Revision: 20275
http://sourceforge.net/p/jmol/code/20275
Author: hansonr
Date: 2015-02-09 13:10:40 +0000 (Mon, 09 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.02.09"
new feature: frame align {atoms} FIXED
-- shifts atom positions in each frame to match first atom in {atoms}
-- unlike just frame align {atoms}, frame * will still show alignment
-- objects such as DRAW and ISOSURFACE will NOT be shifted
-- needs testing
new feature: frame align [modelNo] [pt]
-- FIXED is assumed
-- used in state; shifts a model by a specific amount after removing any
current frame alignment
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/Model.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/Model.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Model.java 2015-02-08 18:38:27 UTC (rev
20274)
+++ trunk/Jmol/src/org/jmol/modelset/Model.java 2015-02-09 13:10:40 UTC (rev
20275)
@@ -33,7 +33,9 @@
import javajs.util.AU;
+import javajs.util.P3;
import javajs.util.SB;
+import javajs.util.T3;
import org.jmol.util.BSUtil;
@@ -96,6 +98,7 @@
public Properties properties;
public SymmetryInterface biosymmetry;
Map<String, Integer> dataFrames;
+ P3 translation;
int dataSourceFrame = -1;
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-02-08 18:38:27 UTC
(rev 20274)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-02-09 13:10:40 UTC
(rev 20275)
@@ -310,17 +310,82 @@
trajectory.morph(m1, m2, f);
}
- public P3[] getFrameOffsets(BS bsAtoms) {
- if (bsAtoms == null)
+ public P3[] translations;
+
+ public P3 getTranslation(int iModel) {
+ return (translations == null || iModel >= translations.length ? null :
translations[iModel]);
+ }
+
+ /**
+ * move atoms by vector pt; used for co-centering with FRAME ALIGN {atoms}
TRUE
+ *
+ * @param iModel
+ * @param pt
+ */
+ public void translateModel(int iModel, T3 pt) {
+ if (pt == null) {
+ P3 t = getTranslation(iModel);
+ if (t == null)
+ return;
+ pt = P3.newP(t);
+ pt.scale(-1);
+ translateModel(iModel, pt);
+ translations[iModel] = null;
+ return;
+ }
+ if (translations == null || translations.length <= iModel)
+ translations = new P3[mc];
+ if (translations[iModel] == null)
+ translations[iModel] = new P3();
+ translations[iModel].add(pt);
+ BS bs = am[iModel].bsAtoms;
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ at[i].add(pt);
+ }
+
+ public P3[] getFrameOffsets(BS bsAtoms, boolean isFull) {
+ if (bsAtoms == null) {
+ if (isFull)
+ for (int i = mc; --i >= 0;) {
+ Model m = am[i];
+ if (!m.isJmolDataFrame && !m.isTrajectory)
+ translateModel(m.modelIndex, null);
+ }
return null;
+ }
+ int i0 = bsAtoms.nextSetBit(0);
+ if (i0 < 0)
+ return null;
+ if (isFull) {
+ BS bs = BSUtil.copy(bsAtoms);
+ P3 pt = null;
+ P3 pdiff = new P3();
+ for (int i = 0; i < mc; i++) {
+ Model m = am[i];
+ if (!m.isJmolDataFrame && !m.isTrajectory) {
+ int j = bs.nextSetBit(0);
+ if (m.bsAtoms.get(j)) {
+ if (pt == null) {
+ pt = P3.newP(at[j]);
+ } else {
+ pdiff.sub2(pt, at[j]);
+ translateModel(i, pdiff);
+ }
+ }
+ }
+ bs.andNot(m.bsAtoms);
+ }
+ return null;
+ }
P3[] offsets = new P3[mc];
- for (int i = 0; i < mc; i++)
+ for (int i = mc; --i >= 0;)
offsets[i] = new P3();
int lastModel = 0;
int n = 0;
P3 offset = offsets[0];
boolean asTrajectory = (trajectory != null && trajectory.steps.size() ==
mc);
int m1 = (asTrajectory ? mc : 1);
+ offsets[0].set(0, 0, 0);
for (int m = 0; m < m1; m++) {
if (asTrajectory)
setTrajectory(m);
@@ -343,7 +408,6 @@
n++;
}
}
- offsets[0].set(0, 0, 0);
return offsets;
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-02-08 18:38:27 UTC
(rev 20274)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-02-09 13:10:40 UTC
(rev 20275)
@@ -5019,9 +5019,14 @@
: (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));
+ boolean isNone = (tokAt(2) == T.none);
+ BS bs = (slen == 2 || isNone ? null : atomExpressionAt(2));
+ if (isNone)
+ iToken = 2;
+ boolean isFixed = (tokAt(iToken + 1) == T.fixed);
+ checkLength(iToken + (isFixed ? 2 : 1));
if (!chk)
- vwr.setFrameOffsets(bs);
+ vwr.setFrameOffsets(bs, isFixed);
return;
}
if (getToken(offset).tok == T.minus) {
@@ -5042,6 +5047,7 @@
int[] frameList = new int[] { -1, -1 };
int nFrames = 0;
float fFrame = 0;
+ P3 frameAlign = null;
boolean haveFileSet = vwr.haveFileSet();
if (isArrayParameter(1)) {
setFrameSet(1);
@@ -5049,6 +5055,13 @@
} else {
for (int i = offset; i < slen; i++) {
switch (getToken(i).tok) {
+ case T.align:
+ // model 2.3 align {0 0 0} // from state
+ if (i != 2)
+ invArg();
+ frameAlign = centerParameter(3);
+ checkLength(i = iToken + 1);
+ break;
case T.all:
case T.times:
checkLength(offset + (isRange ? 2 : 1));
@@ -5088,14 +5101,11 @@
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 = (chk ? -2 : vwr.getModelIndexFromId(id));
+ } else {
+ iFrame = 0; // frame 0.0
}
- iFrame = 0; // frame 0.0
+ useModelNumber = false;
}
if (iFrame == -1) {
checkLength(offset + 1);
@@ -5130,10 +5140,10 @@
}
}
}
+ if (chk)
+ return;
if (isRange && nFrames == 0)
isAll = true;
- if (chk)
- return;
if (isAll) {
vwr.setAnimationOn(false);
vwr.setAnimationRange(-1, -1);
@@ -5151,7 +5161,13 @@
frameList[i] %= 1000000;
int modelIndex = vwr.ms.getModelNumberIndex(frameList[0], useModelNumber,
false);
-
+ if (frameAlign != null) {
+ if (modelIndex >= 0) {
+ vwr.ms.translateModel(modelIndex, null);
+ vwr.ms.translateModel(modelIndex, frameAlign);
+ }
+ return;
+ }
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/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-08 18:38:27 UTC
(rev 20274)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-09 13:10:40 UTC
(rev 20275)
@@ -15,8 +15,21 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
TODO: add 2D graphics panel for Ramachandran and NBO-style 2D graphics -- send
to browser as data uri?
-Jmol.___JmolVersion="14.3.12_2015.02.07"
+Jmol.___JmolVersion="14.3.12_2015.02.09"
+new feature: frame align {atoms} FIXED
+ -- shifts atom positions in each frame to match first atom in {atoms}
+ -- unlike just frame align {atoms}, frame * will still show alignment
+ -- objects such as DRAW and ISOSURFACE will NOT be shifted
+ -- needs testing
+
+new feature: frame align [modelNo] [pt]
+ -- FIXED is assumed
+ -- used in state; shifts a model by a specific amount after removing any
current frame alignment
+
+JmolVersion="14.3.12_2015.02.07"
+released
+
bug fix: set meshScale is not being applied to isosurface contours
bug fix: zoomTo{xxx} 0 does not center (broken in 13.1.16_dev_2013.05.23)
bug fix: appending a model to a model with data can fail
@@ -46,6 +59,7 @@
JmolVersion="14.3.12_2015.02.04"
+released
new feature: print data({*},"xyz")
-- (lower case) writes only atom data lines
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-02-08 18:38:27 UTC
(rev 20274)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-02-09 13:10:40 UTC
(rev 20275)
@@ -574,8 +574,15 @@
if (am.backgroundModelIndex >= 0)
app(commands, "set backgroundModel "
+ vwr.getModelNumberDotted(am.backgroundModelIndex));
- if (vwr.bsFrameOffsets != null)
- app(commands, "frame align " + Escape.eBS(vwr.bsFrameOffsets));
+ if (vwr.tm.bsFrameOffsets != null) {
+ app(commands, "frame align " + Escape.eBS(vwr.tm.bsFrameOffsets));
+ } else if (vwr.ms.translations != null) {
+ for (int i = modelCount; --i >= 0;) {
+ P3 t = (vwr.ms.getTranslation(i));
+ if (t != null)
+ app(commands, "frame " + vwr.ms.getModelNumberDotted(i) + " align "
+ t);
+ }
+ }
app(commands, "frame RANGE "
+ am.getModelSpecial(AnimationManager.FRAME_FIRST) + " "
+ am.getModelSpecial(AnimationManager.FRAME_LAST));
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2015-02-08
18:38:27 UTC (rev 20274)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2015-02-09
13:10:40 UTC (rev 20275)
@@ -1457,7 +1457,7 @@
matrixTransform.setIdentity();
// first, translate the coordinates back to the center
-
+
vectorTemp.sub2(frameOffset, fixedRotationCenter);
matrixTransform.setTranslation(vectorTemp);
@@ -2351,13 +2351,15 @@
****************************************************************/
final P3 frameOffset = new P3();
+ P3[] frameOffsets;
+ public BS bsFrameOffsets;
void setFrameOffset(int modelIndex) {
- if (vwr.frameOffsets == null || modelIndex < 0
- || modelIndex >= vwr.frameOffsets.length)
+ if (frameOffsets == null || modelIndex < 0
+ || modelIndex >= frameOffsets.length)
frameOffset.set(0, 0, 0);
else
- frameOffset.setT(vwr.frameOffsets[modelIndex]);
+ frameOffset.setT(frameOffsets[modelIndex]);
}
/////////// Allow during-rendering mouse operations ///////////
@@ -2643,6 +2645,7 @@
private JmolNavigatorInterface nav;
+
private void navInterrupt() {
if (nav != null)
nav.interrupt();
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-02-08 18:38:27 UTC (rev
20274)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-02-09 13:10:40 UTC (rev
20275)
@@ -2421,7 +2421,7 @@
}
public void clearModelDependentObjects() {
- setFrameOffsets(null);
+ setFrameOffsets(null, false);
stopMinimization();
minimizer = null;
smilesMatcher = null;
@@ -3073,11 +3073,13 @@
return (ms.trajectory == null ? "" : ms.trajectory.getState());
}
- BS bsFrameOffsets;
- P3[] frameOffsets;
-
- public void setFrameOffsets(BS bsAtoms) {
- frameOffsets = ms.getFrameOffsets(bsFrameOffsets = bsAtoms);
+ public void setFrameOffsets(BS bsAtoms, boolean isFull) {
+ tm.bsFrameOffsets = null;
+ if (isFull)
+ clearModelDependentObjects();
+ else
+ tm.bsFrameOffsets = bsAtoms;
+ tm.frameOffsets = ms.getFrameOffsets(bsAtoms, isFull);
}
public void setCurrentModelIndexClear(int modelIndex, boolean
clearBackground) {
@@ -7954,7 +7956,7 @@
BS bsModelAtoms) {
// called from ModelCollection.deleteModel
sm.modifySend(-1, modelIndex, 1, "delete atoms " +
Escape.eBS(bsModelAtoms));
- BSUtil.deleteBits(bsFrameOffsets, bsModelAtoms);
+ BSUtil.deleteBits(tm.bsFrameOffsets, bsModelAtoms);
getDataManager().deleteModelAtoms(firstAtomIndex, nAtoms, bsModelAtoms);
sm.modifySend(-1, modelIndex, -1, "OK");
}
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