Revision: 18282
http://sourceforge.net/p/jmol/code/18282
Author: hansonr
Date: 2013-06-05 03:55:27 +0000 (Wed, 05 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.16_dev_2013.06.04"
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
trunk/Jmol/src/org/jmol/api/JmolAdapter.java
trunk/Jmol/src/org/jmol/modelset/BondCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/modelset/Text.java
trunk/Jmol/src/org/jmol/render/LabelsRenderer.java
trunk/Jmol/src/org/jmol/render/SticksRenderer.java
trunk/Jmol/src/org/jmol/shape/Labels.java
trunk/Jmol/src/org/jmol/util/JmolEdge.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2013-06-04 23:48:28 UTC (rev 18281)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2013-06-05 03:55:27 UTC (rev 18282)
@@ -126,7 +126,8 @@
}
@SuppressWarnings("unchecked")
- void finalizeObject(PyMOLScene pymolScene, ModelSet m, String mepList,
boolean doCache) {
+ void finalizeObject(PyMOLScene pymolScene, ModelSet m, String mepList,
+ boolean doCache) {
ShapeManager sm = m.shapeManager;
int modelIndex = getModelIndex(m);
String sID;
@@ -152,8 +153,7 @@
}
sm.viewer.setObjectProp((String) info, id);
} else {
- sm.viewer.displayAtoms(bsAtoms, id == T.display, false, T.add,
- true);
+ sm.viewer.displayAtoms(bsAtoms, id == T.display, false, T.add, true);
}
return;
case T.define:
@@ -190,7 +190,9 @@
case JC.SHAPE_STICKS:
if (size != -1) {
sm.setShapeSizeBs(JC.SHAPE_STICKS, size, null, bsAtoms);
-
pymolScene.setUniqueBonds(((BS[])sm.getShapePropertyIndex(JC.SHAPE_STICKS,
"sets", 0))[1], id == JC.SHAPE_STICKS);
+ BS bsBonds = ((BS[]) sm.getShapePropertyIndex(JC.SHAPE_STICKS, "sets",
+ 0))[1];
+ pymolScene.setUniqueBonds(bsBonds, id == JC.SHAPE_STICKS);
size = -1;
}
id = JC.SHAPE_STICKS;
@@ -245,10 +247,8 @@
if (doCache)
sb.append(";isosurface cache");
} else {
- //if (argb == 0)
- //sm.setShapePropertyBs(JC.SHAPE_BALLS, "colors", colors, bsAtoms);
- String lighting = (String)((Object[]) info)[0];
- String only = (String)((Object[]) info)[1];
+ String lighting = (String) ((Object[]) info)[0];
+ String only = (String) ((Object[]) info)[1];
only = " only";
BS bsCarve = (BS) ((Object[]) info)[2];
float carveDistance = ((Float) ((Object[]) info)[3]).floatValue();
@@ -261,16 +261,15 @@
}
boolean haveMep = Parser.isOneOf(sID, mepList);
String model = m.models[modelIndex].getModelNumberDotted();
-// BS bsIgnore = sm.viewer.getAtomsWithinRadius(0.1f, bsAtoms, true,
-// new RadiusData(null, 0.1f, EnumType.ABSOLUTE, null));
-// bsIgnore.andNot(bsAtoms);
-// String ignore = " ignore " + Escape.eBS(bsIgnore);
+ // BS bsIgnore = sm.viewer.getAtomsWithinRadius(0.1f, bsAtoms,
true,
+ // new RadiusData(null, 0.1f, EnumType.ABSOLUTE, null));
+ // bsIgnore.andNot(bsAtoms);
+ // String ignore = " ignore " + Escape.eBS(bsIgnore);
String ignore = "";
String type = (size < 0 ? " sasurface " : " solvent ");
- sb.append(" model ")
- .append(model).append(
- resolution).append(" select ").append(Escape.eBS(bsAtoms))
- .append(only).append(ignore).append(type).appendF(Math.abs(size /
1000f));
+ sb.append(" model ").append(model).append(resolution)
+ .append(" select ").append(Escape.eBS(bsAtoms)).append(only)
+ .append(ignore).append(type).appendF(Math.abs(size / 1000f));
if (!haveMep) {
if (argb == 0)
sb.append(" map property color");
@@ -281,7 +280,7 @@
if (translucency > 0)
sb.append(";color isosurface translucent " + translucency);
if (bsCarve != null && !bsCarve.isEmpty())
- sb.append(";isosurface slab within " + carveDistance + " {" + model
+ sb.append(";isosurface slab within " + carveDistance + " {" + model
+ " and " + Escape.eBS(bsCarve) + "}");
if (doCache && !haveMep)
sb.append(";isosurface cache");
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-04 23:48:28 UTC (rev 18281)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-05 03:55:27 UTC (rev 18282)
@@ -33,6 +33,7 @@
import org.jmol.adapter.smarter.Atom;
import org.jmol.adapter.smarter.Bond;
import org.jmol.adapter.smarter.Structure;
+import org.jmol.api.JmolAdapter;
import org.jmol.api.JmolDocument;
import org.jmol.api.PymolAtomReader;
import org.jmol.constant.EnumStructure;
@@ -703,8 +704,9 @@
return;
JmolList<Object> data = listAt(listAt(pymolObject, 2), 0);
int color = PyMOL.getRGB(intAt(listAt(pymolObject, 0), 2));
- pymolScene.addCGO(data, color);
- appendLoadNote("CGO " + PyMOLScene.fixName(objectName));
+ String name = pymolScene.addCGO(data, color);
+ if (name != null)
+ appendLoadNote("CGO " + name);
}
/**
@@ -736,7 +738,7 @@
volumeData = new Hashtable<String, JmolList<Object>>();
volumeData.put(objectName, pymolObject);
if (!isHidden && !isStateScript)
- addJmolObject(T.isosurface, null, objectName);
+ pymolScene.addIsosurface(objectName);
}
pymolObject.addLast(objectName);
}
@@ -847,6 +849,7 @@
}
addBonds(bonds);
addMolStructures();
+ atoms = atomSetCollection.getAtoms();
if (!isStateScript)
createShapeObjects();
ssMapSeq = null;
@@ -879,11 +882,11 @@
*/
private JmolList<Bond> getBondList(JmolList<Object> bonds) {
JmolList<Bond> bondList = new JmolList<Bond>();
- boolean valence = pymolScene.booleanSetting(PyMOL.valence);
+ int asSingle = (pymolScene.booleanSetting(PyMOL.valence) ? 0 :
JmolAdapter.ORDER_AS_SINGLE);
int n = bonds.size();
for (int i = 0; i < n; i++) {
JmolList<Object> b = listAt(bonds, i);
- int order = (valence ? intAt(b, 2) : 1);
+ int order = intAt(b, 2) | asSingle;
if (order < 1 || order > 3)
order = 1;
int ia = intAt(b, 0);
@@ -1151,18 +1154,16 @@
*
*/
private void createShapeObjects() {
- atoms = atomSetCollection.getAtoms();
pymolScene.createShapeObjects(reps, allowSurface && !isHidden, atomCount0,
atomCount);
}
////// end of molecule-specific JmolObjects //////
-
+
///// final processing /////
-
+
/**
- * Create mesh or mep JmolObjects.
- * Caching the volumeData, because it will be needed
- * by org.jmol.jvxl.readers.PyMOLMeshReader
+ * Create mesh or mep JmolObjects. Caching the volumeData, because it will be
+ * needed by org.jmol.jvxl.readers.PyMOLMeshReader
*
*/
private void processMeshes() {
@@ -1192,18 +1193,11 @@
if (surface == null)
continue;
obj.addLast(mapName);
- appendLoadNote("PyMOL object " + objName + " references map " + mapName);
volumeData.put(objName, obj);
volumeData.put("__pymolSurfaceData__", obj);
- if (!isStateScript) {
- JmolObject jo = addJmolObject(tok, null, obj);
- if (isMep) {
- } else {
- jo.setSize(pymolScene.globalSetting(PyMOL.mesh_width));
- jo.argb = PyMOL.getRGB(intAt(listAt(obj, 0), 2));
- }
- jo.translucency = pymolScene.globalSetting(PyMOL.transparency);
- }
+ if (!isStateScript)
+ pymolScene.addMesh(tok, obj, objName, isMep);
+ appendLoadNote("PyMOL object " + objName + " references map " + mapName);
}
}
@@ -1276,10 +1270,6 @@
pymolScene.setAtomInfo(uniqueIDs, cartoonTypes, sequenceNumbers, newChain,
radii);
}
- private JmolObject addJmolObject(int id, BS bsAtoms, Object info) {
- return pymolScene.addJmolObject(id, bsAtoms, info);
- }
-
// generally useful static methods
private static int intAt(JmolList<Object> list, int i) {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-04 23:48:28 UTC (rev 18281)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-05 03:55:27 UTC (rev 18282)
@@ -434,13 +434,14 @@
bs = null;
String info = objectSelectionName;
switch (objectType) {
+ case 0: // doesn't have selected state
+ case PyMOL.OBJECT_GROUP:
+ continue;
case PyMOL.OBJECT_MOLECULE:
bs = viewer.getDefinedAtomSet(info);
if (bs.nextSetBit(0) < 0)
continue;
break;
- case PyMOL.OBJECT_GROUP:
- continue;
case PyMOL.OBJECT_MEASURE:
if (tok == T.display) {
MeasurementData[] mdList = htMeasures.get(name);
@@ -465,7 +466,7 @@
objectName = name;
objectType = getObjectType(name);
objectSelectionName = getSelectionName(name);
- objectNameID = (istate == 0 ? getObjectID(name) : objectSelectionName + "_"
+ objectNameID = (istate == 0 && objectType != 0 ? getObjectID(name) :
objectSelectionName + "_"
+ istate);
objectAtoms = htObjectAtoms.get(name);
objectSettings = htObjectSettings.get(name);
@@ -720,7 +721,8 @@
colixes[i] = (short) atomColorList.get(i).intValue();
jo.setColors(colixes, 0);
jo.setSize(0);
- jo = addJmolObject(JC.SHAPE_STICKS, objectAtoms, null);
+ jo = addJmolObject(JC.SHAPE_STICKS, objectAtoms,
+ Float.valueOf(floatSetting(PyMOL.valence)));
jo.setSize(0);
}
createShapeObject(PyMOL.REP_LINES, reps[PyMOL.REP_LINES]);
@@ -885,11 +887,12 @@
return labelPos;
}
- void addCGO(JmolList<Object> data, int color) {
+ String addCGO(JmolList<Object> data, int color) {
data.addLast(objectName);
JmolObject jo = addJmolObject(JC.SHAPE_CGO, null, data);
jo.argb = color;
jo.translucency = floatSetting(PyMOL.cgo_transparency);
+ return fixName(objectName);
}
boolean addMeasurements(MeasurementData[] mdList, int nCoord,
@@ -1002,7 +1005,7 @@
frameObj = null;
}
- static String fixName(String name) {
+ private static String fixName(String name) {
char[] chars = name.toLowerCase().toCharArray();
for (int i = chars.length; --i >= 0;)
if (!Character.isLetterOrDigit(chars[i]))
@@ -1014,8 +1017,9 @@
return (String) objectInfo.get(name)[0];
}
- int getObjectType(String name) {
- return ((Integer) objectInfo.get(name)[1]).intValue();
+ private int getObjectType(String name) {
+ Object[] o = objectInfo.get(name);
+ return (o == null ? 0 : ((Integer) o[1]).intValue());
}
BS setAtomMap(int[] atomMap, int atomCount0) {
@@ -1568,9 +1572,24 @@
int c = (int) getUniqueFloatDef(id, PyMOL.stick_color,
Integer.MAX_VALUE);
if (c != Integer.MAX_VALUE)
c = PyMOL.getRGB(c);
+ float valence = getUniqueFloatDef(id, PyMOL.valence, Float.NaN);
float t = getUniqueFloatDef(id, PyMOL.stick_transparency, Float.NaN);
- viewer.setBondParameters(thisState - 1, i, rad, c, t);
+ viewer.setBondParameters(thisState - 1, i, null, rad, valence, c, t);
}
}
+ public void addMesh(int tok, JmolList<Object> obj, String objName, boolean
isMep) {
+ JmolObject jo = addJmolObject(tok, null, obj);
+ setObject(objName, -1);
+ if (!isMep) {
+ jo.setSize(floatSetting(PyMOL.mesh_width));
+ jo.argb = PyMOL.getRGB(intAt(listAt(obj, 0), 2));
+ }
+ jo.translucency = floatSetting(PyMOL.transparency);
+ }
+
+ public void addIsosurface(String objectName) {
+ addJmolObject(T.isosurface, null, objectName);
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/api/JmolAdapter.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolAdapter.java 2013-06-04 23:48:28 UTC
(rev 18281)
+++ trunk/Jmol/src/org/jmol/api/JmolAdapter.java 2013-06-05 03:55:27 UTC
(rev 18282)
@@ -56,20 +56,21 @@
****************************************************************/
public abstract class JmolAdapter {
- public final static short ORDER_COVALENT_SINGLE =
JmolEdge.BOND_COVALENT_SINGLE;
- public final static short ORDER_COVALENT_DOUBLE =
JmolEdge.BOND_COVALENT_DOUBLE;
- public final static short ORDER_COVALENT_TRIPLE =
JmolEdge.BOND_COVALENT_TRIPLE;
- public final static short ORDER_AROMATIC = JmolEdge.BOND_AROMATIC;
- public final static short ORDER_AROMATIC_SINGLE =
JmolEdge.BOND_AROMATIC_SINGLE;
- public final static short ORDER_AROMATIC_DOUBLE =
JmolEdge.BOND_AROMATIC_DOUBLE;
- public final static short ORDER_HBOND = JmolEdge.BOND_H_REGULAR;
- public final static short ORDER_STEREO_NEAR = JmolEdge.BOND_STEREO_NEAR;
- public final static short ORDER_STEREO_FAR = JmolEdge.BOND_STEREO_FAR;
- public final static short ORDER_PARTIAL01 = JmolEdge.BOND_PARTIAL01;
- public final static short ORDER_PARTIAL12 = JmolEdge.BOND_PARTIAL12;
- public final static short ORDER_PARTIAL23 = JmolEdge.BOND_PARTIAL23;
- public final static short ORDER_PARTIAL32 = JmolEdge.BOND_PARTIAL32;
- public final static short ORDER_UNSPECIFIED =
JmolEdge.BOND_ORDER_UNSPECIFIED;
+ public final static int ORDER_COVALENT_SINGLE =
JmolEdge.BOND_COVALENT_SINGLE;
+ public final static int ORDER_COVALENT_DOUBLE =
JmolEdge.BOND_COVALENT_DOUBLE;
+ public final static int ORDER_COVALENT_TRIPLE =
JmolEdge.BOND_COVALENT_TRIPLE;
+ public final static int ORDER_AROMATIC = JmolEdge.BOND_AROMATIC;
+ public final static int ORDER_AROMATIC_SINGLE =
JmolEdge.BOND_AROMATIC_SINGLE;
+ public final static int ORDER_AROMATIC_DOUBLE =
JmolEdge.BOND_AROMATIC_DOUBLE;
+ public final static int ORDER_HBOND = JmolEdge.BOND_H_REGULAR;
+ public final static int ORDER_STEREO_NEAR = JmolEdge.BOND_STEREO_NEAR;
+ public final static int ORDER_STEREO_FAR = JmolEdge.BOND_STEREO_FAR;
+ public final static int ORDER_PARTIAL01 = JmolEdge.BOND_PARTIAL01;
+ public final static int ORDER_PARTIAL12 = JmolEdge.BOND_PARTIAL12;
+ public final static int ORDER_PARTIAL23 = JmolEdge.BOND_PARTIAL23;
+ public final static int ORDER_PARTIAL32 = JmolEdge.BOND_PARTIAL32;
+ public final static int ORDER_UNSPECIFIED =
JmolEdge.BOND_ORDER_UNSPECIFIED;
+ public final static int ORDER_AS_SINGLE = JmolEdge.BOND_AS_SINGLE;
public final static EnumQuantumShell getShellEnumeration(int i) { return
EnumQuantumShell.getItem(i); }
public final static int[][] getNewDfCoefMap() { return
EnumQuantumShell.getNewDfCoefMap(); }
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2013-06-04
23:48:28 UTC (rev 18281)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2013-06-05
03:55:27 UTC (rev 18282)
@@ -849,14 +849,28 @@
}
/**
- * used in PyMOL reader to set unique bond settings
+ * used in PyMOL reader to set unique bond settings and for valence
+ *
* @param modelIndex
- * @param i
+ * @param iBond
+ * @param bsBonds
* @param rad
+ * @param pymolValence 1 for "show multiple bonds
* @param argb
* @param trans
*/
- public void setBondParameters(int modelIndex, int i, float rad, int argb,
float trans) {
+ public void setBondParametersBS(int modelIndex, int iBond, BS bsBonds,
+ float rad, float pymolValence, int argb,
+ float trans) {
+ if (bsBonds == null)
+ setBondParameters(modelIndex, iBond, rad, pymolValence, argb, trans);
+ else
+ for (int i = bsBonds.nextSetBit(0); i >= 0; i = bsBonds.nextSetBit(i +
1))
+ setBondParameters(modelIndex, i, rad, pymolValence, argb, trans);
+ }
+
+ public void setBondParameters(int modelIndex, int i, float rad, float
pymolValence,
+ int argb, float trans) {
if (i < 0 || i >= bondCount)
return;
Bond b = bonds[i];
@@ -871,6 +885,10 @@
b.colix = C.getColixTranslucent3(colix, trans != 0, trans);
else if (b.colix != colix)
b.colix = C.copyColixTranslucency(b.colix, colix);
+ if (pymolValence == 1)
+ b.order &= ~JmolEdge.BOND_AS_SINGLE;
+ else if (pymolValence == 0)
+ b.order |= JmolEdge.BOND_AS_SINGLE;
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-06-04 23:48:28 UTC
(rev 18281)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-06-05 03:55:27 UTC
(rev 18282)
@@ -889,30 +889,37 @@
return model.chains[model.chainCount++] = new Chain(model, chainID);
}
- private void iterateOverAllNewBonds(JmolAdapter adapter, Object
atomSetCollection) {
- JmolAdapterBondIterator iterBond =
adapter.getBondIterator(atomSetCollection);
+ private void iterateOverAllNewBonds(JmolAdapter adapter,
+ Object atomSetCollection) {
+ JmolAdapterBondIterator iterBond = adapter
+ .getBondIterator(atomSetCollection);
if (iterBond == null)
return;
short mad = viewer.getMadBond();
- short order;
modelSet.defaultCovalentMad = (jmolData == null ? mad : 0);
boolean haveMultipleBonds = false;
while (iterBond.hasNext()) {
- order = (short) iterBond.getEncodedOrder();
- Bond b = bondAtoms(iterBond.getAtomUniqueID1(),
iterBond.getAtomUniqueID2(), order);
+ int iOrder = iterBond.getEncodedOrder();
+ short order = (short) iOrder;
+ Bond b = bondAtoms(iterBond.getAtomUniqueID1(), iterBond
+ .getAtomUniqueID2(), order);
if (b != null) {
- if (order > 1 && order != JmolEdge.BOND_STEREO_NEAR && order !=
JmolEdge.BOND_STEREO_FAR)
- haveMultipleBonds = true;
+ if (order > 1 && order != JmolEdge.BOND_STEREO_NEAR
+ && order != JmolEdge.BOND_STEREO_FAR)
+ haveMultipleBonds = true;
float radius = iterBond.getRadius();
if (radius > 0)
b.setMad((short) (radius * 2000));
short colix = iterBond.getColix();
if (colix >= 0)
b.setColix(colix);
+ b.order |= (iOrder & JmolEdge.BOND_AS_SINGLE);
}
}
- if (haveMultipleBonds && modelSet.someModelsHaveSymmetry &&
!viewer.getBoolean(T.applysymmetrytobonds))
- Logger.info("ModelSet: use \"set appletSymmetryToBonds TRUE \" to apply
the file-based multiple bonds to symmetry-generated atoms.");
+ if (haveMultipleBonds && modelSet.someModelsHaveSymmetry
+ && !viewer.getBoolean(T.applysymmetrytobonds))
+ Logger
+ .info("ModelSet: use \"set appletSymmetryToBonds TRUE \" to apply
the file-based multiple bonds to symmetry-generated atoms.");
modelSet.defaultCovalentMad = mad;
}
Modified: trunk/Jmol/src/org/jmol/modelset/Text.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Text.java 2013-06-04 23:48:28 UTC (rev
18281)
+++ trunk/Jmol/src/org/jmol/modelset/Text.java 2013-06-05 03:55:27 UTC (rev
18282)
@@ -39,14 +39,8 @@
public float fontScale;
- public String text;
-
public String textUnformatted;
- public String getText() {
- return text;
- }
-
public boolean doFormatText;
public String[] lines;
@@ -59,6 +53,10 @@
private int textWidth;
private int textHeight;
+ private String text;
+ public String getText() {
+ return text;
+ }
private int[] widths;
Modified: trunk/Jmol/src/org/jmol/render/LabelsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/LabelsRenderer.java 2013-06-04 23:48:28 UTC
(rev 18281)
+++ trunk/Jmol/src/org/jmol/render/LabelsRenderer.java 2013-06-05 03:55:27 UTC
(rev 18282)
@@ -105,7 +105,8 @@
if (!atom.isVisible(myVisibilityFlag))
continue;
String label = labelStrings[i];
- if (label == null || label.length() == 0 || labels.mads != null
+ if (label == null
+ || label.length() == 0 || labels.mads != null
&& labels.mads[i] < 0)
continue;
labelColix = labels.getColix2(i, atom, false);
Modified: trunk/Jmol/src/org/jmol/render/SticksRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/SticksRenderer.java 2013-06-04 23:48:28 UTC
(rev 18281)
+++ trunk/Jmol/src/org/jmol/render/SticksRenderer.java 2013-06-05 03:55:27 UTC
(rev 18282)
@@ -87,10 +87,13 @@
if (multipleBondSpacing == 0 && isCartesianExport)
multipleBondSpacing = 0.2f;
multipleBondRadiusFactor = viewer.getFloat(T.multiplebondradiusfactor);
- showMultipleBonds = multipleBondSpacing != 0
- && viewer.getBoolean(T.showmultiplebonds);
modeMultipleBond = viewer.getModeMultipleBond();
- renderWireframe = viewer.getInMotion(true) &&
viewer.getBoolean(T.wireframerotation);
+ showMultipleBonds = (multipleBondSpacing != 0
+ && modeMultipleBond != JC.MULTIBOND_NEVER
+ && viewer.getBoolean(T.showmultiplebonds));
+
+ renderWireframe = viewer.getInMotion(true)
+ && viewer.getBoolean(T.wireframerotation);
ssbondsBackbone = viewer.getBoolean(T.ssbondsbackbone);
hbondsBackbone = viewer.getBoolean(T.hbondsbackbone);
bondsBackbone = hbondsBackbone | ssbondsBackbone;
@@ -192,8 +195,9 @@
bondOrder &= ~JmolEdge.BOND_SULFUR_MASK;
if ((bondOrder & JmolEdge.BOND_COVALENT_MASK) != 0) {
if (!showMultipleBonds
- || modeMultipleBond == JC.MULTIBOND_NEVER
- || (modeMultipleBond == JC.MULTIBOND_NOTSMALL && mad >
JC.madMultipleBondSmallMaximum)) {
+ || (modeMultipleBond == JC.MULTIBOND_NOTSMALL && mad >
JC.madMultipleBondSmallMaximum)
+ || (bondOrder & JmolEdge.BOND_AS_SINGLE) != 0
+ ) {
bondOrder = 1;
}
}
Modified: trunk/Jmol/src/org/jmol/shape/Labels.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Labels.java 2013-06-04 23:48:28 UTC (rev
18281)
+++ trunk/Jmol/src/org/jmol/shape/Labels.java 2013-06-05 03:55:27 UTC (rev
18282)
@@ -440,7 +440,7 @@
if (isScaled) {
text = Text.newLabel(gdata, null, label, (short) 0, (short) 0, 0,
scalePixelsPerMicron, null);
putLabel(i, text);
- } else if (text != null) {
+ } else if (text != null && label != null) {
text.setText(label);
}
if (defaultOffset != zeroOffset)
Modified: trunk/Jmol/src/org/jmol/util/JmolEdge.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/JmolEdge.java 2013-06-04 23:48:28 UTC (rev
18281)
+++ trunk/Jmol/src/org/jmol/util/JmolEdge.java 2013-06-05 03:55:27 UTC (rev
18282)
@@ -37,6 +37,7 @@
// 11 1111 1100 0000 0000
// 76 5432 1098 7654 3210
// | new connection 1 << 17 0x20000
+ // | render as single 1 << 16 0x10000
// | strut 1 << 15 0x08000
// ||| | Hydrogen bond 0x3800 F << 11
// |Stereo 0x400 1 << 10
@@ -68,10 +69,11 @@
public final static int BOND_COVALENT_TRIPLE = 3;
public final static int BOND_COVALENT_QUADRUPLE = 4;
public final static int BOND_ORDER_UNSPECIFIED = 0x11;
- public final static int BOND_ORDER_ANY = 0xFFFF;
+ public final static int BOND_ORDER_ANY = 0x0FFFF;
public final static int BOND_ORDER_NULL = 0x1FFFF;
+ public static final int BOND_STRUT = 0x08000;
+ public final static int BOND_AS_SINGLE = 0x10000;
public final static int BOND_NEW = 0x20000;
- public static final int BOND_STRUT = 0x8000;
public final static int BOND_HBOND_SHIFT = 11;
public final static int BOND_HYDROGEN_MASK = 0xF << 11;
public final static int BOND_H_REGULAR = 1 << 11;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-04 23:48:28 UTC
(rev 18281)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-05 03:55:27 UTC
(rev 18282)
@@ -11,6 +11,8 @@
___JmolVersion="13.1.16_dev_2013.06.04"
+TODO: PyMOL sphere_color -- will require color spacefill ...
+
PyMOL: better scene restore;
bug fix: "display add" by itself should not do anything
bug fix: Hall translation initialization problem
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-06-04 23:48:28 UTC
(rev 18281)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-06-05 03:55:27 UTC
(rev 18282)
@@ -1267,7 +1267,8 @@
private String getTextState(Text t) {
SB s = new SB();
- if (t.text == null || t.isLabelOrHover || t.target.equals("error"))
+ String text = t.getText();
+ if (text == null || t.isLabelOrHover || t.target.equals("error"))
return "";
//set echo top left
//set echo myecho x y
@@ -1305,7 +1306,7 @@
s.append("; ").append(echoCmd).append(" IMAGE /*file*/");
else
s.append("; echo ");
- s.append(Escape.eS(t.text)); // was textUnformatted, but that is not
really the STATE
+ s.append(Escape.eS(text)); // was textUnformatted, but that is not really
the STATE
s.append(";\n");
if (isImage && t.imageScale != 1)
s.append(" ").append(echoCmd).append(" scale
").appendF(t.imageScale).append(";\n");
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-04 23:48:28 UTC (rev
18281)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-05 03:55:27 UTC (rev
18282)
@@ -10005,8 +10005,8 @@
}
}
- public void setBondParameters(int modelIndex, int i, float rad, int argb,
float trans) {
- modelSet.setBondParameters(modelIndex, i, rad, argb, trans);
+ public void setBondParameters(int modelIndex, int i, BS bsBonds, float rad,
float pymolValence, int argb, float trans) {
+ modelSet.setBondParametersBS(modelIndex, i, bsBonds, rad, pymolValence,
argb, trans);
}
}
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