Revision: 20474
http://sourceforge.net/p/jmol/code/20474
Author: hansonr
Date: 2015-05-02 17:46:35 +0000 (Sat, 02 May 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.13_2015.05.02"
bug fix: color atoms property vxyz crashes Jmol if no vibrations
bug fix: with msCIF, select subsystem=1 does not select anything
bug fix: vibrations in trajectories not animating (14.3.6_2014.08.14)
Modified Paths:
--------------
trunk/Jmol/src/javajs/api/GenericCifDataParser.java
trunk/Jmol/src/javajs/util/CifDataParser.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java
trunk/Jmol/src/org/jmol/g3d/CylinderRenderer.java
trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
trunk/Jmol/src/org/jmol/g3d/LineRenderer.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/JmolBioModelSet.java
trunk/Jmol/src/org/jmol/modelset/Model.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/script/ScriptExpr.java
trunk/Jmol/src/org/jmol/thread/VibrationThread.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/javajs/api/GenericCifDataParser.java
===================================================================
--- trunk/Jmol/src/javajs/api/GenericCifDataParser.java 2015-04-30 20:25:08 UTC
(rev 20473)
+++ trunk/Jmol/src/javajs/api/GenericCifDataParser.java 2015-05-02 17:46:35 UTC
(rev 20474)
@@ -38,7 +38,7 @@
String toUnicode(String data);
- void skipLoop() throws Exception;
+ String skipLoop(boolean doReport) throws Exception;
String fixKey(String key);
Modified: trunk/Jmol/src/javajs/util/CifDataParser.java
===================================================================
--- trunk/Jmol/src/javajs/util/CifDataParser.java 2015-04-30 20:25:08 UTC
(rev 20473)
+++ trunk/Jmol/src/javajs/util/CifDataParser.java 2015-05-02 17:46:35 UTC
(rev 20474)
@@ -273,12 +273,24 @@
* @throws Exception
*/
@Override
- public void skipLoop() throws Exception {
+ public String skipLoop(boolean doReport) throws Exception {
String str;
- while ((str = peekToken()) != null && str.charAt(0) == '_')
- getTokenPeeked();
- while (getNextDataToken() != null) {
+ SB ret = (doReport ? new SB() : null);
+ int n = 0;
+ while ((str = peekToken()) != null && str.charAt(0) == '_') {
+ if (ret != null)
+ ret.append(str).append("\n");
+ getTokenPeeked();
+ n++;
}
+ int m = 0;
+ while ((str = getNextDataToken()) != null) {
+ if (ret != null)
+ ret.append(str).append(" ");
+ if ((++m % n) == 0)
+ ret.append("\n");
+ }
+ return (ret == null ? null : ret.toString());
}
/**
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-04-30
20:25:08 UTC (rev 20473)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-05-02
17:46:35 UTC (rev 20474)
@@ -193,7 +193,7 @@
if (key.startsWith("loop_")) {
if (skipping) {
parser.getTokenPeeked();
- parser.skipLoop();
+ parser.skipLoop(false);
} else {
processLoopBlock();
}
@@ -680,7 +680,7 @@
case 0:
break;
case -1:
- parser.skipLoop();
+ parser.skipLoop(false);
//$FALL-THROUGH$
case 1:
return;
@@ -700,7 +700,7 @@
|| key.startsWith("_symmetry_ssg_equiv")) {
if (ignoreFileSymmetryOperators) {
Logger.warn("ignoring file-based symmetry operators");
- parser.skipLoop();
+ parser.skipLoop(false);
} else {
processSymmetryOperationsLoopBlock();
}
@@ -724,7 +724,7 @@
addMore();
return;
}
- parser.skipLoop();
+ parser.skipLoop(false);
}
protected boolean processSubclassLoopBlock() throws Exception {
@@ -827,7 +827,7 @@
parseLoopParameters(atomTypeFields);
for (int i = propertyCount; --i >= 0;)
if (fieldOf[i] == NONE) {
- parser.skipLoop();
+ parser.skipLoop(false);
return;
}
@@ -1014,7 +1014,7 @@
// no coordinates, but valuable information
} else {
// it is a different kind of _atom_site loop block
- parser.skipLoop();
+ parser.skipLoop(false);
return false;
}
int modelField = fieldOf[MODEL_NO];
@@ -1025,7 +1025,7 @@
int modelNo = parseIntStr(field);
if (modelNo != currentModelNo) {
if (iHaveDesiredModel && asc.atomSetCount > 0) {
- parser.skipLoop();
+ parser.skipLoop(false);
// but only this atom loop
skipping = false;
continuing = true;
@@ -1451,7 +1451,7 @@
break;
if (n < 0) {
Logger.warn("required " + FAMILY_SGOP + " key not found");
- parser.skipLoop();
+ parser.skipLoop(false);
return;
}
n = 0;
@@ -1556,7 +1556,7 @@
for (int i = propertyCount; --i >= 0;)
if (propertyOf[i] != CCDC_GEOM_BOND_TYPE && fieldOf[i] == NONE) {
Logger.warn("?que? missing property: " + geomBondFields[i]);
- parser.skipLoop();
+ parser.skipLoop(false);
return;
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java 2015-04-30
20:25:08 UTC (rev 20473)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java 2015-05-02
17:46:35 UTC (rev 20474)
@@ -165,15 +165,15 @@
"*_displace_fourier_param_sin", // 15
"*_displace_fourier_param_modulus",
"*_displace_fourier_param_phase",
- "*_displace_special_func_atom_site_label",
- "*_displace_special_func_sawtooth_ax", // 25
+ "*_displace_special_func_atom_site_label", // 18
+ "*_displace_special_func_sawtooth_ax",
"*_displace_special_func_sawtooth_ay",
"*_displace_special_func_sawtooth_az",
"*_displace_special_func_sawtooth_c",
"*_displace_special_func_sawtooth_w",
"*_occ_fourier_atom_site_label",
"*_occ_fourier_wave_vector_seq_id",
- "*_occ_fourier_param_cos", // 20
+ "*_occ_fourier_param_cos", // 26
"*_occ_fourier_param_sin",
"*_occ_fourier_param_modulus",
"*_occ_fourier_param_phase",
@@ -271,11 +271,17 @@
*/
public int processLoopBlock() throws Exception {
CifReader cr = (CifReader) this.cr;
- if (cr.key.equals("_cell_subsystem_code"))
+ String key = cr.key;
+ if (key.equals("_cell_subsystem_code"))
return processSubsystemLoopBlock();
- if (!cr.key.startsWith("_cell_wave") && !cr.key.contains("fourier")
- && !cr.key.contains("legendre") && !cr.key.contains("_special_func"))
+
+ if (!key.startsWith("_cell_wave") && !key.contains("fourier")
+ && !key.contains("legendre") && !key.contains("_special_func")) {
+ if (key.contains("crenel_ortho"))
+ cr.appendLoadNote("WARNING: Orthogonalized non-Legendre functions not
supported.\nThe following block has been ignored. Use Legendre functions
instead.\n\n"
+ + cr.parser.skipLoop(true) +
"=================================\n");
return 0;
+ }
if (cr.asc.iSet < 0)
cr.asc.newAtomSet();
cr.parseLoopParametersFor(CifReader.FAMILY_ATOM, modulationFields);
@@ -341,35 +347,38 @@
type_id += field;
break;
case JANA_OCC_ABS_LABEL:
- if (type_id == null)
- type_id = "J_O";
+ type_id = "J_O";
pt[0] = pt[2] = 1;
- //$FALL-THROUGH$
+ axis = "0";
+ atomLabel = field;
+ break;
case OCC_SPECIAL_LABEL:
- if (type_id == null)
- type_id = "O_0";
+ type_id = "O_0";
axis = "0";
- //$FALL-THROUGH$
+ atomLabel = field;
+ break;
case DISP_SPEC_LABEL:
- if (type_id == null)
- type_id = "D_S";
- //$FALL-THROUGH$
+ type_id = "D_S";
+ axis = "0";
+ atomLabel = field;
+ break;
+ case SPIN_SPEC_LABEL:
+ type_id = "M_T";
+ axis = "0";
+ atomLabel = field;
+ break;
case LEG_DISP_LABEL:
- if (type_id == null)
- type_id = "D_L";
- //$FALL-THROUGH$
+ type_id = "D_L";
+ atomLabel = field;
+ break;
case LEG_U_LABEL:
- if (type_id == null)
- type_id = "U_L";
- //$FALL-THROUGH$
+ type_id = "U_L";
+ atomLabel = field;
+ break;
case LEG_OCC_LABEL:
- if (type_id == null)
- type_id = "O_L";
- //$FALL-THROUGH$
- case SPIN_SPEC_LABEL:
- if (type_id == null)
- type_id = "M_T";
- //$FALL-THROUGH$
+ type_id = "O_L";
+ atomLabel = field;
+ break;
case FWV_DISP_LABEL:
case FWV_OCC_LABEL:
case FWV_SPIN_LABEL:
@@ -481,6 +490,7 @@
if (!ok)
continue;
switch (type_id.charAt(0)) {
+ case 'C':
case 'D':
case 'O':
case 'M':
Modified: trunk/Jmol/src/org/jmol/g3d/CylinderRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/CylinderRenderer.java 2015-04-30 20:25:08 UTC
(rev 20473)
+++ trunk/Jmol/src/org/jmol/g3d/CylinderRenderer.java 2015-05-02 17:46:35 UTC
(rev 20474)
@@ -169,6 +169,11 @@
private P3 ptA0, ptB0;
void renderBits(short colixA, short colixB, int screen, byte endcaps, int
diameter, P3 ptA, P3 ptB) {
+ Graphics3D g = this.g3d;
+ if (diameter == 0 || diameter == 1) {
+ line3d.plotLineBits(g.getColorArgbOrGray(colixA),
g.getColorArgbOrGray(colixB), ptA, ptB);
+ return;
+ }
if (ptA0 == null) {
ptA0 = new P3();
ptB0 = new P3();
@@ -183,7 +188,6 @@
int ixB = Math.round(ptB.x);
int iyB = Math.round(ptB.y);
int izB = Math.round(ptB.z);
- Graphics3D g = this.g3d;
int codeMinA = g.clipCode3(ixA - r, iyA - r, izA - r);
int codeMaxA = g.clipCode3(ixA + r, iyA + r, izA + r);
int codeMinB = g.clipCode3(ixB - r, iyB - r, izB - r);
@@ -198,10 +202,6 @@
dxBf = ptB.x - ptA.x;
dyBf = ptB.y - ptA.y;
dzBf = ptB.z - ptA.z;
- if (diameter == 0 || diameter == 1) {
- line3d.plotLineClippedBits(g.getColorArgbOrGray(colixA),
g.getColorArgbOrGray(colixB), ptA, ptB, clipped, 0, 0);
- return;
- }
if (diameter > 0) {
this.diameter = diameter;
this.xAf = ptA.x;
Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2015-04-30 20:25:08 UTC (rev
20473)
+++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2015-05-02 17:46:35 UTC (rev
20474)
@@ -1263,13 +1263,14 @@
@Override
public void drawLineBits(short colixA, short colixB, P3 pointA, P3 pointB) {
+ // drawQuadBits, drawTriangleBits
if (!setC(colixA))
colixA = 0;
int argbA = argbCurrent;
if (!setC(colixB))
colixB = 0;
if (colixA != 0 || colixB != 0)
- line3d.plotLineClippedBits(argbA, argbCurrent, pointA, pointB, true, 0,
0);
+ line3d.plotLineBits(argbA, argbCurrent, pointA, pointB);
}
@Override
Modified: trunk/Jmol/src/org/jmol/g3d/LineRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/LineRenderer.java 2015-04-30 20:25:08 UTC
(rev 20473)
+++ trunk/Jmol/src/org/jmol/g3d/LineRenderer.java 2015-05-02 17:46:35 UTC
(rev 20474)
@@ -419,28 +419,41 @@
}
}
+ void plotLineBits(int argbA, int argbB, P3 ptA, P3 ptB) {
+ if (ptA.z <= 1 || ptB.z <= 1)
+ return;
+ boolean clipped = true;
+ switch (getTrimmedLineBits(ptA, ptB)) {
+ case VISIBILITY_OFFSCREEN:
+ return;
+ case VISIBILITY_UNCLIPPED:
+ clipped = false;
+ break;
+ }
+ plotLineClippedBits(argbA, argbB, ptA, ptB, clipped, 0, 0);
+ }
+
void plotDashedLineBits(int argb, int run, int rise, P3 ptA, P3 ptB) {
// measures, axes, bbcage only
- boolean clipped = true;
if (ptA.z <= 1 || ptB.z <= 1)
return;
- if (clipped)
- switch (getTrimmedLineBits(ptA, ptB)) {
- case VISIBILITY_OFFSCREEN:
- return;
- case VISIBILITY_UNCLIPPED:
- clipped = false;
- break;
- default:
- if (ptAtrimmed == null) {
- ptAtrimmed = new P3();
- ptBtrimmed = new P3();
- }
- ptAtrimmed.set(x1t, y1t, z1t);
- ptBtrimmed.set(x2t, y2t, z2t);
- ptA = ptAtrimmed;
- ptB = ptBtrimmed;
+ boolean clipped = true;
+ switch (getTrimmedLineBits(ptA, ptB)) {
+ case VISIBILITY_OFFSCREEN:
+ return;
+ case VISIBILITY_UNCLIPPED:
+ clipped = false;
+ break;
+ default:
+ if (ptAtrimmed == null) {
+ ptAtrimmed = new P3();
+ ptBtrimmed = new P3();
}
+ ptAtrimmed.set(x1t, y1t, z1t);
+ ptBtrimmed.set(x2t, y2t, z2t);
+ ptA = ptAtrimmed;
+ ptB = ptBtrimmed;
+ }
plotLineClippedBits(argb, argb, ptA, ptB, clipped, run, rise);
}
@@ -669,7 +682,7 @@
}
}
- void plotLineClippedBits(int argb1, int argb2, P3 ptA, P3 ptB, boolean
clipped, int run,
+ private void plotLineClippedBits(int argb1, int argb2, P3 ptA, P3 ptB,
boolean clipped, int run,
int rise) {
// standard, dashed or not dashed -- isosurface mesh
int[] zbuf = g3d.zbuf;
@@ -683,7 +696,9 @@
int y = (int) ptA.y;
int z = (int) ptA.z;
int dx = (int) ptB.x - x;
+ int x2 = x + dx;
int dy = (int) ptB.y - y;
+ int y2 = y + dy;
int offset = y * width + x;
int offsetMax = g3d.bufferSize;
//boolean flipflop = (((x ^ y) & 1) != 0);
@@ -716,8 +731,8 @@
// using x
setRastAB(ptA.x, ptA.z, ptB.x, ptB.z);
int twoDxAccumulatedYError = 0;
- int n1 = Math.abs(x + dx - x2t) - 1;
- int n2 = Math.abs(x + dx - x1t) - 1;
+ int n1 = Math.abs(x2 - x2t) - 1;
+ int n2 = Math.abs(x2 - x1t) - 1;
for (int n = dx - 1, nMid = n / 2; --n >= n1;) {
if (n == nMid) {
argb = argb2;
@@ -743,8 +758,8 @@
// using y
setRastAB(ptA.y, ptA.z, ptB.y, ptB.z);
int twoDyAccumulatedXError = 0;
- int n1 = Math.abs(y + dy - y2t) - 1;
- int n2 = Math.abs(y + dy - y1t) - 1;
+ int n1 = Math.abs(y2 - y2t) - 1;
+ int n2 = Math.abs(y2 - y1t) - 1;
for (int n = dy - 1, nMid = n / 2; --n >= n1;) {
if (n == nMid) {
argb = argb2;
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-04-30
20:25:08 UTC (rev 20473)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-05-02
17:46:35 UTC (rev 20474)
@@ -2170,7 +2170,7 @@
}
return bs;
case T.spec_alternate:
- // could be PDB type file with UNK
+ // could be PDB type file with UNK or a modulated CIF file subsystem
String spec = (String) specInfo;
for (int i = ac; --i >= 0;)
if (isAltLoc(at[i].altloc, spec))
Modified: trunk/Jmol/src/org/jmol/modelset/JmolBioModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/JmolBioModelSet.java 2015-04-30
20:25:08 UTC (rev 20473)
+++ trunk/Jmol/src/org/jmol/modelset/JmolBioModelSet.java 2015-05-02
17:46:35 UTC (rev 20474)
@@ -54,9 +54,6 @@
int getBioPolymerCountInModel(int modelIndex);
- void getConformations(int modelIndex, int conformationIndex,
- boolean doSet, BS bsAtoms, BS bsRet);
-
String getFullProteinStructureState(BS bsAtoms, int mode);
BS getIdentifierOrNull(String identifier);
Modified: trunk/Jmol/src/org/jmol/modelset/Model.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Model.java 2015-04-30 20:25:08 UTC (rev
20473)
+++ trunk/Jmol/src/org/jmol/modelset/Model.java 2015-05-02 17:46:35 UTC (rev
20474)
@@ -227,6 +227,15 @@
return null;
}
+ protected BS getConformationBS(int conformationIndex, BS bsSelected) {
+ if (conformationIndex > 0 && conformationIndex >= altLocCount)
+ return null;
+ BS bsConformation = ms.vwr.getModelUndeletedAtomsBitSet(modelIndex);
+ if (bsSelected != null)
+ bsConformation.and(bsSelected);
+ return (bsConformation.nextSetBit(0) < 0 ? null : bsConformation);
+ }
+
public void fixIndices(int modelIndex, int nAtomsDeleted, BS bsDeleted) {
// also in BioModel
fixIndicesM(modelIndex, nAtomsDeleted, bsDeleted);
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-04-30 20:25:08 UTC
(rev 20473)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-05-02 17:46:35 UTC
(rev 20474)
@@ -1446,10 +1446,6 @@
return file * 1000000 + model;
}
- public int getAltLocCountInModel(int modelIndex) {
- return am[modelIndex].altLocCount;
- }
-
public int getChainCountInModelWater(int modelIndex, boolean countWater) {
if (modelIndex < 0) {
int chainCount = 0;
@@ -1572,6 +1568,10 @@
////////////// individual models ////////////////
+ public int getAltLocCountInModel(int modelIndex) {
+ return am[modelIndex].altLocCount;
+ }
+
public int getAltLocIndexInModel(int modelIndex, char alternateLocationID) {
if (alternateLocationID == '\0') {
return 0;
@@ -1616,7 +1616,7 @@
public int getLastVibrationVector(int modelIndex, int tok) {
if (vibrations != null) {
Vibration v;
- int a1 = (modelIndex < 0 || modelIndex >= mc - 1 ? ac : am[modelIndex +
1].firstAtomIndex);
+ int a1 = (modelIndex < 0 || isTrajectory(modelIndex) || modelIndex >= mc
- 1 ? ac : am[modelIndex + 1].firstAtomIndex);
int a0 = (modelIndex <= 0 ? 0 : am[modelIndex].firstAtomIndex);
for (int i = a1; --i >= a0;) {
if ((modelIndex < 0 || at[i].mi == modelIndex)
@@ -3759,6 +3759,39 @@
return v.toArray(new Quat[v.size()]);
}
+ public BS getConformation(int modelIndex, int conformationIndex,
+ boolean doSet, BS bsAtoms) {
+ BS bs = new BS();
+ for (int i = mc; --i >= 0;)
+ if (i == modelIndex || modelIndex < 0) {
+ if (am[i].isBioModel)
+ ((BioModel) am[i]).getConformation(conformationIndex, doSet, bsAtoms,
+ bs);
+ else if (!doSet)
+ getSubsystem(i, conformationIndex, bsAtoms, bs);
+ }
+ return bs;
+ }
+
+ private void getSubsystem(int modelIndex, int conformationIndex, BS bsAtoms,
+ BS bs) {
+ BS bsConformation = am[modelIndex].getConformationBS(conformationIndex,
+ bsAtoms);
+ if (bsConformation == null)
+ return;
+ if (conformationIndex >= 0) {
+ int nAltLocs = getAltLocCountInModel(modelIndex);
+ String altLocs = getAltLocListInModel(modelIndex);
+ BS bsTemp = new BS();
+ for (int c = nAltLocs; --c >= 0;)
+ if (c != conformationIndex)
+ bsConformation.andNot(getAtomBitsMDa(T.spec_alternate,
+ altLocs.substring(c, c + 1), bsTemp));
+ }
+ if (bsConformation.nextSetBit(0) >= 0)
+ bs.or(bsConformation);
+ }
+
///// bio-only methods /////
public BS getSequenceBits(String specInfo, BS bs) {
@@ -3783,13 +3816,6 @@
bioModelset.recalculatePoints(modelIndex);
}
- public BS getConformation(int modelIndex, int conformationIndex, boolean
doSet, BS bsAtoms) {
- BS bs = new BS();
- if (haveBioModels)
- bioModelset.getConformations(modelIndex, conformationIndex, doSet,
bsAtoms, bs);
- return bs;
- }
-
/**
* These are not actual hydrogen bonds. They are N-O bonds in proteins and
* nucleic acids The method is called by AminoPolymer and NucleicPolymer
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-04-30 20:25:08 UTC
(rev 20473)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-05-02 17:46:35 UTC
(rev 20474)
@@ -786,15 +786,6 @@
return s;
}
- @Override
- public void getConformations(int modelIndex, int conformationIndex,
- boolean doSet, BS bsAtoms, BS bsRet) {
- for (int i = ms.mc; --i >= 0;)
- if (i == modelIndex || modelIndex < 0)
- if (ms.am[i].isBioModel)
- ((BioModel) ms.am[i]).getConformation(conformationIndex, doSet,
bsAtoms, bsRet);
- }
-
/**
* @param conformationIndex
* @param doSet
@@ -802,21 +793,17 @@
* @param bsSelected
*/
public void getConformation(int conformationIndex, boolean doSet, BS
bsSelected, BS bsRet) {
- String altLocs = ms.getAltLocListInModel(modelIndex);
- int nAltLocs = ms.getAltLocCountInModel(modelIndex);
- if (conformationIndex > 0 && conformationIndex >= nAltLocs)
+ int nAltLocs = altLocCount;
+ BS bsConformation = getConformationBS(conformationIndex, bsSelected);
+ if (bsConformation == null)
return;
- BS bsConformation = vwr.getModelUndeletedAtomsBitSet(modelIndex);
- if (bsSelected != null)
- bsConformation.and(bsSelected);
- if (bsConformation.nextSetBit(0) < 0)
- return;
if (conformationIndex >= 0) {
if (nAltLocs > 0)
for (int i = bioPolymerCount; --i >= 0;)
bioPolymers[i].getConformation(bsConformation, conformationIndex);
BS bs = new BS();
- for (int c = nAltLocs; --c >= 0;)
+ String altLocs = ms.getAltLocListInModel(modelIndex);
+ for (int c = altLocCount; --c >= 0;)
if (c != conformationIndex)
bsConformation.andNot(ms.getAtomBitsMDa(T.spec_alternate,
altLocs.substring(c, c + 1), bs));
Modified: trunk/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-04-30 20:25:08 UTC
(rev 20473)
+++ trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-05-02 17:46:35 UTC
(rev 20474)
@@ -1771,7 +1771,7 @@
T3 t = atom.atomPropertyTuple(vwr, tok, ptTemp);
switch (minmaxtype) {
case T.allfloat:
- fout[i] = (pt == null ? -1 : t.length());
+ fout[i] = (pt == null ? -1 : t == null ? 0 : t.length());
break;
case T.all:
vout.addLast(t == null ? Integer.valueOf(-1) : P3.newP(t));
Modified: trunk/Jmol/src/org/jmol/thread/VibrationThread.java
===================================================================
--- trunk/Jmol/src/org/jmol/thread/VibrationThread.java 2015-04-30 20:25:08 UTC
(rev 20473)
+++ trunk/Jmol/src/org/jmol/thread/VibrationThread.java 2015-05-02 17:46:35 UTC
(rev 20474)
@@ -71,7 +71,6 @@
} else {
float t = (float) (elapsed % transformManager.vibrationPeriodMs)
/ transformManager.vibrationPeriodMs;
-// t = 0.2f;
transformManager.setVibrationT(t);
vwr.refresh(3, "VibrationThread");
mode = (checkInterrupted(transformManager.vibrationThread) ? FINISH
: MAIN);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-04-30 20:25:08 UTC
(rev 20473)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-05-02 17:46:35 UTC
(rev 20474)
@@ -14,8 +14,14 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.13_2015.04.30d"
+Jmol.___JmolVersion="14.3.13_2015.05.02"
+bug fix: color atoms property vxyz crashes Jmol if no vibrations
+bug fix: with msCIF, select subsystem=1 does not select anything
+bug fix: vibrations in trajectories not animating (14.3.6_2014.08.14)
+
+JmolVersion="14.3.13_2015.04.30d"
+
bug fix: reading Molden file with no MOs crashes Jmol
JmolVersion="14.3.13_2015.04.30c"
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