.notionalUnitcell[i])))
+ for (int i = unitCellParams.length; --i >= 0;)
+ if (unitCellParams[i] != uc.unitCellParams[i]
+ && !(Float.isNaN(unitCellParams[i]) && Float
+ .isNaN(uc.unitCellParams[i])))
return false;
return (fractionalOffset == null ? !uc.hasOffset()
: uc.fractionalOffset == null ? !hasOffset()
Modified: trunk/Jmol/src/org/jmol/util/ModulationSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ModulationSet.java 2015-02-18 22:39:06 UTC
(rev 20304)
+++ trunk/Jmol/src/org/jmol/util/ModulationSet.java 2015-02-18 22:56:05 UTC
(rev 20305)
@@ -551,7 +551,7 @@
private float[] axesLengths;
float[] getAxesLengths() {
- return (axesLengths == null ? (axesLengths =
symmetry.getNotionalUnitCell())
+ return (axesLengths == null ? (axesLengths = symmetry.getUnitCellParams())
: axesLengths);
}
Modified: trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java 2015-02-18 22:39:06 UTC
(rev 20304)
+++ trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java 2015-02-18 22:56:05 UTC
(rev 20305)
@@ -43,7 +43,7 @@
public class SimpleUnitCell {
- protected float[] notionalUnitcell; //6 parameters + optional 16 matrix items
+ protected float[] unitCellParams; //6 parameters + optional 16 matrix items
public M4 matrixCartesianToFractional;
public M4 matrixFractionalToCartesian;
public double volume;
@@ -74,39 +74,39 @@
fractionalOrigin = new P3();
}
- public static SimpleUnitCell newA(float[] parameters) {
+ public static SimpleUnitCell newA(float[] params) {
SimpleUnitCell c = new SimpleUnitCell();
- c.init(parameters);
+ c.init(params);
return c;
}
- protected void init(float[] parameters) {
- if (parameters == null)
- parameters = new float[] {1, 1, 1, 90, 90, 90};
- if (!isValid(parameters))
+ protected void init(float[] params) {
+ if (params == null)
+ params = new float[] {1, 1, 1, 90, 90, 90};
+ if (!isValid(params))
return;
- notionalUnitcell = AU.arrayCopyF(parameters, parameters.length);
+ unitCellParams = AU.arrayCopyF(params, params.length);
- a = parameters[0];
- b = parameters[1];
- c = parameters[2];
- alpha = parameters[3];
- beta = parameters[4];
- gamma = parameters[5];
+ a = params[0];
+ b = params[1];
+ c = params[2];
+ alpha = params[3];
+ beta = params[4];
+ gamma = params[5];
// (int) Float.NaN == 0 (but not in JavaScript!)
- na = Math.max(1, parameters.length >= 25 && !Float.isNaN(parameters[22]) ?
(int) parameters[22] : 1);
- nb = Math.max(1, parameters.length >= 25 && !Float.isNaN(parameters[23]) ?
(int) parameters[23] : 1);
- nc = Math.max(1, parameters.length >= 25 && !Float.isNaN(parameters[24]) ?
(int) parameters[24] : 1);
+ na = Math.max(1, params.length >= 25 && !Float.isNaN(params[22]) ? (int)
params[22] : 1);
+ nb = Math.max(1, params.length >= 25 && !Float.isNaN(params[23]) ? (int)
params[23] : 1);
+ nc = Math.max(1, params.length >= 25 && !Float.isNaN(params[24]) ? (int)
params[24] : 1);
if (a <= 0) {
// must calculate a, b, c alpha beta gamma from Cartesian vectors;
- V3 va = V3.new3(parameters[6], parameters[7], parameters[8]);
- V3 vb = V3.new3(parameters[9], parameters[10], parameters[11]);
- V3 vc = V3.new3(parameters[12], parameters[13], parameters[14]);
+ V3 va = V3.new3(params[6], params[7], params[8]);
+ V3 vb = V3.new3(params[9], params[10], params[11]);
+ V3 vc = V3.new3(params[12], params[13], params[14]);
setABC(va, vb, vc);
if (c < 0) {
- float[] n = AU.arrayCopyF(parameters, -1);
+ float[] n = AU.arrayCopyF(params, -1);
if (b < 0) {
vb.set(0, 0, 1);
vb.cross(vb, va);
@@ -124,7 +124,7 @@
n[13] = vc.y;
n[14] = vc.z;
}
- parameters = n;
+ params = n;
}
}
@@ -144,7 +144,7 @@
setCellParams();
- if (parameters.length > 21 && !Float.isNaN(parameters[21])) {
+ if (params.length > 21 && !Float.isNaN(params[21])) {
// parameters with a 4x4 matrix
// [a b c alpha beta gamma m00 m01 m02 m03 m10 m11.... m20...]
// this is for PDB and CIF reader
@@ -165,20 +165,20 @@
f = 1;
break;
}
- scaleMatrix[i] = parameters[6 + i] * f;
+ scaleMatrix[i] = params[6 + i] * f;
}
matrixCartesianToFractional = M4.newA16(scaleMatrix);
matrixCartesianToFractional.getTranslation(fractionalOrigin);
matrixFractionalToCartesian =
M4.newM4(matrixCartesianToFractional).invert();
- if (parameters[0] == 1)
+ if (params[0] == 1)
setParamsFromMatrix();
- } else if (parameters.length > 14 && !Float.isNaN(parameters[14])) {
+ } else if (params.length > 14 && !Float.isNaN(params[14])) {
// parameters with a 3 vectors
// [a b c alpha beta gamma ax ay az bx by bz cx cy cz...]
M4 m = matrixFractionalToCartesian = new M4();
- m.setColumn4(0, parameters[6] * na, parameters[7] * na, parameters[8] *
na, 0);
- m.setColumn4(1, parameters[9] * nb, parameters[10] * nb, parameters[11]
* nb, 0);
- m.setColumn4(2, parameters[12] * nc, parameters[13] * nc, parameters[14]
* nc, 0);
+ m.setColumn4(0, params[6] * na, params[7] * na, params[8] * na, 0);
+ m.setColumn4(1, params[9] * nb, params[10] * nb, params[11] * nb, 0);
+ m.setColumn4(2, params[12] * nc, params[13] * nc, params[14] * nc, 0);
m.setColumn4(3, 0, 0, 0, 1);
matrixCartesianToFractional =
M4.newM4(matrixFractionalToCartesian).invert();
} else {
@@ -291,8 +291,8 @@
return (dimension == 2);
}
- public final float[] getNotionalUnitCell() {
- return notionalUnitcell;
+ public final float[] getUnitCellParams() {
+ return unitCellParams;
}
public final float[] getUnitCellAsArray(boolean vectorsOnly) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-18 22:39:06 UTC
(rev 20304)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-18 22:56:05 UTC
(rev 20305)
@@ -15,8 +15,14 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
TODO: add 2D graphics panel for Ramachandran and NBO-style 2D graphics -- send
to browser as data uri?
-Jmol.___JmolVersion="14.3.12_2015.02.18"
+Jmol.___JmolVersion="14.2.12_2015.02.18b"
+bug fix: CML reader does not show proper atom names for crystal structures
+bug fix: POV-Ray renderer does not show proper backbone width (since forever)
+bug fix: POV-Ray renderer with a translucent surface shows bonds that should
be hidden (since 13.1)
+bug fix: unitcell info for PDB file biomolecule does not show "biomolecule 1"
+JmolVersion="14.3.12_2015.02.18"
+
bug fix: load filter "biomolecule 1" broken in 14.3.12_2015.02.14
JmolVersion="14.3.12_2015.02.17b"
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