Revision: 20903
http://sourceforge.net/p/jmol/code/20903
Author: hansonr
Date: 2015-12-23 08:23:37 +0000 (Wed, 23 Dec 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.4.1_2015.12.23"
bug fix: PyMOL 1.8 PSE files cannot be read
bug fix: dots broken when colored none
bug fix: color cartoons red blue not saved in state
bug fix: color cartoons red blue flipping red/blue in sheets
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/render/MeshRenderer.java
branches/v14_4/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
branches/v14_4/Jmol/src/org/jmol/shape/AtomShape.java
branches/v14_4/Jmol/src/org/jmol/shapebio/BioShape.java
branches/v14_4/Jmol/src/org/jmol/shapebio/BioShapeCollection.java
branches/v14_4/Jmol/src/org/jmol/shapespecial/Dots.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_4/Jmol/src/org/jmol/viewer/JmolStateCreator.java
branches/v14_4/Jmol/src/org/jmol/viewer/StateCreator.java
branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/jmol/render/MeshRenderer.java
trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
trunk/Jmol/src/org/jmol/shape/AtomShape.java
trunk/Jmol/src/org/jmol/shapebio/BioShape.java
trunk/Jmol/src/org/jmol/shapebio/BioShapeCollection.java
trunk/Jmol/src/org/jmol/shapespecial/Dots.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/JmolStateCreator.java
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: branches/v14_4/Jmol/src/org/jmol/render/MeshRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/render/MeshRenderer.java 2015-12-23
04:42:24 UTC (rev 20902)
+++ branches/v14_4/Jmol/src/org/jmol/render/MeshRenderer.java 2015-12-23
08:23:37 UTC (rev 20903)
@@ -25,8 +25,15 @@
+import javajs.util.AU;
+import javajs.util.M4;
+import javajs.util.P3;
+import javajs.util.P3i;
+import javajs.util.P4;
+import javajs.util.T3;
+import javajs.util.V3;
+
import org.jmol.api.SymmetryInterface;
-import org.jmol.g3d.Graphics3D;
import org.jmol.java.BS;
import org.jmol.script.T;
import org.jmol.shape.Mesh;
@@ -34,14 +41,6 @@
import org.jmol.util.GData;
import org.jmol.util.MeshSurface;
-import javajs.util.AU;
-import javajs.util.M4;
-import javajs.util.P3;
-import javajs.util.P3i;
-import javajs.util.P4;
-import javajs.util.T3;
-import javajs.util.V3;
-
/**
* an abstract class subclasssed by BioShapeRenderer, DrawRenderer, and
IsosurfaceRenderer
*/
Modified: branches/v14_4/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
2015-12-23 04:42:24 UTC (rev 20902)
+++ branches/v14_4/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
2015-12-23 08:23:37 UTC (rev 20903)
@@ -404,10 +404,10 @@
// cartoons and meshRibbon
setNeighbors(i);
- colix = getLeadColix(i);
+ short c0 = colix = getLeadColix(i);
if (!setBioColix(colix))
return;
- colixBack = getLeadColixBack(i);
+ short cb = colixBack = getLeadColixBack(i);
if (doFill && (aspectRatio != 0 || isExport)) {
if (setMads(i, thisTypeOnly) || isExport) {
try {
@@ -415,22 +415,31 @@
&& !createMesh(i, madBeg, madMid, madEnd, aspectRatio, isNucleic
? 4 : 7))
return;
meshes[i].setColix(colix);
- meshes[i].setColixBack(colixBack);
+ meshes[i].setColixBack(cb);
bsRenderMesh.set(i);
- return;
} catch (Exception e) {
bsRenderMesh.clear(i);
meshes[i] = null;
Logger.error("render mesh error hermiteRibbon: " + e.toString());
//System.out.println(e.getMessage());
}
+ return;
}
}
- g3d.drawHermite7(doFill, ribbonBorder, (reversed.get(i) ? -1 : 1) *
(isNucleic ? 4 : 7),
+ boolean isReversed = reversed.get(i);
+ if (isReversed && colixBack != 0) {
+ setColix(colixBack);
+ cb = c0;
+ }
+ g3d.drawHermite7(doFill, ribbonBorder, (isReversed ? -1 : 1) * (isNucleic
? 4 : 7),
ribbonTopScreens[iPrev], ribbonTopScreens[i], ribbonTopScreens[iNext],
ribbonTopScreens[iNext2], ribbonBottomScreens[iPrev],
ribbonBottomScreens[i], ribbonBottomScreens[iNext],
- ribbonBottomScreens[iNext2], (int) aspectRatio, colixBack);
+ ribbonBottomScreens[iNext2], (int) aspectRatio, cb);
+ if (isReversed && colixBack != 0) {
+ setColix(c0);
+ cb = colixBack;
+ }
}
//// cardinal hermite (box or flat) arrow head (cartoon)
Modified: branches/v14_4/Jmol/src/org/jmol/shape/AtomShape.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shape/AtomShape.java 2015-12-23
04:42:24 UTC (rev 20902)
+++ branches/v14_4/Jmol/src/org/jmol/shape/AtomShape.java 2015-12-23
08:23:37 UTC (rev 20903)
@@ -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;
@@ -53,10 +51,6 @@
public int monomerCount;
public BS bsSizeDefault;
- public Group[] getMonomers() {
- return null;
- }
-
@Override
public void initShape() {
// nothing to do
@@ -167,13 +161,8 @@
if ("translucency" == propertyName) {
isActive = true;
boolean isTranslucent = (value.equals("translucent"));
- if (bsColixSet == null)
- bsColixSet = new BS();
+ checkColixLength(C.BLACK, ac);
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
- if (colixes == null) {
- colixes = new short[ac];
- paletteIDs = new byte[ac];
- }
colixes[i] = C.getColixTranslucent3(colixes[i], isTranslucent,
translucentLevel);
if (isTranslucent)
Modified: branches/v14_4/Jmol/src/org/jmol/shapebio/BioShape.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapebio/BioShape.java 2015-12-23
04:42:24 UTC (rev 20902)
+++ branches/v14_4/Jmol/src/org/jmol/shapebio/BioShape.java 2015-12-23
08:23:37 UTC (rev 20903)
@@ -25,10 +25,15 @@
package org.jmol.shapebio;
+import java.util.Map;
+
+import javajs.util.AU;
+import javajs.util.PT;
+import javajs.util.V3;
+
import org.jmol.c.PAL;
import org.jmol.java.BS;
import org.jmol.modelset.Atom;
-import org.jmol.modelset.Group;
import org.jmol.modelset.ModelSet;
import org.jmol.modelsetbio.AlphaPolymer;
import org.jmol.modelsetbio.BioPolymer;
@@ -37,11 +42,9 @@
import org.jmol.modelsetbio.NucleicPolymer;
import org.jmol.shape.AtomShape;
import org.jmol.shape.Mesh;
+import org.jmol.util.BSUtil;
import org.jmol.util.C;
import org.jmol.util.Logger;
-
-import javajs.util.AU;
-import javajs.util.V3;
import org.jmol.viewer.JC;
public class BioShape extends AtomShape {
@@ -66,11 +69,6 @@
public Monomer[] monomers;
- @Override
- public Group[] getMonomers() {
- return monomers;
- }
-
public V3[] wingVectors;
int[] leadAtomIndices;
@@ -285,29 +283,39 @@
void setColixBS(short colix, byte pid, BS bsSelected) {
isActive = true;
if (bsColixSet == null)
- bsColixSet = new BS();
+ bsColixSet = BS.newN(monomerCount);
for (int i = monomerCount; --i >= 0;) {
int atomIndex = leadAtomIndices[i];
if (bsSelected.get(atomIndex)) {
colixes[i] = shape.getColixI(colix, pid, atomIndex);
if (colixesBack != null && colixesBack.length > i)
- colixesBack[i] = 0;
+ colixesBack[i] = C.INHERIT_ALL;
paletteIDs[i] = pid;
bsColixSet.setBitTo(i, colixes[i] != C.INHERIT_ALL);
}
}
}
+ void setColixBack(short colix, BS bsSelected) {
+ if (colixesBack == null)
+ colixesBack = new short[colixes.length];
+ if (colixesBack.length < colixes.length)
+ colixesBack = AU.ensureLengthShort(colixesBack, colixes.length);
+ for (int i = monomerCount; --i >= 0;)
+ if (bsSelected.get(leadAtomIndices[i]))
+ colixesBack[i] = colix;
+ }
+
void setColixes(short[] atomColixes, BS bsSelected) {
isActive = true;
if (bsColixSet == null)
- bsColixSet = new BS();
+ bsColixSet = BS.newN(monomerCount);
for (int i = monomerCount; --i >= 0;) {
int atomIndex = leadAtomIndices[i];
if (bsSelected.get(atomIndex) && i < colixes.length && atomIndex <
atomColixes.length) {
colixes[i] = shape.getColixI(atomColixes[atomIndex], PAL.UNKNOWN.id,
atomIndex);
if (colixesBack != null && i < colixesBack.length)
- colixesBack[i] = 0;
+ colixesBack[i] = C.INHERIT_ALL;
paletteIDs[i] = PAL.UNKNOWN.id;
bsColixSet.set(i);
}
@@ -325,7 +333,7 @@
isActive = true;
if (bsColixSet == null)
- bsColixSet = new BS();
+ bsColixSet = BS.newN(monomerCount);
int n = atomMap.length;
for (int i = monomerCount; --i >= 0;) {
int atomIndex = leadAtomIndices[i];
@@ -344,25 +352,10 @@
}
}
-
-
- void setColixBack(short colix, BS bsSelected) {
- for (int i = monomerCount; --i >= 0;) {
- int atomIndex = leadAtomIndices[i];
- if (bsSelected.get(atomIndex)) {
- if (colixesBack == null)
- colixesBack = new short[colixes.length];
- if (colixesBack.length < colixes.length)
- colixesBack = AU.ensureLengthShort(colixesBack, colixes.length);
- colixesBack[i] = colix;
- }
- }
- }
-
void setTranslucent(boolean isTranslucent, BS bsSelected, float
translucentLevel) {
isActive = true;
if (bsColixSet == null)
- bsColixSet = new BS();
+ bsColixSet = BS.newN(monomerCount);
for (int i = monomerCount; --i >= 0; )
if (bsSelected.get(leadAtomIndices[i])) {
colixes[i] = C.getColixTranslucent3(colixes[i], isTranslucent,
translucentLevel);
@@ -392,4 +385,34 @@
}
}
+ void getBioShapeState(String type, boolean translucentAllowed,
+ Map<String, BS> temp, Map<String, BS> temp2) {
+ if (monomerCount > 0) {
+ if (!isActive || bsSizeSet == null && bsColixSet == null)
+ return;
+ for (int i = 0; i < monomerCount; i++) {
+ int atomIndex1 = monomers[i].firstAtomIndex;
+ int atomIndex2 = monomers[i].lastAtomIndex;
+ if (bsSizeSet != null
+ && (bsSizeSet.get(i) || bsColixSet != null && bsColixSet.get(i)))
{//shapes MUST have been set with a size
+ if (bsSizeDefault.get(i)) {
+ BSUtil.setMapBitSet(temp, atomIndex1, atomIndex2,
+ type + (bsSizeSet.get(i) ? " on" : " off"));
+ } else {
+ BSUtil.setMapBitSet(temp, atomIndex1, atomIndex2,
+ type + " " + PT.escF(mads[i] / 2000f));
+ }
+ }
+ if (bsColixSet == null || !bsColixSet.get(i))
+ continue;
+ String s = getColorCommand(type, paletteIDs[i], colixes[i],
+ translucentAllowed);
+ if (colixesBack != null && colixesBack.length > i
+ && colixesBack[i] != C.INHERIT_ALL)
+ s += " " + C.getHexCode(colixesBack[i]);
+ BSUtil.setMapBitSet(temp2, atomIndex1, atomIndex2, s);
+ }
+ }
+ }
+
}
\ No newline at end of file
Modified: branches/v14_4/Jmol/src/org/jmol/shapebio/BioShapeCollection.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapebio/BioShapeCollection.java
2015-12-23 04:42:24 UTC (rev 20902)
+++ branches/v14_4/Jmol/src/org/jmol/shapebio/BioShapeCollection.java
2015-12-23 08:23:37 UTC (rev 20903)
@@ -25,6 +25,11 @@
package org.jmol.shapebio;
+import java.util.Hashtable;
+import java.util.Map;
+
+import javajs.util.AU;
+
import org.jmol.atomdata.RadiusData;
import org.jmol.c.PAL;
import org.jmol.java.BS;
@@ -35,11 +40,9 @@
import org.jmol.modelsetbio.BioPolymer;
import org.jmol.modelsetbio.Monomer;
import org.jmol.shape.Shape;
-
-import javajs.util.AU;
-
import org.jmol.util.BSUtil;
import org.jmol.util.C;
+import org.jmol.viewer.JC;
/****************************************************************
* Mps stands for Model-Polymer-Shape
*
@@ -180,7 +183,7 @@
for (int i = bioShapes.length; --i >= 0;) {
BioShape bioShape = bioShapes[i];
if (bioShape.monomerCount > 0) {
- bioShape.setColixBS(colix, (byte) 0, bsSelected);
+ bioShape.setColixBS(colix, PAL.PALETTE_VOLATILE, bsSelected);
bioShape.setColixBack(colixBack, bsSelected);
}
}
@@ -201,9 +204,19 @@
@Override
public String getShapeState() {
- return vwr.getAtomShapeSetState(this, bioShapes);
+ // leaving this here because it is so specialized
+ Map<String, BS> temp = new Hashtable<String, BS>();
+ Map<String, BS> temp2 = new Hashtable<String, BS>();
+ String type = JC.shapeClassBases[shapeID];
+ for (int iShape = bioShapes.length; --iShape >= 0;)
+ bioShapes[iShape].getBioShapeState(type, translucentAllowed, temp,
temp2);
+ String s = "\n"
+ + vwr.getCommands(temp, temp2,
+ shapeID == JC.SHAPE_BACKBONE ? "Backbone" : "select");
+ return s;
}
+
void initialize() {
int modelCount = ms.mc;
Model[] models = ms.am;
Modified: branches/v14_4/Jmol/src/org/jmol/shapespecial/Dots.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapespecial/Dots.java 2015-12-23
04:42:24 UTC (rev 20902)
+++ branches/v14_4/Jmol/src/org/jmol/shapespecial/Dots.java 2015-12-23
08:23:37 UTC (rev 20903)
@@ -141,10 +141,8 @@
ec.setMads(mads);
}
mads[thisAtom] = (short) (thisRadius * 1000f);
- if (colixes == null) {
- colixes = new short[ac];
- paletteIDs = new byte[ac];
- }
+ if (colixes == null)
+ checkColixLength(C.BLACK, ac);
colixes[thisAtom] = C.getColix(thisArgb);
bsOn.set(thisAtom);
//all done!
@@ -271,10 +269,8 @@
}
// now, calculate surface for selected atoms
- if (dotsConvexMaps == null && (colixes == null || colixes.length != ac)) {
- colixes = new short[ac];
- paletteIDs = new byte[ac];
- }
+ if (dotsConvexMaps == null && (colixes == null || colixes.length != ac))
+ checkColixLength(C.BLACK, ac);
ec.calculate(rd, maxRadius, bsOn, bsIgnore, !vwr.getBoolean(T.dotsurface),
vwr.getBoolean(T.dotsselectedonly), isSurface, true);
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-23
04:42:24 UTC (rev 20902)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-23
08:23:37 UTC (rev 20903)
@@ -7,9 +7,12 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.1_2015.12.22"
+Jmol.___JmolVersion="14.4.1_2015.12.23"
bug fix: PyMOL 1.8 PSE files cannot be read
+bug fix: dots broken when colored none
+bug fix: color cartoons red blue not saved in state
+bug fix: color cartoons red blue flipping red/blue in sheets
JmolVersion="14.4.1_2015.12.21"
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/JmolStateCreator.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/JmolStateCreator.java
2015-12-23 04:42:24 UTC (rev 20902)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/JmolStateCreator.java
2015-12-23 08:23:37 UTC (rev 20903)
@@ -2,18 +2,17 @@
import java.util.Map;
+import javajs.awt.Font;
+import javajs.util.Lst;
+import javajs.util.SB;
+
import org.jmol.java.BS;
-import org.jmol.modelset.Group;
import org.jmol.modelset.Measurement;
import org.jmol.modelset.TickInfo;
import org.jmol.shape.AtomShape;
import org.jmol.shape.Measures;
import org.jmol.shape.Shape;
-import javajs.awt.Font;
-import javajs.util.Lst;
-import javajs.util.SB;
-
public abstract class JmolStateCreator {
abstract void setViewer(Viewer vwr);
@@ -31,16 +30,11 @@
abstract String getFontLineShapeState(String s, String myType, TickInfo[]
tickInfos);
- abstract void getShapeSetState(AtomShape atomShape, Shape shape, int
monomerCount, Group[] monomers,
- BS bsSizeDefault, Map<String, BS> temp, Map<String, BS>
temp2);
-
abstract String getMeasurementState(Measures shape, Lst<Measurement> mList,
int measurementCount,
Font font3d, TickInfo tickInfo);
abstract String getBondState(Shape shape, BS bsOrderSet, boolean reportAll);
- abstract String getAtomShapeSetState(Shape shape, AtomShape[] shapes);
-
abstract String getShapeState(Shape shape);
abstract String getCommands(Map<String, BS> htDefine, Map<String, BS> htMore,
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/StateCreator.java 2015-12-23
04:42:24 UTC (rev 20902)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/StateCreator.java 2015-12-23
08:23:37 UTC (rev 20903)
@@ -23,17 +23,16 @@
package org.jmol.viewer;
-import javajs.awt.Font;
-import javajs.util.Lst;
-import javajs.util.PT;
-import javajs.util.SB;
-
import java.util.Arrays;
import java.util.Date;
import java.util.Hashtable;
import java.util.Map;
+import javajs.awt.Font;
+import javajs.util.Lst;
import javajs.util.P3;
+import javajs.util.PT;
+import javajs.util.SB;
import org.jmol.api.JmolDataManager;
import org.jmol.api.JmolModulationSet;
@@ -47,7 +46,6 @@
import org.jmol.modelset.AtomCollection;
import org.jmol.modelset.Bond;
import org.jmol.modelset.BondSet;
-import org.jmol.modelset.Group;
import org.jmol.modelset.Measurement;
import org.jmol.modelset.Model;
import org.jmol.modelset.ModelSet;
@@ -968,33 +966,6 @@
}
@Override
- void getShapeSetState(AtomShape as, Shape shape, int monomerCount,
- Group[] monomers, BS bsSizeDefault,
- Map<String, BS> temp, Map<String, BS> temp2) {
- String type = JC.shapeClassBases[shape.shapeID];
- for (int i = 0; i < monomerCount; i++) {
- int atomIndex1 = monomers[i].firstAtomIndex;
- int atomIndex2 = monomers[i].lastAtomIndex;
- if (as.bsSizeSet != null
- && (as.bsSizeSet.get(i) || as.bsColixSet != null
- && as.bsColixSet.get(i))) {//shapes MUST have been set with a
size
- if (bsSizeDefault.get(i)) {
- BSUtil.setMapBitSet(temp, atomIndex1, atomIndex2, type
- + (as.bsSizeSet.get(i) ? " on" : " off"));
- } else {
-
- BSUtil.setMapBitSet(temp, atomIndex1, atomIndex2, type + " "
- + PT.escF(as.mads[i] / 2000f));
- }
- }
- if (as.bsColixSet != null && as.bsColixSet.get(i))
- BSUtil.setMapBitSet(temp2, atomIndex1, atomIndex2, Shape
- .getColorCommand(type, as.paletteIDs[i], as.colixes[i],
- shape.translucentAllowed));
- }
- }
-
- @Override
String getMeasurementState(Measures shape,
Lst<Measurement> mList,
int measurementCount, Font font3d,
@@ -1121,25 +1092,6 @@
}
@Override
- String getAtomShapeSetState(Shape shape, AtomShape[] bioShapes) {
- clearTemp();
- for (int i = bioShapes.length; --i >= 0;) {
- AtomShape bs = bioShapes[i];
- if (bs.monomerCount > 0) {
- if (!bs.isActive || bs.bsSizeSet == null && bs.bsColixSet == null)
- continue;
- vwr.getShapeSetState(bs, shape, bs.monomerCount, bs.getMonomers(),
- bs.bsSizeDefault, temp, temp2);
- }
- }
- String s = "\n"
- + getCommands(temp, temp2,
- shape.shapeID == JC.SHAPE_BACKBONE ? "Backbone" : "select");
- clearTemp();
- return s;
- }
-
- @Override
String getShapeState(Shape shape) {
String s;
switch (shape.shapeID) {
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2015-12-23 04:42:24 UTC
(rev 20902)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2015-12-23 08:23:37 UTC
(rev 20903)
@@ -8972,15 +8972,6 @@
return getStateCreator().getFontLineShapeState(s, myType, tickInfos);
}
- public void getShapeSetState(AtomShape atomShape, Shape shape,
- int monomerCount, Group[] monomers,
- BS bsSizeDefault, Map<String, BS> temp,
- Map<String, BS> temp2) {
- getStateCreator().getShapeSetState(atomShape, shape, monomerCount,
- monomers, bsSizeDefault, temp, temp2);
-
- }
-
public String getMeasurementState(Measures measures, Lst<Measurement> mList,
int measurementCount, Font font3d,
TickInfo ti) {
@@ -8992,10 +8983,6 @@
return getStateCreator().getBondState(shape, bsOrderSet, reportAll);
}
- public String getAtomShapeSetState(Shape shape, AtomShape[] shapes) {
- return getStateCreator().getAtomShapeSetState(shape, shapes);
- }
-
public String getShapeState(Shape shape) {
return getStateCreator().getShapeState(shape);
}
Modified: trunk/Jmol/src/org/jmol/render/MeshRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/MeshRenderer.java 2015-12-23 04:42:24 UTC
(rev 20902)
+++ trunk/Jmol/src/org/jmol/render/MeshRenderer.java 2015-12-23 08:23:37 UTC
(rev 20903)
@@ -25,8 +25,15 @@
+import javajs.util.AU;
+import javajs.util.M4;
+import javajs.util.P3;
+import javajs.util.P3i;
+import javajs.util.P4;
+import javajs.util.T3;
+import javajs.util.V3;
+
import org.jmol.api.SymmetryInterface;
-import org.jmol.g3d.Graphics3D;
import org.jmol.java.BS;
import org.jmol.script.T;
import org.jmol.shape.Mesh;
@@ -34,14 +41,6 @@
import org.jmol.util.GData;
import org.jmol.util.MeshSurface;
-import javajs.util.AU;
-import javajs.util.M4;
-import javajs.util.P3;
-import javajs.util.P3i;
-import javajs.util.P4;
-import javajs.util.T3;
-import javajs.util.V3;
-
/**
* an abstract class subclasssed by BioShapeRenderer, DrawRenderer, and
IsosurfaceRenderer
*/
Modified: trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java 2015-12-23
04:42:24 UTC (rev 20902)
+++ trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java 2015-12-23
08:23:37 UTC (rev 20903)
@@ -404,10 +404,10 @@
// cartoons and meshRibbon
setNeighbors(i);
- colix = getLeadColix(i);
+ short c0 = colix = getLeadColix(i);
if (!setBioColix(colix))
return;
- colixBack = getLeadColixBack(i);
+ short cb = colixBack = getLeadColixBack(i);
if (doFill && (aspectRatio != 0 || isExport)) {
if (setMads(i, thisTypeOnly) || isExport) {
try {
@@ -415,22 +415,31 @@
&& !createMesh(i, madBeg, madMid, madEnd, aspectRatio, isNucleic
? 4 : 7))
return;
meshes[i].setColix(colix);
- meshes[i].setColixBack(colixBack);
+ meshes[i].setColixBack(cb);
bsRenderMesh.set(i);
- return;
} catch (Exception e) {
bsRenderMesh.clear(i);
meshes[i] = null;
Logger.error("render mesh error hermiteRibbon: " + e.toString());
//System.out.println(e.getMessage());
}
+ return;
}
}
- g3d.drawHermite7(doFill, ribbonBorder, (reversed.get(i) ? -1 : 1) *
(isNucleic ? 4 : 7),
+ boolean isReversed = reversed.get(i);
+ if (isReversed && colixBack != 0) {
+ setColix(colixBack);
+ cb = c0;
+ }
+ g3d.drawHermite7(doFill, ribbonBorder, (isReversed ? -1 : 1) * (isNucleic
? 4 : 7),
ribbonTopScreens[iPrev], ribbonTopScreens[i], ribbonTopScreens[iNext],
ribbonTopScreens[iNext2], ribbonBottomScreens[iPrev],
ribbonBottomScreens[i], ribbonBottomScreens[iNext],
- ribbonBottomScreens[iNext2], (int) aspectRatio, colixBack);
+ ribbonBottomScreens[iNext2], (int) aspectRatio, cb);
+ if (isReversed && colixBack != 0) {
+ setColix(c0);
+ cb = colixBack;
+ }
}
//// cardinal hermite (box or flat) arrow head (cartoon)
Modified: trunk/Jmol/src/org/jmol/shape/AtomShape.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/AtomShape.java 2015-12-23 04:42:24 UTC
(rev 20902)
+++ trunk/Jmol/src/org/jmol/shape/AtomShape.java 2015-12-23 08:23:37 UTC
(rev 20903)
@@ -53,10 +53,6 @@
public int monomerCount;
public BS bsSizeDefault;
- public Group[] getMonomers() {
- return null;
- }
-
@Override
public void initShape() {
// nothing to do
@@ -167,13 +163,8 @@
if ("translucency" == propertyName) {
isActive = true;
boolean isTranslucent = (value.equals("translucent"));
- if (bsColixSet == null)
- bsColixSet = new BS();
+ checkColixLength(C.BLACK, ac);
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
- if (colixes == null) {
- colixes = new short[ac];
- paletteIDs = new byte[ac];
- }
colixes[i] = C.getColixTranslucent3(colixes[i], isTranslucent,
translucentLevel);
if (isTranslucent)
Modified: trunk/Jmol/src/org/jmol/shapebio/BioShape.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/BioShape.java 2015-12-23 04:42:24 UTC
(rev 20902)
+++ trunk/Jmol/src/org/jmol/shapebio/BioShape.java 2015-12-23 08:23:37 UTC
(rev 20903)
@@ -25,10 +25,15 @@
package org.jmol.shapebio;
+import java.util.Map;
+
+import javajs.util.AU;
+import javajs.util.PT;
+import javajs.util.V3;
+
import org.jmol.c.PAL;
import org.jmol.java.BS;
import org.jmol.modelset.Atom;
-import org.jmol.modelset.Group;
import org.jmol.modelset.ModelSet;
import org.jmol.modelsetbio.AlphaPolymer;
import org.jmol.modelsetbio.BioPolymer;
@@ -37,11 +42,9 @@
import org.jmol.modelsetbio.NucleicPolymer;
import org.jmol.shape.AtomShape;
import org.jmol.shape.Mesh;
+import org.jmol.util.BSUtil;
import org.jmol.util.C;
import org.jmol.util.Logger;
-
-import javajs.util.AU;
-import javajs.util.V3;
import org.jmol.viewer.JC;
public class BioShape extends AtomShape {
@@ -66,11 +69,6 @@
public Monomer[] monomers;
- @Override
- public Group[] getMonomers() {
- return monomers;
- }
-
public V3[] wingVectors;
int[] leadAtomIndices;
@@ -285,29 +283,39 @@
void setColixBS(short colix, byte pid, BS bsSelected) {
isActive = true;
if (bsColixSet == null)
- bsColixSet = new BS();
+ bsColixSet = BS.newN(monomerCount);
for (int i = monomerCount; --i >= 0;) {
int atomIndex = leadAtomIndices[i];
if (bsSelected.get(atomIndex)) {
colixes[i] = shape.getColixI(colix, pid, atomIndex);
if (colixesBack != null && colixesBack.length > i)
- colixesBack[i] = 0;
+ colixesBack[i] = C.INHERIT_ALL;
paletteIDs[i] = pid;
bsColixSet.setBitTo(i, colixes[i] != C.INHERIT_ALL);
}
}
}
+ void setColixBack(short colix, BS bsSelected) {
+ if (colixesBack == null)
+ colixesBack = new short[colixes.length];
+ if (colixesBack.length < colixes.length)
+ colixesBack = AU.ensureLengthShort(colixesBack, colixes.length);
+ for (int i = monomerCount; --i >= 0;)
+ if (bsSelected.get(leadAtomIndices[i]))
+ colixesBack[i] = colix;
+ }
+
void setColixes(short[] atomColixes, BS bsSelected) {
isActive = true;
if (bsColixSet == null)
- bsColixSet = new BS();
+ bsColixSet = BS.newN(monomerCount);
for (int i = monomerCount; --i >= 0;) {
int atomIndex = leadAtomIndices[i];
if (bsSelected.get(atomIndex) && i < colixes.length && atomIndex <
atomColixes.length) {
colixes[i] = shape.getColixI(atomColixes[atomIndex], PAL.UNKNOWN.id,
atomIndex);
if (colixesBack != null && i < colixesBack.length)
- colixesBack[i] = 0;
+ colixesBack[i] = C.INHERIT_ALL;
paletteIDs[i] = PAL.UNKNOWN.id;
bsColixSet.set(i);
}
@@ -325,7 +333,7 @@
isActive = true;
if (bsColixSet == null)
- bsColixSet = new BS();
+ bsColixSet = BS.newN(monomerCount);
int n = atomMap.length;
for (int i = monomerCount; --i >= 0;) {
int atomIndex = leadAtomIndices[i];
@@ -344,25 +352,10 @@
}
}
-
-
- void setColixBack(short colix, BS bsSelected) {
- for (int i = monomerCount; --i >= 0;) {
- int atomIndex = leadAtomIndices[i];
- if (bsSelected.get(atomIndex)) {
- if (colixesBack == null)
- colixesBack = new short[colixes.length];
- if (colixesBack.length < colixes.length)
- colixesBack = AU.ensureLengthShort(colixesBack, colixes.length);
- colixesBack[i] = colix;
- }
- }
- }
-
void setTranslucent(boolean isTranslucent, BS bsSelected, float
translucentLevel) {
isActive = true;
if (bsColixSet == null)
- bsColixSet = new BS();
+ bsColixSet = BS.newN(monomerCount);
for (int i = monomerCount; --i >= 0; )
if (bsSelected.get(leadAtomIndices[i])) {
colixes[i] = C.getColixTranslucent3(colixes[i], isTranslucent,
translucentLevel);
@@ -392,4 +385,34 @@
}
}
+ void getBioShapeState(String type, boolean translucentAllowed,
+ Map<String, BS> temp, Map<String, BS> temp2) {
+ if (monomerCount > 0) {
+ if (!isActive || bsSizeSet == null && bsColixSet == null)
+ return;
+ for (int i = 0; i < monomerCount; i++) {
+ int atomIndex1 = monomers[i].firstAtomIndex;
+ int atomIndex2 = monomers[i].lastAtomIndex;
+ if (bsSizeSet != null
+ && (bsSizeSet.get(i) || bsColixSet != null && bsColixSet.get(i)))
{//shapes MUST have been set with a size
+ if (bsSizeDefault.get(i)) {
+ BSUtil.setMapBitSet(temp, atomIndex1, atomIndex2,
+ type + (bsSizeSet.get(i) ? " on" : " off"));
+ } else {
+ BSUtil.setMapBitSet(temp, atomIndex1, atomIndex2,
+ type + " " + PT.escF(mads[i] / 2000f));
+ }
+ }
+ if (bsColixSet == null || !bsColixSet.get(i))
+ continue;
+ String s = getColorCommand(type, paletteIDs[i], colixes[i],
+ translucentAllowed);
+ if (colixesBack != null && colixesBack.length > i
+ && colixesBack[i] != C.INHERIT_ALL)
+ s += " " + C.getHexCode(colixesBack[i]);
+ BSUtil.setMapBitSet(temp2, atomIndex1, atomIndex2, s);
+ }
+ }
+ }
+
}
\ No newline at end of file
Modified: trunk/Jmol/src/org/jmol/shapebio/BioShapeCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/BioShapeCollection.java 2015-12-23
04:42:24 UTC (rev 20902)
+++ trunk/Jmol/src/org/jmol/shapebio/BioShapeCollection.java 2015-12-23
08:23:37 UTC (rev 20903)
@@ -25,6 +25,11 @@
package org.jmol.shapebio;
+import java.util.Hashtable;
+import java.util.Map;
+
+import javajs.util.AU;
+
import org.jmol.atomdata.RadiusData;
import org.jmol.c.PAL;
import org.jmol.java.BS;
@@ -35,11 +40,9 @@
import org.jmol.modelsetbio.BioPolymer;
import org.jmol.modelsetbio.Monomer;
import org.jmol.shape.Shape;
-
-import javajs.util.AU;
-
import org.jmol.util.BSUtil;
import org.jmol.util.C;
+import org.jmol.viewer.JC;
/****************************************************************
* Mps stands for Model-Polymer-Shape
*
@@ -67,11 +70,6 @@
public BioShape[] bioShapes;
@Override
- public void initShape() {
- // nothing to do
- }
-
- @Override
public final void initModelSet() {
isBioShape = true;
atoms = ms.at;
@@ -79,6 +77,11 @@
}
@Override
+ public void initShape() {
+ // nothing to do
+ }
+
+ @Override
public int getSizeG(Group group) {
Monomer m = (Monomer) group;
int groupIndex = m.groupIndex;
@@ -180,7 +183,7 @@
for (int i = bioShapes.length; --i >= 0;) {
BioShape bioShape = bioShapes[i];
if (bioShape.monomerCount > 0) {
- bioShape.setColixBS(colix, (byte) 0, bsSelected);
+ bioShape.setColixBS(colix, PAL.PALETTE_VOLATILE, bsSelected);
bioShape.setColixBack(colixBack, bsSelected);
}
}
@@ -201,9 +204,19 @@
@Override
public String getShapeState() {
- return vwr.getAtomShapeSetState(this, bioShapes);
+ // leaving this here because it is so specialized
+ Map<String, BS> temp = new Hashtable<String, BS>();
+ Map<String, BS> temp2 = new Hashtable<String, BS>();
+ String type = JC.shapeClassBases[shapeID];
+ for (int iShape = bioShapes.length; --iShape >= 0;)
+ bioShapes[iShape].getBioShapeState(type, translucentAllowed, temp,
temp2);
+ String s = "\n"
+ + vwr.getCommands(temp, temp2,
+ shapeID == JC.SHAPE_BACKBONE ? "Backbone" : "select");
+ return s;
}
+
void initialize() {
int modelCount = ms.mc;
Model[] models = ms.am;
Modified: trunk/Jmol/src/org/jmol/shapespecial/Dots.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Dots.java 2015-12-23 04:42:24 UTC
(rev 20902)
+++ trunk/Jmol/src/org/jmol/shapespecial/Dots.java 2015-12-23 08:23:37 UTC
(rev 20903)
@@ -141,10 +141,8 @@
ec.setMads(mads);
}
mads[thisAtom] = (short) (thisRadius * 1000f);
- if (colixes == null) {
- colixes = new short[ac];
- paletteIDs = new byte[ac];
- }
+ if (colixes == null)
+ checkColixLength(C.BLACK, ac);
colixes[thisAtom] = C.getColix(thisArgb);
bsOn.set(thisAtom);
//all done!
@@ -271,10 +269,8 @@
}
// now, calculate surface for selected atoms
- if (dotsConvexMaps == null && (colixes == null || colixes.length != ac)) {
- colixes = new short[ac];
- paletteIDs = new byte[ac];
- }
+ if (dotsConvexMaps == null && (colixes == null || colixes.length != ac))
+ checkColixLength(C.BLACK, ac);
ec.calculate(rd, maxRadius, bsOn, bsIgnore, !vwr.getBoolean(T.dotsurface),
vwr.getBoolean(T.dotsselectedonly), isSurface, true);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-23 04:42:24 UTC
(rev 20902)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-23 08:23:37 UTC
(rev 20903)
@@ -62,9 +62,12 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.1_2015.12.22"
+Jmol.___JmolVersion="14.5.1_2015.12.23"
bug fix: PyMOL 1.8 PSE files cannot be read
+bug fix: dots broken when colored none
+bug fix: color cartoons red blue not saved in state
+bug fix: color cartoons red blue flipping red/blue in sheets
JmolVersion="14.5.1_2015.12.21"
Modified: trunk/Jmol/src/org/jmol/viewer/JmolStateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JmolStateCreator.java 2015-12-23
04:42:24 UTC (rev 20902)
+++ trunk/Jmol/src/org/jmol/viewer/JmolStateCreator.java 2015-12-23
08:23:37 UTC (rev 20903)
@@ -2,18 +2,17 @@
import java.util.Map;
+import javajs.awt.Font;
+import javajs.util.Lst;
+import javajs.util.SB;
+
import org.jmol.java.BS;
-import org.jmol.modelset.Group;
import org.jmol.modelset.Measurement;
import org.jmol.modelset.TickInfo;
import org.jmol.shape.AtomShape;
import org.jmol.shape.Measures;
import org.jmol.shape.Shape;
-import javajs.awt.Font;
-import javajs.util.Lst;
-import javajs.util.SB;
-
public abstract class JmolStateCreator {
abstract void setViewer(Viewer vwr);
@@ -31,16 +30,11 @@
abstract String getFontLineShapeState(String s, String myType, TickInfo[]
tickInfos);
- abstract void getShapeSetState(AtomShape atomShape, Shape shape, int
monomerCount, Group[] monomers,
- BS bsSizeDefault, Map<String, BS> temp, Map<String, BS>
temp2);
-
abstract String getMeasurementState(Measures shape, Lst<Measurement> mList,
int measurementCount,
Font font3d, TickInfo tickInfo);
abstract String getBondState(Shape shape, BS bsOrderSet, boolean reportAll);
- abstract String getAtomShapeSetState(Shape shape, AtomShape[] shapes);
-
abstract String getShapeState(Shape shape);
abstract String getCommands(Map<String, BS> htDefine, Map<String, BS> htMore,
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-12-23 04:42:24 UTC
(rev 20902)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-12-23 08:23:37 UTC
(rev 20903)
@@ -23,17 +23,16 @@
package org.jmol.viewer;
-import javajs.awt.Font;
-import javajs.util.Lst;
-import javajs.util.PT;
-import javajs.util.SB;
-
import java.util.Arrays;
import java.util.Date;
import java.util.Hashtable;
import java.util.Map;
+import javajs.awt.Font;
+import javajs.util.Lst;
import javajs.util.P3;
+import javajs.util.PT;
+import javajs.util.SB;
import org.jmol.api.JmolDataManager;
import org.jmol.api.JmolModulationSet;
@@ -47,7 +46,6 @@
import org.jmol.modelset.AtomCollection;
import org.jmol.modelset.Bond;
import org.jmol.modelset.BondSet;
-import org.jmol.modelset.Group;
import org.jmol.modelset.Measurement;
import org.jmol.modelset.Model;
import org.jmol.modelset.ModelSet;
@@ -343,6 +341,7 @@
if (sb.length() > 0)
commands.append(" frame " + ms.getModelNumberDotted(i) +
";\n").appendSB(sb);
}
+
boolean loadUC = false;
if (ms.unitCells != null) {
boolean haveModulation = false;
@@ -973,33 +972,6 @@
}
@Override
- void getShapeSetState(AtomShape as, Shape shape, int monomerCount,
- Group[] monomers, BS bsSizeDefault,
- Map<String, BS> temp, Map<String, BS> temp2) {
- String type = JC.shapeClassBases[shape.shapeID];
- for (int i = 0; i < monomerCount; i++) {
- int atomIndex1 = monomers[i].firstAtomIndex;
- int atomIndex2 = monomers[i].lastAtomIndex;
- if (as.bsSizeSet != null
- && (as.bsSizeSet.get(i) || as.bsColixSet != null
- && as.bsColixSet.get(i))) {//shapes MUST have been set with a
size
- if (bsSizeDefault.get(i)) {
- BSUtil.setMapBitSet(temp, atomIndex1, atomIndex2, type
- + (as.bsSizeSet.get(i) ? " on" : " off"));
- } else {
-
- BSUtil.setMapBitSet(temp, atomIndex1, atomIndex2, type + " "
- + PT.escF(as.mads[i] / 2000f));
- }
- }
- if (as.bsColixSet != null && as.bsColixSet.get(i))
- BSUtil.setMapBitSet(temp2, atomIndex1, atomIndex2, Shape
- .getColorCommand(type, as.paletteIDs[i], as.colixes[i],
- shape.translucentAllowed));
- }
- }
-
- @Override
String getMeasurementState(Measures shape,
Lst<Measurement> mList,
int measurementCount, Font font3d,
@@ -1126,25 +1098,6 @@
}
@Override
- String getAtomShapeSetState(Shape shape, AtomShape[] bioShapes) {
- clearTemp();
- for (int i = bioShapes.length; --i >= 0;) {
- AtomShape bs = bioShapes[i];
- if (bs.monomerCount > 0) {
- if (!bs.isActive || bs.bsSizeSet == null && bs.bsColixSet == null)
- continue;
- vwr.getShapeSetState(bs, shape, bs.monomerCount, bs.getMonomers(),
- bs.bsSizeDefault, temp, temp2);
- }
- }
- String s = "\n"
- + getCommands(temp, temp2,
- shape.shapeID == JC.SHAPE_BACKBONE ? "Backbone" : "select");
- clearTemp();
- return s;
- }
-
- @Override
String getShapeState(Shape shape) {
String s;
switch (shape.shapeID) {
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-12-23 04:42:24 UTC (rev
20902)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-12-23 08:23:37 UTC (rev
20903)
@@ -8972,15 +8972,6 @@
return getStateCreator().getFontLineShapeState(s, myType, tickInfos);
}
- public void getShapeSetState(AtomShape atomShape, Shape shape,
- int monomerCount, Group[] monomers,
- BS bsSizeDefault, Map<String, BS> temp,
- Map<String, BS> temp2) {
- getStateCreator().getShapeSetState(atomShape, shape, monomerCount,
- monomers, bsSizeDefault, temp, temp2);
-
- }
-
public String getMeasurementState(Measures measures, Lst<Measurement> mList,
int measurementCount, Font font3d,
TickInfo ti) {
@@ -8992,10 +8983,6 @@
return getStateCreator().getBondState(shape, bsOrderSet, reportAll);
}
- public String getAtomShapeSetState(Shape shape, AtomShape[] shapes) {
- return getStateCreator().getAtomShapeSetState(shape, shapes);
- }
-
public String getShapeState(Shape shape) {
return getStateCreator().getShapeState(shape);
}
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