Revision: 18266
http://sourceforge.net/p/jmol/code/18266
Author: hansonr
Date: 2013-05-30 20:46:54 +0000 (Thu, 30 May 2013)
Log Message:
-----------
___JmolVersion="13.1.16_dev_2013.05.30c"
PyMOL: adds SASURFACE option (surface_solvent ON), with "carving"
(ProFusion_ABL.pse, scene F6)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLGroup.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/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2013-05-30 16:35:52 UTC (rev 18265)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2013-05-30 20:46:54 UTC (rev 18266)
@@ -233,8 +233,11 @@
} else {
//if (argb == 0)
//sm.setShapePropertyBs(JC.SHAPE_BALLS, "colors", colors, bsAtoms);
- String lighting = ((String[]) info)[0];
- String only = ((String[]) 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();
// not implementing "not only" yet because if we did that, since we
have so
// many sets of atoms, we could have real problems here.
String resolution = "";
@@ -243,10 +246,17 @@
resolution = " resolution 1.5";
}
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);
+ String ignore = "";
+ String type = (size < 0 ? " sasurface " : " solvent ");
sb.append(" model ")
- .append(m.models[modelIndex].getModelNumberDotted()).append(
+ .append(model).append(
resolution).append(" select ").append(Escape.eBS(bsAtoms))
- .append(" only").append(" solvent ").appendF(size / 1000f);
+ .append(only).append(ignore).append(type).appendF(Math.abs(size /
1000f));
if (!haveMep) {
if (argb == 0)
sb.append(" map property color");
@@ -256,6 +266,9 @@
sb.append(";isosurface frontOnly ").append(lighting);
if (translucency > 0)
sb.append(";color isosurface translucent " + translucency);
+ if (bsCarve != null && !bsCarve.isEmpty())
+ 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/PyMOLGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLGroup.java
2013-05-30 16:35:52 UTC (rev 18265)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLGroup.java
2013-05-30 20:46:54 UTC (rev 18266)
@@ -13,7 +13,7 @@
JmolList<Object> object;
boolean visible = true;
boolean occluded = false;
- BS bsAtoms;
+ BS bsAtoms = new BS();
int type;
PyMOLGroup parent;
@@ -35,8 +35,16 @@
return;
}
+ BS addGroupAtoms(BS bs) {
+ bsAtoms.or(bs);
+ if (parent != null)
+ parent.addGroupAtoms(bsAtoms);
+ return bsAtoms;
+ }
+
@Override
public String toString() {
return this.name;
}
+
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-05-30 16:35:52 UTC (rev 18265)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-05-30 20:46:54 UTC (rev 18266)
@@ -116,7 +116,6 @@
private boolean isMovie;
- private Map<String, Object> htNames = new Hashtable<String, Object>();
private int pymolFrame;
private boolean allStates;
private int totalAtomCount;
@@ -382,10 +381,9 @@
}
processDefinitions();
- if (haveScenes)
- processScenes(map, names);
+ processSelections(map);
// no need to render if this is a state script
- pymolScene.setRendering();
+ pymolScene.finalizeEverything();
if (!isStateScript) {
// same idea as for a Jmol state -- session reinitializes
viewer.initialize(true);
@@ -620,7 +618,8 @@
processGadget(pymolObject);
break;
case PyMOL.OBJECT_GROUP:
- pymolScene.addGroup(execObject, null, type);
+ if (parentGroupName == null)
+ parentGroupName = ""; // force creation
break;
case PyMOL.OBJECT_CGO:
msg = "CGO";
@@ -645,10 +644,10 @@
msg = "SURFACE";
break;
}
- if (parentGroupName != null) {
+ if (parentGroupName != null || bsAtoms != null) {
PyMOLGroup group = pymolScene.addGroup(execObject, parentGroupName,
type);
if (bsAtoms != null)
- pymolScene.addGroupAtoms(group, bsAtoms);
+ bsAtoms = group.addGroupAtoms(bsAtoms);
}
if (doExclude) {
int i0 = intAt(startLen, 0);
@@ -807,17 +806,8 @@
JmolList<Object> pymolAtoms = listAt(pymolObject, 7);
- String fname = "__" + PyMOLScene.fixName(objectName);
atomMap = new int[nAtoms];
- BS bsAtoms = (BS) htNames.get(fname);
- if (bsAtoms == null) {
- bsAtoms = BS.newN(atomCount0 + nAtoms);
- Logger.info("PyMOL molecule " + objectName);
- htNames.put(fname, bsAtoms);
- pymolScene.addMolecule(objectName);
- }
- if (haveScenes)
- pymolScene.setAtomMap(atomMap, bsAtoms);
+ BS bsAtoms = pymolScene.setAtomMap(atomMap, atomCount0);
for (int i = 0; i < PyMOL.REP_JMOL_MAX; i++)
reps[i] = BS.newN(1000);
@@ -1218,40 +1208,40 @@
*
*/
private void processDefinitions() {
- addJmolObject(T.define, null, htNames);
- String s = viewer.getAtomDefs(htNames);
+ String s = viewer.getAtomDefs(pymolScene.setAtomDefs());
if (s.length() > 2)
s = s.substring(0, s.length() - 2);
appendLoadNote(s);
}
/**
- * A PyMOL scene consists of one or more of:
- * view
- * frame
- * visibilities, by object
- * colors, by color
- * reps, by type
- * currently just extracts viewpoint
+ * A PyMOL scene consists of one or more of: view frame visibilities, by
+ * object colors, by color reps, by type currently just extracts viewpoint
*
* @param map
- * @param names
*/
@SuppressWarnings("unchecked")
- private void processScenes(Map<String, Object> map, JmolList<Object>names) {
- JmolList<Object> order = getMapList(map, "scene_order");
- Map<String, Object> scenes = (Map<String, Object>) map.get("scene_dict");
- finalizeSceneData();
- Map<String, JmolList<Object>> htObjNames = PyMOLScene.listToMap(names);
- Map<String, JmolList<Object>> htSecrets =
PyMOLScene.listToMap(getMapList(map, "selector_secrets"));
- for (int i = 0; i < order.size(); i++) {
- String name = stringAt(order, i);
- JmolList<Object> thisScene = getMapList(scenes, name);
- if (thisScene == null)
- continue;
- pymolScene.buildScene(name, thisScene, htObjNames, htSecrets);
- appendLoadNote("scene: " + name);
+ private void processSelections(Map<String, Object> map) {
+ if (!pymolScene.needSelections())
+ return;
+ Map<String, JmolList<Object>> htObjNames = PyMOLScene.listToMap(getMapList(
+ map, "names"));
+ if (haveScenes) {
+ JmolList<Object> order = getMapList(map, "scene_order");
+ Map<String, Object> scenes = (Map<String, Object>) map.get("scene_dict");
+ finalizeSceneData();
+ Map<String, JmolList<Object>> htSecrets = PyMOLScene
+ .listToMap(getMapList(map, "selector_secrets"));
+ for (int i = 0; i < order.size(); i++) {
+ String name = stringAt(order, i);
+ JmolList<Object> thisScene = getMapList(scenes, name);
+ if (thisScene == null)
+ continue;
+ pymolScene.buildScene(name, thisScene, htObjNames, htSecrets);
+ appendLoadNote("scene: " + name);
+ }
}
+ pymolScene.setCarveSets(htObjNames);
}
////////////////// set the rendering ////////////////
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-05-30 16:35:52 UTC (rev 18265)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-05-30 20:46:54 UTC (rev 18266)
@@ -34,7 +34,7 @@
*
*/
class PyMOLScene implements JmolSceneGenerator {
-
+
private Viewer viewer;
private int pymolVersion;
@@ -45,7 +45,7 @@
BS bsLabeled = new BS();
BS bsHydrogen = new BS();
BS bsNoSurface = new BS();
-
+
// private -- only needed for file reading
private Map<Float, BS> htSpacefill = new Hashtable<Float, BS>();
@@ -85,6 +85,8 @@
// private -- needed for processing Scenes
private BS bsCartoon = new BS();
+ private Map<String, BS> htCarveSets = new Hashtable<String, BS>();
+ private Map<String, BS> htDefinedAtoms = new Hashtable<String, BS>();
private Map<String, Boolean> htHiddenObjects = new Hashtable<String,
Boolean>();
private JmolList<String> moleculeNames = new JmolList<String>();
private JmolList<JmolObject> jmolObjects = new JmolList<JmolObject>();
@@ -116,6 +118,7 @@
private String objectName;
private String objectNameID;
+ private String objectSelectionName;
private int objectType;
private BS objectAtoms;
private boolean objectHidden;
@@ -136,7 +139,10 @@
private String mepList;
private boolean doCache;
-
+ private boolean haveScenes;
+ private BS bsCarve;
+ private boolean solventAccessible;
+
void setStateCount(int stateCount) {
this.stateCount = stateCount;
}
@@ -162,9 +168,9 @@
objectHidden = isHidden;
objectNameID = (objectName == null ? null : PyMOLScene.fixName(objectName
+ ext));
-
objectSettings = new Hashtable<Integer, JmolList<Object>>();
if (objectName != null) {
+ objectSelectionName = getSelectionName(name);
if (groupName != null) {
htObjectGroups.put(objectName, groupName);
htObjectGroups.put(objectNameID, groupName);
@@ -173,7 +179,8 @@
Integer.valueOf(type) });
htObjectSettings.put(objectName, objectSettings);
if (list != null && list.size() != 0) {
- Logger.info(objectName + " local settings: " + list.toString());
+ if (Logger.debugging)
+ Logger.info(objectName + " local settings: " + list.toString());
for (int i = list.size(); --i >= 0;) {
JmolList<Object> setting = (JmolList<Object>) list.get(i);
objectSettings.put((Integer) setting.get(0), setting);
@@ -193,6 +200,16 @@
cartoonRockets = booleanSetting(PyMOL.cartoon_cylindrical_helices);
surfaceMode = (int) floatSetting(PyMOL.surface_mode);
surfaceColor = (int) floatSetting(PyMOL.surface_color);
+ solventAccessible = booleanSetting(PyMOL.surface_solvent);
+ String carveSet = stringSetting(PyMOL.surface_carve_selection).trim();
+ if (carveSet.length() == 0) {
+ bsCarve = null;
+ } else {
+ bsCarve = htCarveSets.get(carveSet);
+ if (bsCarve == null)
+ htCarveSets.put(carveSet, bsCarve = new BS());
+ }
+
//solventAsSpheres = getBooleanSetting(PyMOL.sphere_solvent); - this is
for SA-Surfaces
labelPosition = new P3();
try {
@@ -250,7 +267,7 @@
// {name : [ visFlag, repOn, objVis, color ], ...}
// As far as I can tell, repOn is not useful, and objVis
// is only used for measurements.
-
+
Map<String, Object> visibilities = (Map<String, Object>) thisScene.get(1);
smap.put("visibilities", visibilities);
@@ -282,7 +299,7 @@
smap.put("colors", colors);
addJmolObject(T.scene, null, smap).objectNameID = name;
}
-
+
/**
* Generate the saved scene.
*
@@ -302,10 +319,11 @@
addJmolObject(T.frame, null, Integer.valueOf(frame.intValue() - 1));
try {
int istate = (frame == null ? 0 : frame.intValue());
- generateVisibilities((Map<String, Object>) scene.get("visibilities"),
istate);
+ generateVisibilities((Map<String, Object>) scene.get("visibilities"),
+ istate);
generateColors((Object[]) scene.get("colors"), istate);
generateShapes((Object[]) scene.get("moleculeReps"), istate);
- setRendering();
+ finalizeEverything();
finalizeObjects();
} catch (Exception e) {
System.out.println("PyMOLScene exception " + e);
@@ -322,15 +340,19 @@
Object[] item = (Object[]) colors[i];
int color = ((Integer) item[0]).intValue();
int icolor = PyMOL.getRGB(color);
- BS bs = new BS();
JmolList<Object> molecules = (JmolList<Object>) item[1];
- // all states will be colored?
- for (int j = molecules.size(); --j >= 0;)
- selectAllAtoms(listAt(molecules, j), istate, bs);
+ BS bs = getSelectionAtoms(molecules, istate, new BS());
addJmolObject(JC.SHAPE_BALLS, bs, null).argb = icolor;
}
}
+ private BS getSelectionAtoms(JmolList<Object> molecules, int istate, BS bs) {
+ if (molecules != null)
+ for (int j = molecules.size(); --j >= 0;)
+ selectAllAtoms(listAt(molecules, j), istate, bs);
+ return bs;
+ }
+
private void selectAllAtoms(JmolList<Object> obj, int istate, BS bs) {
String name = (String) obj.get(0);
setObject(name, istate);
@@ -352,7 +374,7 @@
BS bs = new BS();
addJmolObject(T.hide, null, null);
for (Entry<String, PyMOLGroup> e : groups.entrySet())
- e.getValue().visible = true;
+ e.getValue().visible = true;
for (Entry<String, Object> e : vis.entrySet()) {
String name = e.getKey();
if (name.equals("all"))
@@ -380,8 +402,8 @@
JmolList<Object> list = (JmolList<Object>) e.getValue();
int tok = (objectHidden ? T.hide : T.display);
bs = null;
- String info = "__" + fixName(name);
- switch (getObjectType(name)) {
+ String info = objectSelectionName;
+ switch (objectType) {
case PyMOL.OBJECT_MOLECULE:
bs = viewer.getDefinedAtomSet(info);
if (bs.nextSetBit(0) < 0)
@@ -412,8 +434,9 @@
private void setObject(String name, int istate) {
objectName = name;
objectType = getObjectType(name);
- objectNameID = (istate == 0 ? getObjectID(name) : "__" + fixName(name)
- + "_" + istate);
+ objectSelectionName = getSelectionName(name);
+ objectNameID = (istate == 0 ? getObjectID(name) : objectSelectionName + "_"
+ + istate);
objectAtoms = htObjectAtoms.get(name);
objectSettings = htObjectSettings.get(name);
String groupName = htObjectGroups.get(objectName);
@@ -475,12 +498,13 @@
return getColorPt(c.get(2));
}
- void setObjects(String mepList, boolean doCache,
- int baseModelIndex, int baseAtomIndex, boolean haveScenes) {
+ void setObjects(String mepList, boolean doCache, int baseModelIndex,
+ int baseAtomIndex, boolean haveScenes) {
this.baseModelIndex = baseModelIndex;
this.baseAtomIndex = baseAtomIndex;
this.mepList = mepList;
this.doCache = doCache;
+ this.haveScenes = haveScenes;
clearReaderData(!haveScenes);
finalizeObjects();
}
@@ -583,19 +607,24 @@
occludedObjects.put(objectNameID, Boolean.TRUE);
htHiddenObjects.put(objectName, Boolean.TRUE);
}
- if (parent != null)
+ if (parent != null && parent.length() != 0)
getGroup(parent).addList(myGroup);
return myGroup;
}
- void addGroupAtoms(PyMOLGroup group, BS bsAtoms) {
- group.bsAtoms = bsAtoms;
+ private PyMOLGroup getGroup(String name) {
+ PyMOLGroup g = groups.get(name);
+ if (g == null) {
+ groups.put(name, (g = new PyMOLGroup(name)));
+ defineAtoms(name, g.bsAtoms);
+ }
+ return g;
}
/**
* Create group JmolObjects, and set hierarchical visibilities
*/
- void setRendering() {
+ void finalizeEverything() {
viewer.setStringProperty("measurementUnits", "ANGSTROMS");
viewer.setBooleanProperty("zoomHeight", true);
setGroupVisibilities();
@@ -612,17 +641,36 @@
addJmolObject(T.hidden, bsHidden, null);
}
+ void setCarveSets(Map<String, JmolList<Object>> htObjNames) {
+ if (htCarveSets.isEmpty())
+ return;
+ for (Entry<String, BS> e: htCarveSets.entrySet())
+ getSelectionAtoms(listAt(htObjNames.get(e.getKey()), 5), 0,
e.getValue());
+ }
+
private void setGroupVisibilities() {
if (groups != null) {
Collection<PyMOLGroup> list = groups.values();
+ BS bsAll = new BS();
for (PyMOLGroup g : list) {
- if (g.parent != null)
- continue;
- setGroupVisible(g, true);
+ bsAll.or(g.bsAtoms);
+ if (g.parent == null) // top
+ setGroupVisible(g, true);
+ else if (g.list.isEmpty()) // bottom
+ g.addGroupAtoms(new BS());
}
+ defineAtoms("all", bsAll);
}
}
+ private void defineAtoms(String name, BS bs) {
+ htDefinedAtoms.put(getSelectionName(name), bs);
+ }
+
+ private static String getSelectionName(String name) {
+ return "__" + fixName(name);
+ }
+
void createShapeObjects(BS[] reps, boolean allowSurface, int atomCount0,
int atomCount) {
if (atomCount >= 0) {
@@ -752,6 +800,20 @@
}
}
+ @SuppressWarnings("unchecked")
+ String stringSetting(int i) {
+ try {
+ JmolList<Object> setting = null;
+ if (objectSettings != null)
+ setting = objectSettings.get(Integer.valueOf(i));
+ if (setting == null)
+ setting = (JmolList<Object>) settings.get(i);
+ return setting.get(2).toString();
+ } catch (Exception e) {
+ return null;
+ }
+ }
+
static P3 pointAt(JmolList<Object> list, int i, P3 pt) {
pt.set(floatAt(list, i++), floatAt(list, i++), floatAt(list, i));
return pt;
@@ -785,9 +847,9 @@
return labelPos;
}
- boolean addMeasurements(MeasurementData[] mdList, int nCoord,
JmolList<Object> list, BS bsReps,
- int color, JmolList<Object> offsets,
- boolean haveLabels) {
+ boolean addMeasurements(MeasurementData[] mdList, int nCoord,
+ JmolList<Object> list, BS bsReps, int color,
+ JmolList<Object> offsets, boolean haveLabels) {
boolean isNew = (mdList == null);
int n = (isNew ? list.size() / 3 / nCoord : mdList.length);
if (n == 0)
@@ -821,13 +883,13 @@
offset = floatsAt(listAt(offsets, index), 0, new float[7], 7);
if (offset == null)
offset = setLabelPosition(labelPosition, new float[7]);
- md = mdList[index] = new MeasurementData(objectNameID + "_" + (index +
1),
- viewer, points);
+ md = mdList[index] = new MeasurementData(objectNameID + "_"
+ + (index + 1), viewer, points);
md.note = objectName;
} else {
md = mdList[index];
offset = md.text.pymolOffset;
- }
+ }
int nDigits = (int) floatSetting(MEAS_DIGITS[nCoord - 2]);
String strFormat = nCoord + ": "
+ (drawLabel ? "%0." + (nDigits < 0 ? 1 : nDigits) + "VALUE" : "");
@@ -884,7 +946,6 @@
atomColorList.addLast(Integer.valueOf(getColix(atomColor, translucency)));
}
-
void setFrameObject(int type, Object info) {
if (info != null) {
frameObj = getJmolObject(type, null, info);
@@ -901,20 +962,28 @@
for (int i = chars.length; --i >= 0;)
if (!Character.isLetterOrDigit(chars[i]))
chars[i] = '_';
- return String.valueOf(chars);
+ return String.valueOf(chars);
}
String getObjectID(String name) {
- return (String)objectInfo.get(name)[0];
+ return (String) objectInfo.get(name)[0];
}
int getObjectType(String name) {
- return ((Integer)objectInfo.get(name)[1]).intValue();
+ return ((Integer) objectInfo.get(name)[1]).intValue();
}
- void setAtomMap(int[] atomMap, BS bsAtoms) {
+ BS setAtomMap(int[] atomMap, int atomCount0) {
htAtomMap.put(objectNameID, atomMap);
- htObjectAtoms.put(objectName, bsAtoms);
+ BS bsAtoms = htDefinedAtoms.get(objectSelectionName);
+ if (bsAtoms == null) {
+ bsAtoms = BS.newN(atomCount0 + atomMap.length);
+ Logger.info("PyMOL molecule " + objectName);
+ htDefinedAtoms.put(objectSelectionName, bsAtoms);
+ htObjectAtoms.put(objectName, bsAtoms);
+ moleculeNames.addLast(objectName);
+ }
+ return bsAtoms;
}
private final static int[] MEAS_DIGITS = { PyMOL.label_distance_digits,
@@ -1034,7 +1103,8 @@
private void fixReps(BS[] reps) {
htSpacefill.clear();
bsCartoon.clearAll();
- for (int iAtom = objectAtoms.nextSetBit(0); iAtom >= 0; iAtom =
objectAtoms.nextSetBit(iAtom + 1)) {
+ for (int iAtom = objectAtoms.nextSetBit(0); iAtom >= 0; iAtom = objectAtoms
+ .nextSetBit(iAtom + 1)) {
float rad = 0;
int uniqueID = (reader == null ? uniqueIDs[iAtom] : reader
.getUniqueID(iAtom));
@@ -1089,9 +1159,9 @@
}
}
}
-
+
reps[PyMOL.REP_CARTOON].and(bsCartoon);
- cleanSingletons(reps[PyMOL.REP_CARTOON]);
+ cleanSingletons(reps[PyMOL.REP_CARTOON]);
cleanSingletons(reps[PyMOL.REP_RIBBON]);
cleanSingletons(reps[PyMOL.REP_JMOL_TRACE]);
cleanSingletons(reps[PyMOL.REP_JMOL_PUTTY]);
@@ -1176,9 +1246,8 @@
jo.rd = new RadiusData(null, f, RadiusData.EnumType.FACTOR,
EnumVdw.AUTO);
break;
case PyMOL.REP_CARTOON:
- createCartoonObject("H",
- (cartoonRockets ? PyMOL.cartoon_helix_radius
- : PyMOL.cartoon_oval_length));
+ createCartoonObject("H", (cartoonRockets ? PyMOL.cartoon_helix_radius
+ : PyMOL.cartoon_oval_length));
createCartoonObject("S", PyMOL.cartoon_rect_length);
createCartoonObject("L", PyMOL.cartoon_loop_radius);
createCartoonObject(" ", PyMOL.cartoon_loop_radius);
@@ -1189,10 +1258,12 @@
jo.translucency = floatSetting(PyMOL.transparency);
break;
case PyMOL.REP_SURFACE: // = 2;
- jo = addJmolObject(T.isosurface, bs, new String[] {
+ float withinDistance = floatSetting(PyMOL.surface_carve_cutoff);
+ jo = addJmolObject(T.isosurface, bs, new Object[] {
booleanSetting(PyMOL.two_sided_lighting) ? "FULLYLIT" : "FRONTLIT",
- (surfaceMode == 3 || surfaceMode == 4) ? " only" : "" });
- jo.setSize(floatSetting(PyMOL.solvent_radius));
+ (surfaceMode == 3 || surfaceMode == 4) ? " only" : "",
+ bsCarve, Float.valueOf(withinDistance)});
+ jo.setSize(floatSetting(PyMOL.solvent_radius) * (solventAccessible ? -1
: 1));
jo.translucency = floatSetting(PyMOL.transparency);
if (surfaceColor >= 0)
jo.argb = PyMOL.getRGB(surfaceColor);
@@ -1353,9 +1424,7 @@
htHiddenObjects.put(g.name, Boolean.TRUE);
switch (g.type) {
case PyMOL.OBJECT_MOLECULE:
- if (g.bsAtoms != null) {
- bsHidden.or(g.bsAtoms);
- }
+ bsHidden.or(g.bsAtoms);
break;
default:
// a group?
@@ -1367,13 +1436,6 @@
}
}
- private PyMOLGroup getGroup(String name) {
- PyMOLGroup g = groups.get(name);
- if (g == null)
- groups.put(name, (g = new PyMOLGroup(name)));
- return g;
- }
-
private float getUniqueFloat(int uniqueID, int i) {
float f;
switch (i) {
@@ -1399,13 +1461,8 @@
return bs;
}
- public void addMolecule(String objectName) {
- moleculeNames .addLast(objectName);
- }
-
/**
- * return a map of lists of the type:
- * [ [name1,...], [name2,...], ...]
+ * return a map of lists of the type: [ [name1,...], [name2,...], ...]
*
* @param list
* @return Hashtable
@@ -1415,10 +1472,25 @@
for (int i = list.size(); --i >= 0;) {
JmolList<Object> item = PyMOLScene.listAt(list, i);
if (item != null && item.size() > 0)
- map.put((String)item.get(0), item);
+ map.put((String) item.get(0), item);
}
return map;
}
+ Map<String, Object> setAtomDefs() {
+ setGroupVisibilities();
+ Map<String, Object> defs = new Hashtable<String, Object>();
+ for (Entry<String, BS> e: htDefinedAtoms.entrySet()) {
+ BS bs = e.getValue();
+ if (!bs.isEmpty())
+ defs.put(e.getKey(), bs);
+ }
+ addJmolObject(T.define, null, defs);
+ return defs;
+ }
+ public boolean needSelections() {
+ return haveScenes || !htCarveSets.isEmpty();
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-05-30 16:35:52 UTC
(rev 18265)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-05-30 20:46:54 UTC
(rev 18266)
@@ -9,8 +9,9 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.16_dev_2013.05.30b"
+___JmolVersion="13.1.16_dev_2013.05.30c"
+PyMOL: adds SASURFACE option (surface_solvent ON), with "carving"
(ProFusion_ABL.pse, scene F6)
new feature: restore SCENE "xxxx" nSec
new feature: Scene menu
-- PyMOL scene names, in order
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