Revision: 20244
http://sourceforge.net/p/jmol/code/20244
Author: hansonr
Date: 2015-01-27 13:49:18 +0000 (Tue, 27 Jan 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.01.26"
new feature: frame [1 3 5 6]
-- sets limited number of frames for animation and frame *
-- same as animation frame [1 3 5 6]; frame *
bug fix: @3 for "atomno=3" should not extend to models that are not part of the
current model set
-- commonly used for shortcut at the console
-- provides a function distinct from "atomno=3"
new feature: CGO PostScript option
bug fix: CGO LINE_LOOP not closing
bug fix: configuration 1 broken
bug fix: display configuration=1 broken (in Jmol 12.0, 2011)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/ScriptExpr.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-01-27
05:24:40 UTC (rev 20243)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-01-27
13:49:18 UTC (rev 20244)
@@ -278,7 +278,7 @@
return (i < 0 ? null : at[i].group.getQuaternion(qtype));
}
- public int getAtomIndexFromAtomNumber(int atomNumber, BS bsVisibleFrames) {
+ public int getFirstAtomIndexFromAtomNumber(int atomNumber, BS
bsVisibleFrames) {
//definitely want FIRST (model) not last here
for (int i = 0; i < ac; i++) {
Atom atom = at[i];
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-01-27 05:24:40 UTC
(rev 20243)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-01-27 13:49:18 UTC
(rev 20244)
@@ -4079,6 +4079,21 @@
return ret;
}
+ public BS getAtomsFromAtomNumberInFrame(int atomNumber) {
+ BS bs = new BS();
+ BS bsModels = vwr.getVisibleFramesBitSet();
+ for (int i = ac; --i >= 0;) {
+ Atom atom = at[i];
+ if (!bsModels.get(atom.mi)) {
+ i = am[atom.mi].firstAtomIndex;
+ continue;
+ }
+ if (atom.getAtomNumber() == atomNumber)
+ bs.set(i);
+ }
+ return bs;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-01-27 05:24:40 UTC
(rev 20243)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-01-27 13:49:18 UTC
(rev 20244)
@@ -2754,20 +2754,10 @@
vwr.setAnimDisplay(bs);
return;
case T.frame:
- if (isArrayParameter(2)) {
- int[] frames = expandFloatArray(
- floatParameterSet(2, 0, Integer.MAX_VALUE), 1);
- checkLength(iToken + 1);
- if (chk)
- return;
- Map<String, Object> movie = new Hashtable<String, Object>();
- if (frames.length > 0)
- movie.put("frames", frames);
- movie.put("currentFrame", Integer.valueOf(0));
- vwr.am.setMovie(movie);
- } else {
+ if (isArrayParameter(2))
+ setFrameSet(2);
+ else
cmdModel(2);
- }
break;
case T.mode:
float startDelay = 1,
@@ -2823,6 +2813,19 @@
}
}
+ private void setFrameSet(int i) throws ScriptException {
+ int[] frames = expandFloatArray(
+ floatParameterSet(i, 0, Integer.MAX_VALUE), 1);
+ checkLength(iToken + 1);
+ if (chk)
+ return;
+ Map<String, Object> movie = new Hashtable<String, Object>();
+ if (frames.length > 0)
+ movie.put("frames", frames);
+ movie.put("currentFrame", Integer.valueOf(0));
+ vwr.am.setMovie(movie);
+ }
+
private void cmdAxes(int index) throws ScriptException {
// axes (index==1) or set axes (index==2)
TickInfo tickInfo = tickParamAsStr(index, true, true, false);
@@ -4960,9 +4963,9 @@
}
/**
- * ONE difference between FRAME and MODEL:
- * model 1 sets model NAMED one in the case of PDB
- * frame 1 always sets the first model
+ * ONE difference between FRAME and MODEL: model 1 sets model NAMED one in
the
+ * case of PDB frame 1 always sets the first model
+ *
* @param offset
* @throws ScriptException
*/
@@ -4994,8 +4997,7 @@
return;
BS bsa = new BS();
bsa.set(i);
- vwr.setCurrentModelIndex(vwr.ms.getModelBS(bsa, false).nextSetBit(
- 0));
+ vwr.setCurrentModelIndex(vwr.ms.getModelBS(bsa, false).nextSetBit(0));
return;
case T.create:
iToken = 1;
@@ -5028,8 +5030,7 @@
if (checkLength23() > 0)
if (!chk)
vwr.setFrameTitleObj(slen == 2 ? "@{_modelName}"
- : (tokAt(2) == T.varray ? SV.strListValue(st[2])
- : paramAsStr(2)));
+ : (tokAt(2) == T.varray ? SV.strListValue(st[2]) :
paramAsStr(2)));
return;
case T.align:
BS bs = (slen == 2 || tokAt(2) == T.none ? null : atomExpressionAt(2));
@@ -5056,87 +5057,91 @@
int nFrames = 0;
float fFrame = 0;
boolean haveFileSet = vwr.haveFileSet();
-
- for (int i = offset; i < slen; i++) {
- switch (getToken(i).tok) {
- case T.all:
- case T.times:
- checkLength(offset + (isRange ? 2 : 1));
- isAll = true;
- break;
- case T.minus: // ignore
- if (nFrames != 1)
- invArg();
- isHyphen = true;
- break;
- case T.none:
- checkLength(offset + 1);
- break;
- case T.decimal:
- useModelNumber = false;
- if ((fFrame = floatParameter(i)) < 0) {
- checkLength(i + 1);
- if (!chk)
- vwr.am.morph(-fFrame);
- return;
- }
- //$FALL-THROUGH$
- case T.integer:
- case T.string:
- if (nFrames == 2)
- invArg();
- int iFrame = (theTok == T.string ? getFloatEncodedInt((String)
theToken.value)
- : theToken.intValue);
- if (iFrame < 0 && nFrames == 1) {
+ if (isArrayParameter(1)) {
+ setFrameSet(1);
+ isAll = true;
+ } else {
+ for (int i = offset; i < slen; i++) {
+ switch (getToken(i).tok) {
+ case T.all:
+ case T.times:
+ checkLength(offset + (isRange ? 2 : 1));
+ isAll = true;
+ break;
+ case T.minus: // ignore
+ if (nFrames != 1)
+ invArg();
isHyphen = true;
- iFrame = -iFrame;
- if (haveFileSet && iFrame < 1000000)
- iFrame *= 1000000;
- }
- if (theTok == T.decimal && haveFileSet && fFrame == (int) fFrame)
- iFrame = (int) fFrame * 1000000;
- if (iFrame == Integer.MAX_VALUE) {
- if (i == 1) {
- String id = theToken.value.toString();
- int modelIndex = (chk ? -1 : vwr.getModelIndexFromId(id));
- if (modelIndex >= 0) {
- checkLength(2);
- vwr.setCurrentModelIndex(modelIndex);
- return;
+ break;
+ case T.none:
+ checkLength(offset + 1);
+ break;
+ case T.decimal:
+ useModelNumber = false;
+ if ((fFrame = floatParameter(i)) < 0) {
+ checkLength(i + 1);
+ if (!chk)
+ vwr.am.morph(-fFrame);
+ return;
+ }
+ //$FALL-THROUGH$
+ case T.integer:
+ case T.string:
+ if (nFrames == 2)
+ invArg();
+ int iFrame = (theTok == T.string ? getFloatEncodedInt((String)
theToken.value)
+ : theToken.intValue);
+ if (iFrame < 0 && nFrames == 1) {
+ isHyphen = true;
+ iFrame = -iFrame;
+ if (haveFileSet && iFrame < 1000000)
+ iFrame *= 1000000;
+ }
+ if (theTok == T.decimal && haveFileSet && fFrame == (int) fFrame)
+ iFrame = (int) fFrame * 1000000;
+ if (iFrame == Integer.MAX_VALUE) {
+ if (i == 1) {
+ String id = theToken.value.toString();
+ int modelIndex = (chk ? -1 : vwr.getModelIndexFromId(id));
+ if (modelIndex >= 0) {
+ checkLength(2);
+ vwr.setCurrentModelIndex(modelIndex);
+ return;
+ }
}
+ iFrame = 0; // frame 0.0
}
- iFrame = 0; // frame 0.0
- }
- if (iFrame == -1) {
- checkLength(offset + 1);
- if (!chk)
- vwr.setAnimation(T.prev);
+ if (iFrame == -1) {
+ checkLength(offset + 1);
+ if (!chk)
+ vwr.setAnimation(T.prev);
+ return;
+ }
+ if (iFrame >= 1000 && iFrame < 1000000 && haveFileSet)
+ iFrame = (iFrame / 1000) * 1000000 + (iFrame % 1000); // initial
way
+ if (!useModelNumber && iFrame == 0 && nFrames == 0)
+ isAll = true; // 0.0 means ALL; 0 means "all in this range
+ if (iFrame >= 1000000)
+ useModelNumber = false;
+ frameList[nFrames++] = iFrame;
+ break;
+ case T.play:
+ isPlay = true;
+ break;
+ case T.range:
+ isRange = true;
+ break;
+ case T.property:
+ propName = stringParameter(3);
+ SV sv = setVariable(4, -1, "", false);
+ if (sv != null)
+ prop = SV.oValue(sv);
+ i = slen;
+ break;
+ default:
+ frameControl(offset);
return;
}
- if (iFrame >= 1000 && iFrame < 1000000 && haveFileSet)
- iFrame = (iFrame / 1000) * 1000000 + (iFrame % 1000); // initial way
- if (!useModelNumber && iFrame == 0 && nFrames == 0)
- isAll = true; // 0.0 means ALL; 0 means "all in this range
- if (iFrame >= 1000000)
- useModelNumber = false;
- frameList[nFrames++] = iFrame;
- break;
- case T.play:
- isPlay = true;
- break;
- case T.range:
- isRange = true;
- break;
- case T.property:
- propName = stringParameter(3);
- SV sv = setVariable(4, -1, "", false);
- if (sv != null)
- prop = SV.oValue(sv);
- i = slen;
- break;
- default:
- frameControl(offset);
- return;
}
}
if (isRange && nFrames == 0)
@@ -5160,7 +5165,7 @@
frameList[i] %= 1000000;
int modelIndex = vwr.ms.getModelNumberIndex(frameList[0], useModelNumber,
false);
-
+
int modelIndex2 = -1;
if (haveFileSet && modelIndex < 0 && frameList[0] != 0) {
// may have frame 2.0 or frame 2 meaning the range of models in file 2
Modified: trunk/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-01-27 05:24:40 UTC
(rev 20243)
+++ trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-01-27 13:49:18 UTC
(rev 20244)
@@ -2323,7 +2323,7 @@
v = (vt.tok == T.varray ? vt : SV.oValue(vt));
} else {
if (tokAt(i) == T.integer) {
- v = vwr.ms.getAtoms(T.atomno, Integer.valueOf(st[i].intValue));
+ v = vwr.ms.getAtomsFromAtomNumberInFrame(st[i].intValue);
} else {
v = getParameter(var, T.nada, true);
}
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-01-27 05:24:40 UTC
(rev 20243)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-01-27 13:49:18 UTC
(rev 20244)
@@ -1127,7 +1127,7 @@
ptFloat = (ptFloat + 1) % 2;
rangeMinMax[ptFloat] = iParam;
} else {
- atomIndex = vwr.getAtomIndexFromAtomNumber(iParam);
+ atomIndex = vwr.ms.getFirstAtomIndexFromAtomNumber(iParam,
vwr.getVisibleFramesBitSet());
if (!chk && atomIndex < 0)
return;
if (value != null)
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-27 05:24:40 UTC
(rev 20243)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-27 13:49:18 UTC
(rev 20244)
@@ -19,6 +19,14 @@
Jmol.___JmolVersion="14.3.12_2015.01.26"
+new feature: frame [1 3 5 6]
+ -- sets limited number of frames for animation and frame *
+ -- same as animation frame [1 3 5 6]; frame *
+
+bug fix: @3 for "atomno=3" should not extend to models that are not part of
the current model set
+ -- commonly used for shortcut at the console
+ -- provides a function distinct from "atomno=3"
+
new feature: CGO PostScript option
bug fix: CGO LINE_LOOP not closing
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-01-27 05:24:40 UTC (rev
20243)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-01-27 13:49:18 UTC (rev
20244)
@@ -2783,11 +2783,6 @@
null, atomIndexNot, allowCyclic, true);
}
- public int getAtomIndexFromAtomNumber(int atomNumber) {
- return ms.getAtomIndexFromAtomNumber(atomNumber,
- getVisibleFramesBitSet());
- }
-
@Override
public BS getElementsPresentBitSet(int modelIndex) {
return ms.getElementsPresentBitSet(modelIndex);
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
