Revision: 20865
http://sourceforge.net/p/jmol/code/20865
Author: hansonr
Date: 2015-11-18 15:28:51 +0000 (Wed, 18 Nov 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.4.0_2015.11.18"
bug fix: loading mmCIF files where label_asym_id != auth_asym_id will apply
biomolecule symmetry to wrong chain
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
branches/v14_4/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
branches/v14_4/Jmol/src/org/jmol/console/GenericConsole.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptMathProcessor.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
trunk/Jmol/src/org/jmol/console/GenericConsole.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-11-16 15:39:29 UTC (rev 20864)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-11-18 15:28:51 UTC (rev 20865)
@@ -30,7 +30,6 @@
import javajs.util.M4;
import javajs.util.P3;
import javajs.util.PT;
-import javajs.util.Rdr;
import javajs.util.SB;
import org.jmol.adapter.smarter.Atom;
@@ -841,6 +840,7 @@
M4 mident = M4.newM4(null);
String[] ops = PT.split((String) biomolecule.get("operators"), ",");
String assemblies = (String) biomolecule.get("assemblies");
+ biomolecule.put("asemblyIdAtoms", assemblyIdAtoms);
P3 sum = new P3();
int count = 0;
int nAtoms = 0;
@@ -851,10 +851,8 @@
chainlist += ":" + id + ";";
if (assemblyIdAtoms != null) {
BS bs = assemblyIdAtoms.get(id);
- if (bs != null) {
- //System.out.println(id + " " + bs.cardinality());
+ if (bs != null)
bsAll.or(bs);
- }
} else if (isCourseGrained) {
P3 asum = chainAtomMap.get(id);
int c = chainAtomCounts.get(id)[0];
Modified: branches/v14_4/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
2015-11-16 15:39:29 UTC (rev 20864)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
2015-11-18 15:28:51 UTC (rev 20865)
@@ -1083,6 +1083,8 @@
firstSymmetryAtom = atomMax++;
break;
}
+ Map<String, BS> assemblyIdAtoms = (Map<String, BS>) thisBiomolecule
+ .get("asemblyIdAtoms");
if (filter.indexOf("#<") >= 0) {
len = Math.min(len,
PT.parseInt(filter.substring(filter.indexOf("#<") + 2)) - 1);
@@ -1090,6 +1092,7 @@
}
for (int iAtom = firstSymmetryAtom; iAtom < atomMax; iAtom++)
atoms[iAtom].bsSymmetry = BSUtil.newAndSetBit(0);
+ BS bsAtoms = asc.bsAtoms;
for (int i = (biomtchains == null ? 1 : 0); i < len; i++) {
if (filter.indexOf("!#") >= 0) {
if (filter.indexOf("!#" + (i + 1) + ";") >= 0)
@@ -1100,12 +1103,21 @@
}
M4 mat = biomts.get(i);
String chains = (biomtchains == null ? null : biomtchains.get(i));
-
+ if (chains != null && assemblyIdAtoms != null) {
+ // must use label_asym_id, not auth_asym_id // bug fix 11/18/2015
+ bsAtoms = new BS();
+ for (Entry<String, BS> e : assemblyIdAtoms.entrySet())
+ if (chains.indexOf(":" + e.getKey() + ";") >= 0)
+ bsAtoms.or(e.getValue());
+ if (asc.bsAtoms != null)
+ bsAtoms.and(asc.bsAtoms);
+ chains = null;
+ }
for (int iAtom = firstSymmetryAtom; iAtom < atomMax; iAtom++) {
- if (asc.bsAtoms != null && !asc.bsAtoms.get(iAtom))
- continue;
- if (chains != null
- && chains.indexOf(":" + acr.vwr.getChainIDStr(atoms[iAtom].chainID)
+ if (bsAtoms != null
+ && !bsAtoms.get(iAtom)
+ || chains != null
+ && chains.indexOf(":" + acr.vwr.getChainIDStr(atoms[i].chainID)
+ ";") < 0)
continue;
try {
Modified: branches/v14_4/Jmol/src/org/jmol/console/GenericConsole.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/console/GenericConsole.java
2015-11-16 15:39:29 UTC (rev 20864)
+++ branches/v14_4/Jmol/src/org/jmol/console/GenericConsole.java
2015-11-18 15:28:51 UTC (rev 20865)
@@ -375,12 +375,18 @@
}
private void outputMsg(String message) {
- if (message == null) {
+ int n = (message == null ? -1 : message.length());
+ switch (n) {
+ case -1:
output.setText("");
return;
+ default:
+ if (message.charAt(n - 1) == '\n')
+ break;
+ //$FALL-THROUGH$
+ case 0:
+ message += "\n";
}
- if (message.charAt(message.length() - 1) != '\n')
- message += "\n";
output.append(message);
}
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2015-11-16 15:39:29 UTC (rev 20864)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2015-11-18 15:28:51 UTC (rev 20865)
@@ -1255,7 +1255,7 @@
return (isDecimal(x2) || isDecimal(x1) ? addXFloat(x1.asFloat()
* x2.asFloat()) : addXInt(x1.asInt() * x2.asInt()));
}
- pt = (x1.tok == T.matrix3f ? ptValue(x2)
+ pt = (x1.tok == T.matrix3f || x1.tok == T.matrix4f ? ptValue(x2)
: x2.tok == T.matrix3f ? ptValue(x1) : null);
pt4 = (x1.tok == T.matrix4f ? planeValue(x2)
: x2.tok == T.matrix4f ? planeValue(x1) : null);
@@ -1268,9 +1268,10 @@
// pt * m
M3 m3b = M3.newM3((M3) x2.value);
m3b.transpose();
- m3b.rotate(pt);
+ P3 pt1 = P3.newP(pt);
+ m3b.rotate(pt1);
return (x1.tok == T.varray ? addX(SV.getVariableAF(new float[] {
- pt.x, pt.y, pt.z })) : addXPt(pt));
+ pt1.x, pt1.y, pt1.z })) : addXPt(pt1));
}
if (pt4 != null)
// q * m --> q
@@ -1283,9 +1284,10 @@
if (pt4 != null) {
M4 m4b = M4.newM4((M4) x2.value);
m4b.transpose();
- m4b.transform(pt4);
+ P4 pt41 = P4.newPt(pt4);
+ m4b.transform(pt41);
return (x1.tok == T.varray ? addX(SV.getVariableAF(new float[] {
- pt4.x, pt4.y, pt4.z, pt4.w })) : addXPt4(pt4));
+ pt41.x, pt41.y, pt41.z, pt41.w })) : addXPt4(pt41));
}
break;
}
@@ -1293,9 +1295,10 @@
case T.matrix3f:
M3 m3 = (M3) x1.value;
if (pt != null) {
- m3.rotate(pt);
+ P3 pt1 = P3.newP(pt);
+ m3.rotate(pt1);
return (x2.tok == T.varray ? addX(SV.getVariableAF(new float[] {
- pt.x, pt.y, pt.z })) : addXPt(pt));
+ pt1.x, pt1.y, pt1.z })) : addXPt(pt1));
}
switch (x2.tok) {
case T.matrix3f:
@@ -1315,9 +1318,10 @@
case T.matrix4f:
M4 m4 = (M4) x1.value;
if (pt != null) {
- m4.rotTrans(pt);
+ P3 pt1 = P3.newP(pt);
+ m4.rotTrans(pt1);
return (x2.tok == T.varray ? addX(SV.getVariableAF(new float[] {
- pt.x, pt.y, pt.z })) : addXPt(pt));
+ pt1.x, pt1.y, pt1.z })) : addXPt(pt1));
}
if (pt4 != null) {
m4.transform(pt4);
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-16
15:39:29 UTC (rev 20864)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-18
15:28:51 UTC (rev 20865)
@@ -8,11 +8,16 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.0_2015.11.12"
+Jmol.___JmolVersion="14.4.0_2015.11.18"
+bug fix: loading mmCIF files where label_asym_id != auth_asym_id will apply
biomolecule symmetry to wrong chain
+
+JmolVersion="14.4.0_2015.11.13"
+
+bug fix: echo "" fails in applet
bug fix: 3x3 and 4x4 matrix multiplication of points changes the point itself.
-Jmol.___JmolVersion="14.4.0_2015.11.06"
+JmolVersion="14.4.0_2015.11.06"
bug fix: restoring bonds to a model having fewer bonds than the model for
which they were saved throws an exception
bug fix: CIF reader does not read incommensurately modulated magCIF files
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-11-16 15:39:29 UTC (rev 20864)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-11-18 15:28:51 UTC (rev 20865)
@@ -30,7 +30,6 @@
import javajs.util.M4;
import javajs.util.P3;
import javajs.util.PT;
-import javajs.util.Rdr;
import javajs.util.SB;
import org.jmol.adapter.smarter.Atom;
@@ -841,6 +840,7 @@
M4 mident = M4.newM4(null);
String[] ops = PT.split((String) biomolecule.get("operators"), ",");
String assemblies = (String) biomolecule.get("assemblies");
+ biomolecule.put("asemblyIdAtoms", assemblyIdAtoms);
P3 sum = new P3();
int count = 0;
int nAtoms = 0;
@@ -851,10 +851,8 @@
chainlist += ":" + id + ";";
if (assemblyIdAtoms != null) {
BS bs = assemblyIdAtoms.get(id);
- if (bs != null) {
- //System.out.println(id + " " + bs.cardinality());
+ if (bs != null)
bsAll.or(bs);
- }
} else if (isCourseGrained) {
P3 asum = chainAtomMap.get(id);
int c = chainAtomCounts.get(id)[0];
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java 2015-11-16
15:39:29 UTC (rev 20864)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java 2015-11-18
15:28:51 UTC (rev 20865)
@@ -1010,7 +1010,6 @@
}
int particleMode = (filter.indexOf("BYCHAIN") >= 0 ? PARTICLE_CHAIN
: filter.indexOf("BYSYMOP") >= 0 ? PARTICLE_SYMOP : PARTICLE_NONE);
-
doNormalize = false;
Lst<M4> biomts = (Lst<M4>) thisBiomolecule.get("biomts");
Lst<String> biomtchains = (Lst<String>) thisBiomolecule.get("chains");
@@ -1083,6 +1082,8 @@
firstSymmetryAtom = atomMax++;
break;
}
+ Map<String, BS> assemblyIdAtoms = (Map<String, BS>) thisBiomolecule
+ .get("asemblyIdAtoms");
if (filter.indexOf("#<") >= 0) {
len = Math.min(len,
PT.parseInt(filter.substring(filter.indexOf("#<") + 2)) - 1);
@@ -1090,6 +1091,7 @@
}
for (int iAtom = firstSymmetryAtom; iAtom < atomMax; iAtom++)
atoms[iAtom].bsSymmetry = BSUtil.newAndSetBit(0);
+ BS bsAtoms = asc.bsAtoms;
for (int i = (biomtchains == null ? 1 : 0); i < len; i++) {
if (filter.indexOf("!#") >= 0) {
if (filter.indexOf("!#" + (i + 1) + ";") >= 0)
@@ -1100,12 +1102,21 @@
}
M4 mat = biomts.get(i);
String chains = (biomtchains == null ? null : biomtchains.get(i));
-
+ if (chains != null && assemblyIdAtoms != null) {
+ // must use label_asym_id, not auth_asym_id // bug fix 11/18/2015
+ bsAtoms = new BS();
+ for (Entry<String, BS> e : assemblyIdAtoms.entrySet())
+ if (chains.indexOf(":" + e.getKey() + ";") >= 0)
+ bsAtoms.or(e.getValue());
+ if (asc.bsAtoms != null)
+ bsAtoms.and(asc.bsAtoms);
+ chains = null;
+ }
for (int iAtom = firstSymmetryAtom; iAtom < atomMax; iAtom++) {
- if (asc.bsAtoms != null && !asc.bsAtoms.get(iAtom))
- continue;
- if (chains != null
- && chains.indexOf(":" + acr.vwr.getChainIDStr(atoms[iAtom].chainID)
+ if (bsAtoms != null
+ && !bsAtoms.get(iAtom)
+ || chains != null
+ && chains.indexOf(":" + acr.vwr.getChainIDStr(atoms[i].chainID)
+ ";") < 0)
continue;
try {
Modified: trunk/Jmol/src/org/jmol/console/GenericConsole.java
===================================================================
--- trunk/Jmol/src/org/jmol/console/GenericConsole.java 2015-11-16 15:39:29 UTC
(rev 20864)
+++ trunk/Jmol/src/org/jmol/console/GenericConsole.java 2015-11-18 15:28:51 UTC
(rev 20865)
@@ -375,12 +375,18 @@
}
private void outputMsg(String message) {
- if (message == null) {
+ int n = (message == null ? -1 : message.length());
+ switch (n) {
+ case -1:
output.setText("");
return;
+ default:
+ if (message.charAt(n - 1) == '\n')
+ break;
+ //$FALL-THROUGH$
+ case 0:
+ message += "\n";
}
- if (message.charAt(message.length() - 1) != '\n')
- message += "\n";
output.append(message);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-16 15:39:29 UTC
(rev 20864)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-18 15:28:51 UTC
(rev 20865)
@@ -62,13 +62,17 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.0_2015.11.12"
+Jmol.___JmolVersion="14.5.0_2015.11.18"
+bug fix: loading mmCIF files where label_asym_id != auth_asym_id will apply
biomolecule symmetry to wrong chain
+
+JmolVersion="14.5.0_2015.11.13"
+
+bug fix: echo "" fails in applet
bug fix: 3x3 and 4x4 matrix multiplication of points changes the point itself.
+JmolVersion="14.5.0_2015.11.06"
-Jmol.___JmolVersion="14.5.0_2015.11.06"
-
bug fix: restoring bonds to a model having fewer bonds than the model for
which they were saved throws an exception
bug fix: CIF reader does not read incommensurately modulated magCIF files
bug fix: WRITE xxx.ZIP crashes Jmol
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