Revision: 20918
http://sourceforge.net/p/jmol/code/20918
Author: hansonr
Date: 2016-01-04 12:48:02 +0000 (Mon, 04 Jan 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.1_2016.01.04"
bug fix: setting cartoons on for phosphorus-only polymers fails
bug fix: setting default label properties using select none;.... fails
bug fix: undocumented model-based draw [array of points] broken
-- points only
-- selects from visible frames (frame *, for example)
-- load cyclohexane_movie.xyz; frame *; draw @{{C5}.split().sub({1,0,0})
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/modelsetbio/PhosphorusPolymer.java
branches/v14_4/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
branches/v14_4/Jmol/src/org/jmol/renderbio/CartoonRenderer.java
branches/v14_4/Jmol/src/org/jmol/renderbio/NucleicRenderer.java
branches/v14_4/Jmol/src/org/jmol/shape/Labels.java
branches/v14_4/Jmol/src/org/jmol/shapespecial/Draw.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/modelsetbio/PhosphorusPolymer.java
trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
trunk/Jmol/src/org/jmol/renderbio/CartoonRenderer.java
trunk/Jmol/src/org/jmol/renderbio/NucleicRenderer.java
trunk/Jmol/src/org/jmol/shape/AtomShape.java
trunk/Jmol/src/org/jmol/shape/Labels.java
trunk/Jmol/src/org/jmol/shapespecial/Draw.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/modelsetbio/PhosphorusPolymer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelsetbio/PhosphorusPolymer.java
2016-01-04 12:37:07 UTC (rev 20917)
+++ branches/v14_4/Jmol/src/org/jmol/modelsetbio/PhosphorusPolymer.java
2016-01-04 12:48:02 UTC (rev 20918)
@@ -23,7 +23,7 @@
*/
package org.jmol.modelsetbio;
-class PhosphorusPolymer extends BioPolymer {
+public class PhosphorusPolymer extends BioPolymer {
PhosphorusPolymer(Monomer[] monomers) {
setP(monomers);
Modified: branches/v14_4/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
2016-01-04 12:37:07 UTC (rev 20917)
+++ branches/v14_4/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
2016-01-04 12:48:02 UTC (rev 20918)
@@ -26,10 +26,11 @@
import org.jmol.c.STR;
import org.jmol.java.BS;
-import org.jmol.modelset.Atom; //import org.jmol.modelsetbio.AlphaMonomer;
+import org.jmol.modelset.Atom;
import org.jmol.modelsetbio.CarbohydratePolymer;
import org.jmol.modelsetbio.Monomer;
-import org.jmol.modelsetbio.NucleicPolymer; //import
org.jmol.modelsetbio.ProteinStructure;
+import org.jmol.modelsetbio.NucleicPolymer;
+import org.jmol.modelsetbio.PhosphorusPolymer;
import org.jmol.render.MeshRenderer;
import org.jmol.script.T;
import org.jmol.shape.Mesh;
@@ -73,6 +74,7 @@
protected Monomer[] monomers;
protected boolean isNucleic;
+ protected boolean isPhosphorusOnly;
protected boolean isCarbohydrate;
protected BS bsVisible = new BS();
protected P3[] ribbonTopScreens;
@@ -224,6 +226,7 @@
// isNucleic = bioShape.bioPolymer.isNucleic();
isNucleic = bioShape.bioPolymer instanceof NucleicPolymer;
+ isPhosphorusOnly = !isNucleic && bioShape.bioPolymer instanceof
PhosphorusPolymer;
isCarbohydrate = bioShape.bioPolymer instanceof CarbohydratePolymer;
haveControlPointScreens = false;
wingVectors = bioShape.wingVectors;
Modified: branches/v14_4/Jmol/src/org/jmol/renderbio/CartoonRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/renderbio/CartoonRenderer.java
2016-01-04 12:37:07 UTC (rev 20917)
+++ branches/v14_4/Jmol/src/org/jmol/renderbio/CartoonRenderer.java
2016-01-04 12:48:02 UTC (rev 20918)
@@ -38,7 +38,7 @@
protected void renderBioShape(BioShape bioShape) {
if (!setupRR(bioShape, false))
return;
- if (isNucleic) {
+ if (isNucleic || isPhosphorusOnly) {
if (nucleicRenderer == null)
nucleicRenderer = (NucleicRenderer)
Interface.getInterface("org.jmol.renderbio.NucleicRenderer", vwr, "render");
calcScreenControlPoints();
@@ -75,6 +75,9 @@
boolean doRockets = false;
for (int i = monomerCount; --i >= 0;) {
// runs backwards, so it can render the heads first
+ if (monomers[i].getStructure() != null && !(monomers[i].getStructure()
instanceof ProteinStructure)) {
+ System.out.println("BUG HERE IN CARTOONRENDERER");
+ }
thisStructure = (ProteinStructure) monomers[i].getStructure();
if (thisStructure != previousStructure) {
lastWasSheet = false;
Modified: branches/v14_4/Jmol/src/org/jmol/renderbio/NucleicRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/renderbio/NucleicRenderer.java
2016-01-04 12:37:07 UTC (rev 20917)
+++ branches/v14_4/Jmol/src/org/jmol/renderbio/NucleicRenderer.java
2016-01-04 12:48:02 UTC (rev 20918)
@@ -101,14 +101,15 @@
}
private void renderNucleicBaseStep(int im) {
- NucleicMonomer nucleotide=
- (NucleicMonomer) bsr.monomers[im];
- short thisMad= bsr.mads[im];
- if (rScr[0] == null) {
- for (int i = 10; --i >= 0; )
+ if (bsr.isPhosphorusOnly)
+ return;
+ NucleicMonomer nucleotide = (NucleicMonomer) bsr.monomers[im];
+ short thisMad = bsr.mads[im];
+ if (rScr[0] == null) {
+ for (int i = 10; --i >= 0;)
rScr[i] = new P3();
- for (int i = 5; --i >= 0; )
- rScr5[i] = new P3();
+ for (int i = 5; --i >= 0;)
+ rScr5[i] = new P3();
baseScreen = new P3();
basePt = new P3();
rPt[9] = new P3(); // ribose center
@@ -163,8 +164,8 @@
basePt.setT(stepPt);
nucleotide.getRiboseRing5Points(rPt);
P3 c = rPt[9];
- c.set(0, 0, 0);
- for (int i = 0; i < 5; i++)
+ c.set(0, 0, 0);
+ for (int i = 0; i < 5; i++)
c.add(rPt[i]);
c.scale(0.2f);
transformPoints(10, rPt, rScr);
Modified: branches/v14_4/Jmol/src/org/jmol/shape/Labels.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shape/Labels.java 2016-01-04 12:37:07 UTC
(rev 20917)
+++ branches/v14_4/Jmol/src/org/jmol/shape/Labels.java 2016-01-04 12:48:02 UTC
(rev 20918)
@@ -140,6 +140,10 @@
setScaling();
LabelToken[][] tokens = null;
int nbs = checkStringLength(bsSelected.length());
+ if (defaultColix != C.INHERIT_ALL || defaultPaletteID != 0)
+ checkColixLength(defaultColix, bsSelected.length());
+ if (defaultBgcolix != C.INHERIT_ALL)
+ checkBgColixLength(defaultBgcolix, bsSelected.length());
if (value instanceof Lst) {
Lst<SV> list = (Lst<SV>) value;
int n = list.size();
@@ -490,9 +494,9 @@
setZPos(i, JC.LABEL_ZPOS_GROUP, true);
if (defaultPointer != JC.LABEL_POINTER_NONE)
setPointer(i, defaultPointer);
- if (defaultColix != 0 || defaultPaletteID != 0)
+ if (defaultColix != C.INHERIT_ALL || defaultPaletteID != 0)
setLabelColix(i, defaultColix, defaultPaletteID);
- if (defaultBgcolix != 0)
+ if (defaultBgcolix != C.INHERIT_ALL)
setBgcolix(i, defaultBgcolix);
if (defaultFontId != zeroFontId)
setFont(i, defaultFontId);
Modified: branches/v14_4/Jmol/src/org/jmol/shapespecial/Draw.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapespecial/Draw.java 2016-01-04
12:37:07 UTC (rev 20917)
+++ branches/v14_4/Jmol/src/org/jmol/shapespecial/Draw.java 2016-01-04
12:48:02 UTC (rev 20918)
@@ -357,7 +357,7 @@
modelInfo[1]++; // counts vertices
return;
}
-
+
if ("offset" == propertyName) {
offset = V3.newV((P3) value);
if (thisMesh != null)
@@ -366,9 +366,9 @@
}
if ("atomSet" == propertyName) {
- if (BSUtil.cardinalityOf((BS) value) == 0)
+ BS bsAtoms = (BS) value;
+ if (bsAtoms.isEmpty())
return;
- BS bsAtoms = (BS) value;
vData.addLast(new Object[] { Integer.valueOf(PT_BITSET), bsAtoms });
//nbitsets++;
if (isCircle && diameter == 0 && width == 0)
@@ -377,12 +377,12 @@
}
if ("coords" == propertyName) {
- addPoints(PT_COORD, value, false);
+ addPoints(PT_COORD, value);
return;
}
if ("modelBasedPoints" == propertyName) {
- addPoints(PT_MODEL_BASED_POINTS, value, true);
+ addPoints(PT_MODEL_BASED_POINTS, value);
return;
}
@@ -416,27 +416,38 @@
setPropertySuper(propertyName, value, bs);
}
- private void addPoints(int type, Object value, boolean allowNull) {
+ private void addPoints(int type, Object value) {
@SuppressWarnings("unchecked")
Lst<SV> pts = (Lst<SV>) value;
Integer key = Integer.valueOf(type);
+ boolean isModelPoints = (type == PT_MODEL_BASED_POINTS);
+ if (isModelPoints)
+ vData.addLast(new Object[] { key, pts });
for (int i = 0, n = pts.size(); i < n; i++) {
SV v = pts.get(i);
P3 pt;
switch (v.tok) {
case T.bitset:
- if (!allowNull && ((BS) v.value).isEmpty())
+ if (!isModelPoints && ((BS) v.value).isEmpty())
continue;
pt = vwr.ms.getAtomSetCenter((BS) v.value);
break;
+ case T.point3f:
+ if (isModelPoints)
+ continue;
+ //$FALL-THROUGH$
default:
pt = SV.ptValue(v);
}
- vData.addLast(new Object[] { key, pt });
+ if (isModelPoints) {
+ pts.set(i, SV.getVariable(pt));
+ } else {
+ vData.addLast(new Object[] { key, pt });
+ }
}
}
- private void deleteModels(int modelIndex) {
+private void deleteModels(int modelIndex) {
//int firstAtomDeleted = ((int[])((Object[])value)[2])[1];
//int nAtomsDeleted = ((int[])((Object[])value)[2])[2];
for (int i = meshCount; --i >= 0;) {
@@ -495,6 +506,13 @@
@Override
public boolean getPropertyData(String property, Object[] data) {
+ if (property == "keys") {
+ @SuppressWarnings("unchecked")
+ Lst<String> keys = (data[1] instanceof Lst<?> ? (Lst<String>) data[1] :
new Lst<String>());
+ data[1] = keys;
+ keys.addLast("getSpinAxis");
+ // will continue on to super
+ }
if (property == "getCenter") {
String id = (String) data[0];
int index = ((Integer) data[1]).intValue();
@@ -520,7 +538,7 @@
return getCommand(m);
if (property == "type")
return Integer.valueOf(m == null ? EnumDrawType.NONE.id : m.drawType.id);
- return getPropMC(property);
+ return getPropMC(property, index);
}
private T3 getSpinCenter(String axisID, int vertexIndex, int modelIndex) {
@@ -700,9 +718,8 @@
MeshSurface slabData;
private void addPoint(T3 newPt, int iModel) {
- boolean isOK = (iModel < 0 || bsAllModels.get(iModel));
if (makePoints) {
- if (!isOK)
+ if (newPt == null || iModel >= 0 && !bsAllModels.get(iModel))
return;
ptList[nPoints] = P3.newP(newPt);
if (newPt.z == Float.MAX_VALUE || newPt.z == -Float.MAX_VALUE)
@@ -822,6 +839,8 @@
bs.and(bsModel);
if (bs.length() > 0)
addPoint(vwr.ms.getAtomSetCenter(bs), j);
+ } else if (point instanceof SV) {
+ addPoint(SV.ptValue((SV) point), j);
}
}
break;
@@ -873,7 +892,8 @@
if (nVertices == 3 && isPlane)
isPlane = false;
length = Float.MAX_VALUE;
- thisMesh.diameter = 0;
+ if (isVector)
+ thisMesh.diameter = 0;
} else if (nVertices == 2 && isVector) {
ptList[1].add(ptList[0]);
}
@@ -1159,7 +1179,7 @@
T3 v = pickedMesh.vs[pickedMesh.pis[pickedModel][pickedVertex]];
int modelIndex = pickedMesh.modelIndex;
BS bs = ((DrawMesh) pickedMesh).modelFlags;
- if (modelIndex < 0 && bs != null && BSUtil.cardinalityOf(bs) == 1)
+ if (modelIndex < 0 && BSUtil.cardinalityOf(bs) == 1)
modelIndex = bs.nextSetBit(0);
Map<String, Object> map = null;
if (action != 0)
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-01-04
12:37:07 UTC (rev 20917)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-01-04
12:48:02 UTC (rev 20918)
@@ -7,7 +7,16 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.1_2016.01.01"
+Jmol.___JmolVersion="14.4.1_2016.01.04"
+
+bug fix: setting cartoons on for phosphorus-only polymers fails
+bug fix: setting default label properties using select none;.... fails
+bug fix: undocumented model-based draw [array of points] broken
+ -- points only
+ -- selects from visible frames (frame *, for example)
+ -- load cyclohexane_movie.xyz; frame *; draw @{{C5}.split().sub({1,0,0})
+
+JmolVersion="14.4.1_2016.01.01"
released
bug fix: file dropping of JVXL files does not work
Modified: trunk/Jmol/src/org/jmol/modelsetbio/PhosphorusPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/PhosphorusPolymer.java 2016-01-04
12:37:07 UTC (rev 20917)
+++ trunk/Jmol/src/org/jmol/modelsetbio/PhosphorusPolymer.java 2016-01-04
12:48:02 UTC (rev 20918)
@@ -23,7 +23,7 @@
*/
package org.jmol.modelsetbio;
-class PhosphorusPolymer extends BioPolymer {
+public class PhosphorusPolymer extends BioPolymer {
PhosphorusPolymer(Monomer[] monomers) {
setP(monomers);
Modified: trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java 2016-01-04
12:37:07 UTC (rev 20917)
+++ trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java 2016-01-04
12:48:02 UTC (rev 20918)
@@ -26,10 +26,11 @@
import org.jmol.c.STR;
import org.jmol.java.BS;
-import org.jmol.modelset.Atom; //import org.jmol.modelsetbio.AlphaMonomer;
+import org.jmol.modelset.Atom;
import org.jmol.modelsetbio.CarbohydratePolymer;
import org.jmol.modelsetbio.Monomer;
-import org.jmol.modelsetbio.NucleicPolymer; //import
org.jmol.modelsetbio.ProteinStructure;
+import org.jmol.modelsetbio.NucleicPolymer;
+import org.jmol.modelsetbio.PhosphorusPolymer;
import org.jmol.render.MeshRenderer;
import org.jmol.script.T;
import org.jmol.shape.Mesh;
@@ -73,6 +74,7 @@
protected Monomer[] monomers;
protected boolean isNucleic;
+ protected boolean isPhosphorusOnly;
protected boolean isCarbohydrate;
protected BS bsVisible = new BS();
protected P3[] ribbonTopScreens;
@@ -224,6 +226,7 @@
// isNucleic = bioShape.bioPolymer.isNucleic();
isNucleic = bioShape.bioPolymer instanceof NucleicPolymer;
+ isPhosphorusOnly = !isNucleic && bioShape.bioPolymer instanceof
PhosphorusPolymer;
isCarbohydrate = bioShape.bioPolymer instanceof CarbohydratePolymer;
haveControlPointScreens = false;
wingVectors = bioShape.wingVectors;
Modified: trunk/Jmol/src/org/jmol/renderbio/CartoonRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/CartoonRenderer.java 2016-01-04
12:37:07 UTC (rev 20917)
+++ trunk/Jmol/src/org/jmol/renderbio/CartoonRenderer.java 2016-01-04
12:48:02 UTC (rev 20918)
@@ -38,7 +38,7 @@
protected void renderBioShape(BioShape bioShape) {
if (!setupRR(bioShape, false))
return;
- if (isNucleic) {
+ if (isNucleic || isPhosphorusOnly) {
if (nucleicRenderer == null)
nucleicRenderer = (NucleicRenderer)
Interface.getInterface("org.jmol.renderbio.NucleicRenderer", vwr, "render");
calcScreenControlPoints();
@@ -75,6 +75,9 @@
boolean doRockets = false;
for (int i = monomerCount; --i >= 0;) {
// runs backwards, so it can render the heads first
+ if (monomers[i].getStructure() != null && !(monomers[i].getStructure()
instanceof ProteinStructure)) {
+ System.out.println("BUG HERE IN CARTOONRENDERER");
+ }
thisStructure = (ProteinStructure) monomers[i].getStructure();
if (thisStructure != previousStructure) {
lastWasSheet = false;
Modified: trunk/Jmol/src/org/jmol/renderbio/NucleicRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/NucleicRenderer.java 2016-01-04
12:37:07 UTC (rev 20917)
+++ trunk/Jmol/src/org/jmol/renderbio/NucleicRenderer.java 2016-01-04
12:48:02 UTC (rev 20918)
@@ -101,14 +101,15 @@
}
private void renderNucleicBaseStep(int im) {
- NucleicMonomer nucleotide=
- (NucleicMonomer) bsr.monomers[im];
- short thisMad= bsr.mads[im];
- if (rScr[0] == null) {
- for (int i = 10; --i >= 0; )
+ if (bsr.isPhosphorusOnly)
+ return;
+ NucleicMonomer nucleotide = (NucleicMonomer) bsr.monomers[im];
+ short thisMad = bsr.mads[im];
+ if (rScr[0] == null) {
+ for (int i = 10; --i >= 0;)
rScr[i] = new P3();
- for (int i = 5; --i >= 0; )
- rScr5[i] = new P3();
+ for (int i = 5; --i >= 0;)
+ rScr5[i] = new P3();
baseScreen = new P3();
basePt = new P3();
rPt[9] = new P3(); // ribose center
@@ -163,8 +164,8 @@
basePt.setT(stepPt);
nucleotide.getRiboseRing5Points(rPt);
P3 c = rPt[9];
- c.set(0, 0, 0);
- for (int i = 0; i < 5; i++)
+ c.set(0, 0, 0);
+ for (int i = 0; i < 5; i++)
c.add(rPt[i]);
c.scale(0.2f);
transformPoints(10, rPt, rScr);
Modified: trunk/Jmol/src/org/jmol/shape/AtomShape.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/AtomShape.java 2016-01-04 12:37:07 UTC
(rev 20917)
+++ trunk/Jmol/src/org/jmol/shape/AtomShape.java 2016-01-04 12:48:02 UTC
(rev 20918)
@@ -25,16 +25,14 @@
package org.jmol.shape;
+import javajs.util.AU;
+
import org.jmol.atomdata.RadiusData;
import org.jmol.atomdata.RadiusData.EnumType;
import org.jmol.c.PAL;
import org.jmol.c.VDW;
import org.jmol.java.BS;
import org.jmol.modelset.Atom;
-import org.jmol.modelset.Group;
-
-import javajs.util.AU;
-
import org.jmol.util.BSUtil;
import org.jmol.util.C;
Modified: trunk/Jmol/src/org/jmol/shape/Labels.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Labels.java 2016-01-04 12:37:07 UTC (rev
20917)
+++ trunk/Jmol/src/org/jmol/shape/Labels.java 2016-01-04 12:48:02 UTC (rev
20918)
@@ -140,6 +140,10 @@
setScaling();
LabelToken[][] tokens = null;
int nbs = checkStringLength(bsSelected.length());
+ if (defaultColix != C.INHERIT_ALL || defaultPaletteID != 0)
+ checkColixLength(defaultColix, bsSelected.length());
+ if (defaultBgcolix != C.INHERIT_ALL)
+ checkBgColixLength(defaultBgcolix, bsSelected.length());
if (value instanceof Lst) {
Lst<SV> list = (Lst<SV>) value;
int n = list.size();
@@ -490,9 +494,9 @@
setZPos(i, JC.LABEL_ZPOS_GROUP, true);
if (defaultPointer != JC.LABEL_POINTER_NONE)
setPointer(i, defaultPointer);
- if (defaultColix != 0 || defaultPaletteID != 0)
+ if (defaultColix != C.INHERIT_ALL || defaultPaletteID != 0)
setLabelColix(i, defaultColix, defaultPaletteID);
- if (defaultBgcolix != 0)
+ if (defaultBgcolix != C.INHERIT_ALL)
setBgcolix(i, defaultBgcolix);
if (defaultFontId != zeroFontId)
setFont(i, defaultFontId);
Modified: trunk/Jmol/src/org/jmol/shapespecial/Draw.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Draw.java 2016-01-04 12:37:07 UTC
(rev 20917)
+++ trunk/Jmol/src/org/jmol/shapespecial/Draw.java 2016-01-04 12:48:02 UTC
(rev 20918)
@@ -377,12 +377,12 @@
}
if ("coords" == propertyName) {
- addPoints(PT_COORD, value, false);
+ addPoints(PT_COORD, value);
return;
}
if ("modelBasedPoints" == propertyName) {
- addPoints(PT_MODEL_BASED_POINTS, value, true);
+ addPoints(PT_MODEL_BASED_POINTS, value);
return;
}
@@ -416,23 +416,34 @@
setPropertySuper(propertyName, value, bs);
}
- private void addPoints(int type, Object value, boolean allowNull) {
+ private void addPoints(int type, Object value) {
@SuppressWarnings("unchecked")
Lst<SV> pts = (Lst<SV>) value;
Integer key = Integer.valueOf(type);
+ boolean isModelPoints = (type == PT_MODEL_BASED_POINTS);
+ if (isModelPoints)
+ vData.addLast(new Object[] { key, pts });
for (int i = 0, n = pts.size(); i < n; i++) {
SV v = pts.get(i);
P3 pt;
switch (v.tok) {
case T.bitset:
- if (!allowNull && ((BS) v.value).isEmpty())
+ if (!isModelPoints && ((BS) v.value).isEmpty())
continue;
pt = vwr.ms.getAtomSetCenter((BS) v.value);
break;
+ case T.point3f:
+ if (isModelPoints)
+ continue;
+ //$FALL-THROUGH$
default:
pt = SV.ptValue(v);
}
- vData.addLast(new Object[] { key, pt });
+ if (isModelPoints) {
+ pts.set(i, SV.getVariable(pt));
+ } else {
+ vData.addLast(new Object[] { key, pt });
+ }
}
}
@@ -707,9 +718,8 @@
MeshSurface slabData;
private void addPoint(T3 newPt, int iModel) {
- boolean isOK = (iModel < 0 || bsAllModels.get(iModel));
if (makePoints) {
- if (!isOK)
+ if (newPt == null || iModel >= 0 && !bsAllModels.get(iModel))
return;
ptList[nPoints] = P3.newP(newPt);
if (newPt.z == Float.MAX_VALUE || newPt.z == -Float.MAX_VALUE)
@@ -829,6 +839,8 @@
bs.and(bsModel);
if (bs.length() > 0)
addPoint(vwr.ms.getAtomSetCenter(bs), j);
+ } else if (point instanceof SV) {
+ addPoint(SV.ptValue((SV) point), j);
}
}
break;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-01-04 12:37:07 UTC
(rev 20917)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-01-04 12:48:02 UTC
(rev 20918)
@@ -63,8 +63,17 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.1_2016.01.01"
+Jmol.___JmolVersion="14.5.1_2016.01.04"
+bug fix: setting default label properties using select none;.... fails
+bug fix: setting cartoons on for phosphorus-only polymers fails
+bug fix: undocumented model-based draw [array of points] broken
+ -- points only
+ -- selects from visible frames (frame *, for example)
+ -- load cyclohexane_movie.xyz; frame *; draw @{{C5}.split().sub({1,0,0})
+
+JmolVersion="14.5.1_2016.01.01"
+
bug fix: file dropping of JVXL files does not work
bug fix: Mesh capper not working for multiple cuts due to unclosed surface cut
-- for example: load maleic.cif 1;select on atomindex=6;lcaocartoon scale 1.0
CAP unitcell "cpk"
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