Revision: 20475
http://sourceforge.net/p/jmol/code/20475
Author: hansonr
Date: 2015-05-02 17:47:14 +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:
--------------
branches/v14_2/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java
branches/v14_2/Jmol/src/org/jmol/modelset/JmolBioModelSet.java
branches/v14_2/Jmol/src/org/jmol/modelset/Model.java
branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java
branches/v14_2/Jmol/src/org/jmol/modelsetbio/BioModel.java
branches/v14_2/Jmol/src/org/jmol/script/ScriptExpr.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_2/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java
2015-05-02 17:46:35 UTC (rev 20474)
+++ branches/v14_2/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java
2015-05-02 17:47:14 UTC (rev 20475)
@@ -345,15 +345,19 @@
type_id = "J_O";
pt[0] = pt[2] = 1;
//$FALL-THROUGH$
+ case DISP_SPEC_LABEL:
+ if (type_id == null)
+ type_id = "D_S";
+ //$FALL-THROUGH$
+ case SPIN_SPEC_LABEL:
+ if (type_id == null)
+ type_id = "M_T";
+ //$FALL-THROUGH$
case OCC_SPECIAL_LABEL:
if (type_id == null)
type_id = "O_0";
axis = "0";
//$FALL-THROUGH$
- case DISP_SPEC_LABEL:
- if (type_id == null)
- type_id = "D_S";
- //$FALL-THROUGH$
case LEG_DISP_LABEL:
if (type_id == null)
type_id = "D_L";
@@ -366,10 +370,6 @@
if (type_id == null)
type_id = "O_L";
//$FALL-THROUGH$
- case SPIN_SPEC_LABEL:
- if (type_id == null)
- type_id = "M_T";
- //$FALL-THROUGH$
case FWV_DISP_LABEL:
case FWV_OCC_LABEL:
case FWV_SPIN_LABEL:
Modified: branches/v14_2/Jmol/src/org/jmol/modelset/JmolBioModelSet.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelset/JmolBioModelSet.java
2015-05-02 17:46:35 UTC (rev 20474)
+++ branches/v14_2/Jmol/src/org/jmol/modelset/JmolBioModelSet.java
2015-05-02 17:47:14 UTC (rev 20475)
@@ -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: branches/v14_2/Jmol/src/org/jmol/modelset/Model.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelset/Model.java 2015-05-02
17:46:35 UTC (rev 20474)
+++ branches/v14_2/Jmol/src/org/jmol/modelset/Model.java 2015-05-02
17:47:14 UTC (rev 20475)
@@ -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: branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java 2015-05-02
17:46:35 UTC (rev 20474)
+++ branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java 2015-05-02
17:47:14 UTC (rev 20475)
@@ -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: branches/v14_2/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-05-02
17:46:35 UTC (rev 20474)
+++ branches/v14_2/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-05-02
17:47:14 UTC (rev 20475)
@@ -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: branches/v14_2/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/ScriptExpr.java 2015-05-02
17:46:35 UTC (rev 20474)
+++ branches/v14_2/Jmol/src/org/jmol/script/ScriptExpr.java 2015-05-02
17:47:14 UTC (rev 20475)
@@ -1767,7 +1767,7 @@
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: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-05-02
17:46:35 UTC (rev 20474)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-05-02
17:47:14 UTC (rev 20475)
@@ -4,8 +4,14 @@
# THIS IS THE RELEASE BRANCH
# BUG FIXES ONLY, PLEASE
-Jmol.___JmolVersion="14.2.13_2015.04.30d"
+Jmol.___JmolVersion="14.2.13_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
(14.2/3.12_2015.02.06)
+bug fix: vibrations in trajectories not animating (14.2/3.6_2014.08.14)
+
+JmolVersion="14.2.13_2015.04.30d"
+
bug fix: reading Molden file with no MOs crashes Jmol
JmolVersion="14.2.13_2015.04.27"
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