Revision: 20852
http://sourceforge.net/p/jmol/code/20852
Author: hansonr
Date: 2015-10-30 12:08:02 +0000 (Fri, 30 Oct 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.4.0_2015.10.30"
bug fix: polyhedron volume will be incorrect if there is a
face triangle that has no edges visible (requires a six or more sided
face)
bug fix: nested if...{...if... } else {...} gives compiler syntax error:
if (i=1) {
print "i=1"
if (j=1)
print "j != 1"
} else { // } closes if (j=1) instead of if (i=1) {
print "i != 1"
}
bug fix: empty format crashes Jmol -- print "testing".format("")
bug fix: after CALCULATE HYDROGENS TRUE and then deleting hydrogens, hydrogens
are not added to aromatic rings in PDB models
bug fix: reading saved state after adding hydrogen atoms results in infinite
loop
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/modelset/BondCollection.java
branches/v14_4/Jmol/src/org/jmol/modelsetbio/BioModel.java
branches/v14_4/Jmol/src/org/jmol/script/SV.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptCompiler.java
branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedron.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelset/BondCollection.java
2015-10-30 12:07:20 UTC (rev 20851)
+++ branches/v14_4/Jmol/src/org/jmol/modelset/BondCollection.java
2015-10-30 12:08:02 UTC (rev 20852)
@@ -493,17 +493,17 @@
}
}
// now test non-O atoms
- for (int i = bsTest.nextSetBit(0); i >= 0; i = bsTest.nextSetBit(i + 1)) {
- bond = bo[i];
- if (!assignAromaticDouble(bond))
+ for (int i = bsTest.nextSetBit(0); i >= 0; i = bsTest.nextSetBit(i + 1))
+ if (!assignAromaticDouble(bond = bo[i]))
assignAromaticSingle(bond);
- }
// all done: do the actual assignments and clear arrays.
+ BS bsModels = new BS();
for (int i = i0; i >= 0; i = (isAll ? i - 1 : bsBonds.nextSetBit(i + 1))) {
bond = bo[i];
if (bsAromaticDouble.get(i)) {
if (!bond.is(Edge.BOND_AROMATIC_DOUBLE)) {
bsAromatic.set(i);
+ bsModels.set(bond.atom1.mi);
bond.setOrder(Edge.BOND_AROMATIC_DOUBLE);
}
} else if (bsAromaticSingle.get(i) || bond.isAromatic()) {
@@ -513,6 +513,10 @@
}
}
}
+ Model[] models = ((ModelSet) this).am;
+ for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i +
1))
+ if (models[i].isBioModel)
+ models[i].isPdbWithMultipleBonds = true;
assignAromaticNandO(bsBonds);
Modified: branches/v14_4/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-10-30
12:07:20 UTC (rev 20851)
+++ branches/v14_4/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-10-30
12:08:02 UTC (rev 20852)
@@ -121,10 +121,10 @@
Atom[] at = ms.at;
Model[] am = ms.am;
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
- if (iLast != i - 1)
- monomerIndexCurrent = -1;
+ if (at[i].group.isAdded(i))
+ continue;
monomerIndexCurrent = at[i].group.setProteinStructureType(type,
- monomerIndexCurrent);
+ iLast == i - 1 ? -1 : monomerIndexCurrent);
int modelIndex = at[i].mi;
ms.proteinStructureTainted = am[modelIndex].structureTainted = true;
iLast = i = at[i].group.lastAtomIndex;
@@ -136,10 +136,14 @@
i = am[modelIndex].firstAtomIndex + am[modelIndex].act;
continue;
}
- iLast = at[i].group.getStrucNo();
- if (iLast < 1000 && iLast > lastStrucNo[modelIndex])
- lastStrucNo[modelIndex] = iLast;
- i = at[i].group.lastAtomIndex + 1;
+ Group g = at[i].group;
+ if (!g.isAdded(i)) {
+ iLast = g.getStrucNo();
+ if (iLast < 1000 && iLast > lastStrucNo[modelIndex])
+ lastStrucNo[modelIndex] = iLast;
+ i = g.lastAtomIndex;
+ }
+ i++;
}
for (int i = 0; i < ms.ac;) {
int modelIndex = at[i].mi;
@@ -147,9 +151,13 @@
i = am[modelIndex].firstAtomIndex + am[modelIndex].act;
continue;
}
- if (at[i].group.getStrucNo() > 1000)
- at[i].group.setStrucNo(++lastStrucNo[modelIndex]);
- i = at[i].group.lastAtomIndex + 1;
+ Group g = at[i].group;
+ if (!g.isAdded(i)) {
+ i = g.lastAtomIndex;
+ if (g.getStrucNo() > 1000)
+ g.setStrucNo(++lastStrucNo[modelIndex]);
+ }
+ i++;
}
}
Modified: branches/v14_4/Jmol/src/org/jmol/script/SV.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/SV.java 2015-10-30 12:07:20 UTC
(rev 20851)
+++ branches/v14_4/Jmol/src/org/jmol/script/SV.java 2015-10-30 12:08:02 UTC
(rev 20852)
@@ -1284,8 +1284,10 @@
}
}
// use values to replace codes in format string
+ String[] format = PT.split(PT.rep(sValue(args[0]), "%%", "\1"), "%");
+ if (format.length == 0)
+ return "";
SB sb = new SB();
- String[] format = PT.split(PT.rep(sValue(args[0]), "%%", "\1"), "%");
sb.append(format[0]);
for (int i = 1; i < format.length; i++) {
Object ret = sprintf(PT.formatCheck("%" + format[i]),
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-10-30
12:07:20 UTC (rev 20851)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-10-30
12:08:02 UTC (rev 20852)
@@ -143,7 +143,7 @@
private String ident, identLC;
private Lst<T> vPush = new Lst<T>();
private int pushCount;
- private ScriptFlowContext lastFlowContext;
+ private ScriptFlowContext forceFlowContext;
synchronized ScriptContext compile(String filename, String script,
boolean isPredefining, boolean isSilent,
@@ -333,7 +333,7 @@
isEndOfCommand = false;
needRightParen = false;
lastFlowCommand = null;
- lastFlowContext = null;
+ forceFlowContext = null;
theTok = T.nada;
short iLine = 1;
@@ -731,7 +731,7 @@
if (lastFlowCommand.tok != T.process && (tokAt(0) == T.leftbrace))
ltoken.remove(0);
lastFlowCommand = null;
- lastFlowContext = flowContext;
+ forceFlowContext = flowContext;
// lastFlowImplicitEnd = flowContext.nextFlowImplicitEnd;
}
}
@@ -823,7 +823,7 @@
} else if (n > 0 && !haveENDIF || isOneLine) {
forceFlowEnd(flowContext.token);
if (!isOneLine) {
- lastFlowContext.forceEndIf = true;
+ forceFlowContext.forceEndIf = true;
}
}
isEndOfCommand = true;
@@ -1542,12 +1542,12 @@
// specifically for else { but not elseIf ( ) {
isEndOfCommand = true;
ScriptFlowContext f = (flowContext != null && flowContext.addLine == 0
- || lastFlowContext == null ? flowContext : lastFlowContext);
+ || forceFlowContext == null ? flowContext : forceFlowContext);
if (f != null) {
f.addLine = 0;
f.forceEndIf = false;
lastToken = T.tokenLeftBrace;
- lastFlowContext = f;
+ forceFlowContext = f;
}
return CONTINUE;
}
@@ -1684,10 +1684,10 @@
// unexpectedly allows if (x) { print x else print y}
fixFlowAddLine(flowContext);
if (lltoken.get(iCommand - 1)[0].tok == T.end
- && lastFlowContext != null && lastFlowContext.forceEndIf
- && lastFlowContext.addLine > 0
- && isFlowIfContextOK(lastFlowContext)) {
- flowContext = lastFlowContext;
+ && forceFlowContext != null && forceFlowContext.forceEndIf
+ && forceFlowContext.addLine > 0
+ && isFlowIfContextOK(forceFlowContext)) {
+ flowContext = forceFlowContext;
flowContext.forceEndIf = true;
lltoken.remove(--iCommand);
} else if (flowContext != null && flowContext.addLine > 0) {
@@ -2152,7 +2152,7 @@
}
private int forceFlowEnd(T token) {
T t0 = tokenCommand;
- lastFlowContext = flowContext;
+ forceFlowContext = flowContext;
token = flowStart(token);
if (!checkFlowEnd(token.tok, (String) token.value, ichBrace, false))
return ERROR;
Modified: branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
2015-10-30 12:07:20 UTC (rev 20851)
+++ branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
2015-10-30 12:08:02 UTC (rev 20852)
@@ -735,7 +735,7 @@
*
* @param points
* @param nPoints
- * @param planes
+ * @param triangles
* @param normals
* @param index
* @param pTemp
@@ -747,12 +747,12 @@
* @param bsTemp
* @return true if valid
*/
- private boolean checkFace(P3[] points, int nPoints, int[][] planes,
+ private boolean checkFace(P3[] points, int nPoints, int[][] triangles,
V3[] normals, int index, P4 pTemp, V3 vNorm,
V3 vAC, Map<Integer, Object[]> htNormMap,
Map<String, Object> htEdgeMap, float planarParam,
BS bsTemp) {
- int[] p1 = planes[index];
+ int[] p1 = triangles[index];
// Check here for a 3D convex hull:
int i0 = p1[0];
Modified: branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedron.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedron.java
2015-10-30 12:07:20 UTC (rev 20851)
+++ branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedron.java
2015-10-30 12:08:02 UTC (rev 20852)
@@ -243,10 +243,7 @@
if (bsFlat.cardinality() < triangles.length)
for (int i = triangles.length; --i >= 0;) {
int[] face = triangles[i];
- for (int j = face.length - 2; --j >= 0;)
- if (face[j + 2] >= 0)
- v += triangleVolume(face[j], face[j + 1], face[j + 2], vAB, vAC,
- vTemp);
+ v += triangleVolume(face[0], face[1], face[2], vAB, vAC, vTemp);
}
return Float.valueOf(v / 6);
}
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-30
12:07:20 UTC (rev 20851)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-30
12:08:02 UTC (rev 20852)
@@ -7,8 +7,28 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.0_2015.10.28"
+Jmol.___JmolVersion="14.4.0_2015.10.30"
+bug fix: polyhedron volume will be incorrect if there is a
+ face triangle that has no edges visible (requires a six or more sided
face)
+
+bug fix: nested if...{...if... } else {...} gives compiler syntax error:
+
+ if (i=1) {
+ print "i=1"
+ if (j=1)
+ print "j != 1"
+ } else { // } closes if (j=1) instead of if (i=1) {
+ print "i != 1"
+ }
+
+bug fix: empty format crashes Jmol -- print "testing".format("")
+bug fix: after CALCULATE HYDROGENS TRUE and then deleting hydrogens, hydrogens
are not added to aromatic rings in PDB models
+bug fix: reading saved state after adding hydrogen atoms results in infinite
loop
+
+
+JmolVersion="14.4.0_2015.10.28"
+
bug fix: XODYDATA file reader does not read bond info or formal charge //
changes in 14.4.0_2015.10.28
JmolVersion="14.4.0_2015.10.24"
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