Revision: 18305
http://sourceforge.net/p/jmol/code/18305
Author: hansonr
Date: 2013-06-07 19:15:26 +0000 (Fri, 07 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.17"
TODO: PyMOL uniqueAtomSettings for selected atom settings
new feature: set translucent
-- default TRUE : translucent objects are fully translucent
-- FALSE: translucent object are opaque to other translucent objects
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.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/JmolRendererInterface.java
trunk/Jmol/src/org/jmol/export/Export3D.java
trunk/Jmol/src/org/jmol/exportjs/Export3D.java
trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/shape/AtomShape.java
trunk/Jmol/src/org/jmol/shapebio/BioShapeCollection.java
trunk/Jmol/src/org/jmol/util/GData.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateManager.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
2013-06-06 22:17:52 UTC (rev 18304)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2013-06-07 19:15:26 UTC (rev 18305)
@@ -199,7 +199,6 @@
id = JC.SHAPE_BALLS;
break;
case JC.SHAPE_BALLS:
- color = "colorballs";
break;
case JC.SHAPE_TRACE:
case JC.SHAPE_BACKBONE:
@@ -219,6 +218,16 @@
}
switch (id) {
+ case JC.SHAPE_DOTS:
+ case JC.SHAPE_BALLS:
+ case JC.SHAPE_STARS:
+ case JC.SHAPE_ELLIPSOIDS: // not implemented
+ if (info instanceof Object[]) {
+ sm.loadShape(id);
+ sm.setShapePropertyBs(id, "params", info, bsAtoms);
+ return;
+ }
+ break;
case JC.SHAPE_MEASURES:
if (modelIndex < 0)
return;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java 2013-06-06
22:17:52 UTC (rev 18304)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java 2013-06-07
19:15:26 UTC (rev 18305)
@@ -59,7 +59,8 @@
"labels","nb_spheres",
"cartoon","ribbon","lines",
"mesh","dots","dashes",
- "nonbonded"};//',"slice"};
+ "nonbonded","cell","cgo","callback","extent",
+ "slice","angles","dihedrals","ellipsoid","volume"};
final static int REP_STICKS = 0;
@@ -74,14 +75,7 @@
final static int REP_DOTS = 9; // dots; also used for objMap
final static int REP_DASHES = 10; // for measurements
final static int REP_NONBONDED = 11;
- final static int REP_MAX = 12;
-
- // a continuation of PyMOL.REP_xxx
- final static int REP_JMOL_TRACE = 12;
- final static int REP_JMOL_PUTTY = 13;
- final static int REP_JMOL_MAX = 14;
-
- // ???
+
final static int REP_CELL = 12; // for objMesh, objSurface
final static int REP_CGO = 13; // for sculpt mode, objAlignment, objCGO
final static int REP_CALLBACK = 14; // for objCallback
@@ -89,8 +83,17 @@
final static int REP_SLICE = 16; // for objSlice
final static int REP_ANGLES = 17;
final static int REP_DIHEDRALS = 18;
+ final static int REP_ELLIPSOID = 19;
+ final static int REP_VOLUME = 20;
+ final static int REP_MAX = 21;
+ // a continuation of PyMOL.REP_xxx
+ final static int REP_JMOL_TRACE = 21;
+ final static int REP_JMOL_PUTTY = 22;
+ final static int REP_JMOL_MAX = 23;
+
+ // ???
// flag 24:
@@ -6242,18 +6245,22 @@
public static float getDefaultSetting(int i, int pymolVersion) {
switch (i) {
- case stick_color:
- return -1;
case label_size:
return 14;
+ case line_color:
+ case stick_color:
case label_distance_digits:
case label_angle_digits:
case label_dihedral_digits:
+ case ellipsoid_color:
return -1;
case ray_pixel_scale:
+ case ellipsoid_scale:
return 1;
default:
Logger.info("PyMOL " + pymolVersion + " does not have setting " + i);
+ //$FALL-THROUGH$
+ case ellipsoid_transparency:
return 0;
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-06 22:17:52 UTC (rev 18304)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-07 19:15:26 UTC (rev 18305)
@@ -1025,6 +1025,9 @@
int flags = intAt(a, 24);
//System.out.println(atomCount + " " + group3 + " " + serNo + " " +
Integer.toHexString(flags));
boolean bonded = (intAt(a, 25) != 0);
+
+ // repurposing vectorX,Y,Z
+
int uniqueID = (a.size() > 40 && intAt(a, 40) == 1 ? intAt(a, 32) : -1);
atom.vectorX = uniqueID;
atom.vectorY = cartoonType;
@@ -1034,7 +1037,7 @@
}
//if (uniqueID > 0)
//pymolScene.setUnique(uniqueID, atom);
- pymolScene.setAtomColor(uniqueID, atomColor);
+ pymolScene.setAtomColor(atomColor);
processAtom2(atom, serNo, x, y, z, formalCharge);
// set pymolScene bit sets and create labels
@@ -1261,13 +1264,15 @@
uniqueIDs[i] = getUniqueID(i);
sequenceNumbers[i] = getSequenceNumber(i);
radii[i] = getVDW(i);
- if (lastAtomChain != atoms[i].chainID || lastAtomSet !=
atoms[i].atomSetIndex) {
+ if (lastAtomChain != atoms[i].chainID
+ || lastAtomSet != atoms[i].atomSetIndex) {
newChain[i] = true;
lastAtomChain = atoms[i].chainID;
lastAtomSet = atoms[i].atomSetIndex;
}
}
- pymolScene.setAtomInfo(uniqueIDs, cartoonTypes, sequenceNumbers, newChain,
radii);
+ pymolScene.setAtomInfo(uniqueIDs, cartoonTypes, sequenceNumbers,
+ newChain, radii);
}
// generally useful static methods
@@ -1288,9 +1293,11 @@
private static BS getBsReps(JmolList<Object> list) {
BS bsReps = new BS();
- for (int i = 0; i < PyMOL.REP_MAX; i++)
+ int n = Math.min(list.size(), PyMOL.REP_MAX);
+ for (int i = 0; i < n; i++) {
if (intAt(list, i) == 1)
bsReps.set(i);
+ }
return bsReps;
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-06 22:17:52 UTC (rev 18304)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-07 19:15:26 UTC (rev 18305)
@@ -34,6 +34,37 @@
*
*/
class PyMOLScene implements JmolSceneGenerator {
+
+//accounted for:
+//
+// dot_color
+// ellipsoid_color
+// ellipsoid_transparency
+// ellipsoid_scale
+// label_color
+// label_position
+// nonbonded_transparency
+// sphere_color
+// sphere_scale
+// sphere_transparency
+//
+//TODO needed:
+//
+// cartoon_color
+// mesh_color
+// ribbon_color
+// surface_color
+// transparency (surface only)
+//
+//special (probably) PyMOL-only:
+//
+// ladder_color
+// ladder_mode
+// ladder_radius
+// ring_color
+// ring_mode
+// ring_radius
+// ring_width
private Viewer viewer;
private int pymolVersion;
@@ -58,29 +89,30 @@
private Map<String, PyMOLGroup> groups;
private Map<Integer, JmolList<Object>> objectSettings;
- private void clearReaderData(boolean isAll) {
+ private void clearReaderData() {
reader = null;
colixes = null;
atomColorList = null;
objectSettings = null;
stateSettings = null;
- if (!isAll)
+ if (haveScenes)
return;
+ settings = null;
groups = null;
labels = null;
+ ssMapAtom = null;
htSpacefill = null;
- ssMapAtom = null;
htAtomMap = null;
htMeasures = null;
htObjectGroups = null;
htObjectAtoms = null;
htObjectSettings = null;
htStateSettings = null;
+ htHiddenObjects = null;
objectInfo = null;
- settings = null;
occludedObjects = null;
- htHiddenObjects = null;
- bsHidden = bsNucleic = bsNonbonded = bsLabeled = bsHydrogen = bsNoSurface
= bsCartoon = null;
+ bsHidden = bsNucleic = bsNonbonded = bsLabeled = bsHydrogen = bsNoSurface
+ = bsCartoon = null;
}
// private -- needed for processing Scenes
@@ -114,6 +146,7 @@
bsUniqueBonds.set(index);
}
private int bgRgb;
+ private int dotColor;
private int surfaceMode;
private int surfaceColor;
private int sphereColor;
@@ -123,6 +156,7 @@
private float labelSize;
private float meshWidth;
private float nonbondedSize;
+ private float nonbondedTranslucency;
private float sphereScale;
private float sphereTranslucency;
private float stickTranslucency;
@@ -137,7 +171,7 @@
private String objectNameID;
private String objectJmolName;
private int objectType;
- private BS objectAtoms;
+ private BS bsAtoms;
private boolean objectHidden;
// during file loading we have a reader, but after that we must rely on data
saved by the server
@@ -178,6 +212,7 @@
this.pymolVersion = pymolVersion;
this.haveScenes = haveScenes;
setVersionSettings();
+ settings.trimToSize();
bgRgb = colorSetting(listAt(settings, PyMOL.bg_rgb));
pointAt((JmolList<Object>) listAt(settings, PyMOL.label_position).get(2),
0, labelPosition0);
@@ -227,7 +262,9 @@
private void getObjectSettings() {
transparency = floatSetting(PyMOL.transparency);
+ dotColor = (int) floatSetting(PyMOL.dot_color);
nonbondedSize = floatSetting(PyMOL.nonbonded_size);
+ nonbondedTranslucency = floatSetting(PyMOL.nonbonded_transparency);
sphereScale = floatSetting(PyMOL.sphere_scale);
sphereColor = (int) floatSetting(PyMOL.sphere_color);
cartoonTranslucency = floatSetting(PyMOL.cartoon_transparency);
@@ -298,7 +335,7 @@
objectJmolName = getJmolName(name);
objectNameID = (istate == 0 && objectType != 0 ? getObjectID(name) :
objectJmolName + "_"
+ istate);
- objectAtoms = htObjectAtoms.get(name);
+ bsAtoms = htObjectAtoms.get(name);
objectSettings = htObjectSettings.get(name);
stateSettings = htStateSettings.get(name+"_" + istate);
String groupName = htObjectGroups.get(name);
@@ -594,7 +631,7 @@
this.baseAtomIndex = baseAtomIndex;
this.mepList = mepList;
this.doCache = doCache;
- clearReaderData(!haveScenes);
+ clearReaderData();
finalizeObjects();
if (!haveScenes) {
uniqueSettings = null;
@@ -777,16 +814,16 @@
int atomCount) {
if (atomCount >= 0) {
// initial creation, not just going to this scene
- objectAtoms = BSUtil.newBitSet2(atomCount0, atomCount);
+ bsAtoms = BSUtil.newBitSet2(atomCount0, atomCount);
JmolObject jo;
// from reader
- jo = addJmolObject(T.atoms, objectAtoms, null);
+ jo = addJmolObject(T.atoms, bsAtoms, null);
colixes = ArrayUtil.ensureLengthShort(colixes, atomCount);
for (int i = atomCount; --i >= atomCount0;)
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, bsAtoms, null);
jo.setSize(0);
}
createShapeObject(PyMOL.REP_LINES, reps[PyMOL.REP_LINES]);
@@ -827,7 +864,7 @@
createShapeObject(i, reps[i]);
continue;
}
- objectAtoms = null;
+ bsAtoms = null;
}
void addLabel(int atomIndex, int uniqueID, int atomColor,
@@ -852,9 +889,7 @@
labelPos[i] = floatAt(labelOffset, i);
}
labels.put(Integer.valueOf(atomIndex), newTextLabel(label, labelPos,
- icolor, (int) getUniqueFloatDef(uniqueID, PyMOL.label_font_id,
- labelFontId), getUniqueFloatDef(uniqueID, PyMOL.label_size,
- labelSize)));
+ icolor, labelFontId, labelSize));
}
float getUniqueFloatDef(int id, int key, float defaultValue) {
@@ -1018,7 +1053,8 @@
SB getViewScript(JmolList<Object> view) {
SB sb = new SB();
float[] pymolView = getPymolView(view, true);
- sb.append(";set zshadePower 1;set traceAlpha "
+ sb.append(";set translucent " + (globalSetting(PyMOL.transparency_mode) !=
2)
+ + ";set zshadePower 1;set traceAlpha "
+ (globalSetting(PyMOL.cartoon_round_helices) != 0));
boolean rockets = cartoonRockets;
sb.append(";set cartoonRockets " + rockets);
@@ -1051,10 +1087,8 @@
.get(5)));
}
- void setAtomColor(int uniqueID, int atomColor) {
- float translucency = getUniqueFloatDef(uniqueID, PyMOL.sphere_transparency,
- sphereTranslucency);
- atomColorList.addLast(Integer.valueOf(getColix(atomColor, translucency)));
+ void setAtomColor(int atomColor) {
+ atomColorList.addLast(Integer.valueOf(getColix(atomColor, 0)));
}
void setFrameObject(int type, Object info) {
@@ -1215,17 +1249,17 @@
private void fixReps(BS[] reps) {
htSpacefill.clear();
bsCartoon.clearAll();
- for (int iAtom = objectAtoms.nextSetBit(0); iAtom >= 0; iAtom = objectAtoms
+ for (int iAtom = bsAtoms.nextSetBit(0); iAtom >= 0; iAtom = bsAtoms
.nextSetBit(iAtom + 1)) {
float rad = 0;
int uniqueID = (reader == null ? uniqueIDs[iAtom] : reader
.getUniqueID(iAtom));
if (reps[PyMOL.REP_SPHERES].get(iAtom)) {
rad = (reader == null ? radii[iAtom] : reader.getVDW(iAtom))
- * getUniqueFloat(uniqueID, PyMOL.sphere_scale);
+ * getUniqueFloatDef(uniqueID, PyMOL.sphere_scale, sphereScale);
} else if (reps[PyMOL.REP_NBSPHERES].get(iAtom)) {
// Penta_vs_mutants calcium
- rad = getUniqueFloat(uniqueID, PyMOL.nonbonded_size);
+ rad = nonbondedSize;
}
if (rad != 0) {
Float r = Float.valueOf(rad);
@@ -1291,7 +1325,7 @@
private void cleanSingletons(BS bs) {
if (bs.isEmpty())
return;
- bs.and(objectAtoms);
+ bs.and(bsAtoms);
BS bsr = new BS();
int n = bs.length();
int pass = 0;
@@ -1334,7 +1368,6 @@
*/
private void createShapeObject(int shapeID, BS bs) {
// add more to implement
- float f;
if (bs.isEmpty())
return;
JmolObject jo = null;
@@ -1343,61 +1376,27 @@
bs.and(bsNonbonded);
if (bs.isEmpty())
return;
- jo = addJmolObject(JC.SHAPE_STARS, bs, null);
- jo.rd = new RadiusData(null, nonbondedSize / 2,
- RadiusData.EnumType.FACTOR, EnumVdw.AUTO);
+ setUniqueObjects(JC.SHAPE_STARS, bs, 0, 0, PyMOL.nonbonded_transparency,
nonbondedTranslucency, 0, nonbondedSize, 0.5f);
break;
case PyMOL.REP_NBSPHERES:
case PyMOL.REP_SPHERES:
- jo = addJmolObject(JC.SHAPE_BALLS, bs, null);
- f = sphereColor;
- if (f != -1)
- jo.argb = PyMOL.getRGB((int) f);
- jo.translucency = sphereTranslucency;
+ setUniqueObjects(JC.SHAPE_BALLS, bs, PyMOL.sphere_color, sphereColor,
PyMOL.sphere_transparency, sphereTranslucency, PyMOL.sphere_scale, sphereScale,
1);
break;
+ case PyMOL.REP_ELLIPSOID:
+ float ellipsoidTranslucency = floatSetting(PyMOL.ellipsoid_transparency);
+ int ellipsoidColor = (int) floatSetting(PyMOL.ellipsoid_color);
+ float ellipsoidScale = floatSetting(PyMOL.ellipsoid_scale);
+ setUniqueObjects(JC.SHAPE_ELLIPSOIDS, bs, PyMOL.ellipsoid_color,
ellipsoidColor, PyMOL.ellipsoid_transparency, ellipsoidTranslucency,
PyMOL.ellipsoid_scale, ellipsoidScale, 1);
+ break;
case PyMOL.REP_DOTS:
- jo = addJmolObject(JC.SHAPE_DOTS, bs, null);
- f = sphereScale;
- jo.rd = new RadiusData(null, f, RadiusData.EnumType.FACTOR,
EnumVdw.AUTO);
+ setUniqueObjects(JC.SHAPE_DOTS, bs, PyMOL.dot_color, dotColor, 0, 0,
PyMOL.sphere_scale, sphereScale, 1);
break;
- case PyMOL.REP_CARTOON:
- 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);
- break;
- case PyMOL.REP_MESH: // = 8;
- jo = addJmolObject(T.isosurface, bs, null);
- jo.setSize(floatSetting(PyMOL.solvent_radius));
- jo.translucency = transparency;
- break;
- case PyMOL.REP_SURFACE: // = 2;
- 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" : "",
- bsCarve, Float.valueOf(withinDistance)});
- jo.setSize(floatSetting(PyMOL.solvent_radius) * (solventAccessible ? -1
: 1));
- jo.translucency = transparency;
- if (surfaceColor >= 0)
- jo.argb = PyMOL.getRGB(surfaceColor);
- break;
case PyMOL.REP_LABELS: // = 3;
bs.and(bsLabeled);
if (bs.isEmpty())
return;
jo = addJmolObject(JC.SHAPE_LABELS, bs, labels);
break;
- case PyMOL.REP_JMOL_PUTTY:
- createPuttyObject(bs);
- break;
- case PyMOL.REP_JMOL_TRACE:
- createTraceObject(bs);
- break;
- case PyMOL.REP_RIBBON: // backbone or trace, depending
- createRibbonObject(bs);
- break;
case PyMOL.REP_LINES:
jo = addJmolObject(T.wireframe, bs, null);
jo.setSize(floatSetting(PyMOL.line_width) / 15);
@@ -1413,11 +1412,74 @@
if (col >= 0)
jo.argb = PyMOL.getRGB(col);
break;
+ case PyMOL.REP_CARTOON:
+ 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);
+ break;
+ case PyMOL.REP_JMOL_PUTTY:
+ createPuttyObject(bs);
+ break;
+ case PyMOL.REP_JMOL_TRACE:
+ createTraceObject(bs);
+ break;
+ case PyMOL.REP_RIBBON: // backbone or trace, depending
+ createRibbonObject(bs);
+ break;
+ case PyMOL.REP_SURFACE: // = 2;
+ // unique translucency here involves creating ghost surfaces
+ 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" : "",
+ bsCarve, Float.valueOf(withinDistance)});
+ jo.setSize(floatSetting(PyMOL.solvent_radius) * (solventAccessible ? -1
: 1));
+ jo.translucency = transparency;
+ if (surfaceColor >= 0)
+ jo.argb = PyMOL.getRGB(surfaceColor);
+ break;
+ case PyMOL.REP_MESH: // = 8;
+ jo = addJmolObject(T.isosurface, bs, null);
+ jo.setSize(floatSetting(PyMOL.solvent_radius));
+ jo.translucency = transparency;
+ break;
default:
Logger.error("Unprocessed representation type " + shapeID);
}
}
+ private void setUniqueObjects(int shape, BS bs,
+ int setColor, int color,
+ int setTrans, float trans,
+ int setSize, float size, float f) {
+ int n = bs.cardinality();
+ short[] colixes = (setColor == 0 ? null : new short[n]);
+ float[] atrans = (setTrans == 0 ? null : new float[n]);
+ float[] sizes = new float[n];
+ for (int pt=0, i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1),
pt++) {
+ int id = (uniqueIDs == null ? -1 : uniqueIDs[i]);
+ if (colixes != null) {
+ int c = (int) getUniqueFloatDef(id, setColor, color);
+ if (c > 0)
+ colixes[pt] = getColix(c, 0);
+ }
+ if (atrans != null) {
+ atrans[pt] = getUniqueFloatDef(id, setTrans, trans);
+ }
+ sizes[pt] = getUniqueFloatDef(id, setSize, size) * f;
+ }
+ addJmolObject(shape, bs, new Object[] {colixes, atrans, sizes});
+
+// case PyMOL.REP_DOTS:
+ // addJmolObject(JC.SHAPE_DOTS, bs, null).rd = new RadiusData(null,
+ // value1, RadiusData.EnumType.FACTOR, EnumVdw.AUTO);
+// case PyMOL.REP_NONBONDED:
+ // addJmolObject(JC.SHAPE_STARS, bs, null).rd = new RadiusData(null,
+ // f / 2, RadiusData.EnumType.FACTOR, EnumVdw.AUTO);
+ }
+
/**
* Create a BALLS JmolObject for each radius.
*
@@ -1557,24 +1619,6 @@
}
}
- private float getUniqueFloat(int uniqueID, int i) {
- float f;
- switch (i) {
- case PyMOL.sphere_transparency:
- f = sphereTranslucency;
- break;
- case PyMOL.sphere_scale:
- f = sphereScale;
- break;
- case PyMOL.nonbonded_size:
- f = nonbondedSize;
- break;
- default:
- return 0;
- }
- return getUniqueFloatDef(uniqueID, i, f);
- }
-
BS getSSMapAtom(String ssType) {
BS bs = ssMapAtom.get(ssType);
if (bs == null)
Modified: trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java 2013-06-06
22:17:52 UTC (rev 18304)
+++ trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java 2013-06-07
19:15:26 UTC (rev 18305)
@@ -343,4 +343,6 @@
P3 navigationOffset,
float navigationDepthPercent);
+ public abstract boolean getTranslucentCoverOnly();
+
}
Modified: trunk/Jmol/src/org/jmol/export/Export3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/Export3D.java 2013-06-06 22:17:52 UTC
(rev 18304)
+++ trunk/Jmol/src/org/jmol/export/Export3D.java 2013-06-07 19:15:26 UTC
(rev 18305)
@@ -903,5 +903,9 @@
g3d.renderAllStrings(this);
}
+ public boolean getTranslucentCoverOnly() {
+ return g3d.getTranslucentCoverOnly();
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/exportjs/Export3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/exportjs/Export3D.java 2013-06-06 22:17:52 UTC
(rev 18304)
+++ trunk/Jmol/src/org/jmol/exportjs/Export3D.java 2013-06-07 19:15:26 UTC
(rev 18305)
@@ -900,5 +900,9 @@
// g3d only
}
+ public boolean getTranslucentCoverOnly() {
+ return g3d.getTranslucentCoverOnly();
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2013-06-06 22:17:52 UTC (rev
18304)
+++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2013-06-07 19:15:26 UTC (rev
18305)
@@ -198,11 +198,6 @@
private boolean addAllPixels;
private boolean haveTranslucentObjects;
- protected boolean translucentCoverOnly = false;
- public void setTranslucentCoverOnly(boolean TF) {
- translucentCoverOnly = TF;
- }
-
protected int[] pbuf;
protected int[] pbufT;
protected int[] zbuf;
@@ -264,7 +259,7 @@
}
@Override
- public void beginRendering(Matrix3f rotationMatrix, boolean isImageWrite) {
+ public void beginRendering(Matrix3f rotationMatrix, boolean translucentMode,
boolean isImageWrite) {
if (currentlyRendering)
endRendering();
if (windowWidth != newWindowWidth || windowHeight != newWindowHeight
@@ -285,6 +280,7 @@
isPass2 = false;
colixCurrent = 0;
haveTranslucentObjects = false;
+ translucentCoverOnly = !translucentMode;
addAllPixels = true;
if (pbuf == null) {
platform.allocateBuffers(windowWidth, windowHeight,
Modified: trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
2013-06-06 22:17:52 UTC (rev 18304)
+++ trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
2013-06-07 19:15:26 UTC (rev 18305)
@@ -166,6 +166,7 @@
mySlabValue = Math.round(pt2f.z + r * (1 - meshSlabValue / 50f));
}
}
+ boolean tcover = g3d.getTranslucentCoverOnly();
g3d.setTranslucentCoverOnly(imesh.frontOnly);
thePlane = imesh.jvxlData.jvxlPlane;
vertexValues = imesh.vertexValues;
@@ -177,7 +178,7 @@
} else {
isOK = renderMesh(imesh);
}
- g3d.setTranslucentCoverOnly(false);
+ g3d.setTranslucentCoverOnly(tcover);
return isOK;
}
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2013-06-06 22:17:52 UTC (rev
18304)
+++ trunk/Jmol/src/org/jmol/script/T.java 2013-06-07 19:15:26 UTC (rev
18305)
@@ -1040,8 +1040,9 @@
public final static int testflag1 = booleanparam | 184;
public final static int testflag2 = booleanparam | 186;
public final static int testflag3 = booleanparam | 188;
- public final static int testflag4 = booleanparam | 190;
- public final static int tracealpha = booleanparam | 191;
+ public final static int testflag4 = booleanparam | 189;
+ public final static int tracealpha = booleanparam | 190;
+ public final static int translucent = booleanparam | 191;
public final static int twistedsheets = booleanparam | 192;
public final static int usearcball = booleanparam | 193;
public final static int useminimizationthread = booleanparam | 194;
@@ -1274,7 +1275,6 @@
final static int torsion = misc | 350;
final static int transform = misc | 352;
public final static int translation = misc | 354;
- public final static int translucent = misc | 356;
public final static int triangles = misc | 358;
final static int url = misc | 360 | expression;
final static int user = misc | 362;
Modified: trunk/Jmol/src/org/jmol/shape/AtomShape.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/AtomShape.java 2013-06-06 22:17:52 UTC
(rev 18304)
+++ trunk/Jmol/src/org/jmol/shape/AtomShape.java 2013-06-07 19:15:26 UTC
(rev 18305)
@@ -28,6 +28,7 @@
import org.jmol.atomdata.RadiusData;
import org.jmol.atomdata.RadiusData.EnumType;
import org.jmol.constant.EnumPalette;
+import org.jmol.constant.EnumVdw;
import org.jmol.modelset.Atom;
import org.jmol.modelset.Group;
import org.jmol.util.ArrayUtil;
@@ -98,8 +99,6 @@
for (int i = i0; i >= 0; i = (isAll ? i - 1 : bsSelected.nextSetBit(i +
1))) {
Atom atom = atoms[i];
mads[i] = atom.calculateMad(viewer, rd);
- //System.out.println("atomshape - setSize " + i + " " + rd);
-// System.out.println("atomSHape " + atom + " mad=" + mads[i]);
bsSizeSet.setBitTo(i, isVisible);
atom.setShapeVisibility(myVisibilityFlag, isVisible);
}
@@ -116,20 +115,34 @@
setColixAndPalette(colix, pid, i);
return;
}
- if ("colors" == propertyName) {
+ if ("params" == propertyName) {
isActive = true;
Object[] data = (Object[]) value;
short[] colixes = (short[]) data[0];
- float translucency = ((Float) data[1]).floatValue();
+ float[] atrans = (float[]) data[1];
+ float[] sizes = (float[]) data[2];
+ RadiusData rd = new RadiusData(null, 0, RadiusData.EnumType.FACTOR,
+ EnumVdw.AUTO);
if (bsColixSet == null)
bsColixSet = new BS();
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
- if (i >= colixes.length)
- continue;
- short colix = colixes[i];
- if (translucency > 0.01f)
- colix = C.getColixTranslucent3(colix, true, translucency);
+ if (bsSizeSet == null)
+ bsSizeSet = new BS();
+ int i0 = bs.nextSetBit(0);
+ if (mads == null && i0 >= 0)
+ mads = new short[atomCount];
+ for (int i = i0, pt = 0; i >= 0; i = bs.nextSetBit(i + 1), pt++) {
+ short colix = (colixes == null ? 0 : colixes[pt]);
+ if (colix == 0)
+ colix = C.INHERIT_ALL;
+ float f = (atrans == null ? 0 : atrans[pt]);
+ if (f > 0.01f)
+ colix = C.getColixTranslucent3(colix, true, f);
setColixAndPalette(colix, EnumPalette.UNKNOWN.id, i);
+ rd.value = sizes[pt];
+ Atom atom = atoms[i];
+ boolean isVisible = ((mads[i] = atom.calculateMad(viewer, rd)) > 0);
+ bsSizeSet.setBitTo(i, isVisible);
+ atom.setShapeVisibility(myVisibilityFlag, isVisible);
}
return;
}
Modified: trunk/Jmol/src/org/jmol/shapebio/BioShapeCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/BioShapeCollection.java 2013-06-06
22:17:52 UTC (rev 18304)
+++ trunk/Jmol/src/org/jmol/shapebio/BioShapeCollection.java 2013-06-07
19:15:26 UTC (rev 18305)
@@ -154,7 +154,7 @@
bioShape.setTranslucent(isTranslucent, bsSelected, translucency);
}
}
- return;
+ return;
}
if ("colorPhase" == propertyName) {
// cartoons and ribbons only
Modified: trunk/Jmol/src/org/jmol/util/GData.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/GData.java 2013-06-06 22:17:52 UTC (rev
18304)
+++ trunk/Jmol/src/org/jmol/util/GData.java 2013-06-07 19:15:26 UTC (rev
18305)
@@ -13,6 +13,14 @@
public ApiPlatform apiPlatform;
+ public boolean translucentCoverOnly = false;
+ public void setTranslucentCoverOnly(boolean TF) {
+ translucentCoverOnly = TF;
+ }
+ public boolean getTranslucentCoverOnly() {
+ return translucentCoverOnly;
+ }
+
protected int windowWidth, windowHeight;
protected int displayMinX, displayMaxX, displayMinY, displayMaxY;
protected boolean antialiasThisFrame;
@@ -517,9 +525,10 @@
/**
* @param stereoRotationMatrix
- * @param isImageWrite TODO
+ * @param translucentMode
+ * @param isImageWrite
*/
- public void beginRendering(Matrix3f stereoRotationMatrix, boolean
isImageWrite) {
+ public void beginRendering(Matrix3f stereoRotationMatrix, boolean
translucentMode, boolean isImageWrite) {
}
public void endRendering() {
@@ -681,4 +690,5 @@
public void renderAllStrings(Object jmolRenderer) {
// only in Graphics3D
}
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-06 22:17:52 UTC
(rev 18304)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-07 19:15:26 UTC
(rev 18305)
@@ -11,6 +11,12 @@
___JmolVersion="13.1.17"
+TODO: PyMOL uniqueAtomSettings for selected atom settings
+
+new feature: set translucent
+ -- default TRUE : translucent objects are fully translucent
+ -- FALSE: translucent object are opaque to other translucent objects
+
=============================================================================
JmolVersion="13.1.16_a"
@@ -19,9 +25,6 @@
-- zoomHeight TRUE
-- measurementUnits ANGSTROMS
-TODO: PyMOL uniqueAtomSettings should override scene color settings
-TODO: PyMOL uniqueAtomSettings for all atom settings
-
new feature: color BALLS
-- distinct from color ATOMS because it doesn't get inherited
-- for PyMOL compatability with sphere_color
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-06-06 22:17:52 UTC
(rev 18304)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-06-07 19:15:26 UTC
(rev 18305)
@@ -156,6 +156,7 @@
JC.DEFAULT_BOND_TOLERANCE);
viewer.setFloatProperty("minBondDistance",
JC.DEFAULT_MIN_BOND_DISTANCE);
+ viewer.setBooleanProperty("translucent", true);
}
void setJmolDefaults() {
@@ -972,6 +973,7 @@
setB("testFlag3", testFlag3);
setB("testFlag4", testFlag4);
setB("traceAlpha", traceAlpha);
+ setB("translucent", translucent);
setB("twistedSheets", twistedSheets);
setB("useArcBall", useArcBall);
setB("useMinimizationThread", useMinimizationThread);
@@ -1141,6 +1143,7 @@
boolean rocketBarrels = false;
float sheetSmoothing = 1; // 0: traceAlpha on alphas for helix, 1 on
midpoints
boolean traceAlpha = true;
+ boolean translucent = true;
boolean twistedSheets = false;
//misc
@@ -1466,7 +1469,7 @@
boolean haveSetStructureList;
private String[] userDatabases;
-
+
public void setStructureList(float[] list, EnumStructure type) {
haveSetStructureList = true;
structureList.put(type, list);
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-06 22:17:52 UTC (rev
18304)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-07 19:15:26 UTC (rev
18305)
@@ -4173,8 +4173,7 @@
Object image = null;
try {
- gdata.beginRendering(transformManager.getStereoRotationMatrix(isDouble),
- isImageWrite);
+ beginRendering(isDouble, isImageWrite);
render();
gdata.endRendering();
image = gdata.getScreenImage(isImageWrite);
@@ -4186,6 +4185,12 @@
return image;
}
+ private void beginRendering(boolean isDouble, boolean isImageWrite) {
+ gdata.beginRendering(transformManager.getStereoRotationMatrix(isDouble),
+ global.translucent,
+ isImageWrite);
+ }
+
private boolean antialiasDisplay;
public boolean isAntialiased() {
@@ -4249,13 +4254,11 @@
boolean mergeImages = (graphic == null && isStereoDouble());
Object imageBuffer;
if (transformManager.stereoMode.isBiColor()) {
- gdata.beginRendering(transformManager.getStereoRotationMatrix(true),
- isImageWrite);
+ beginRendering(true, isImageWrite);
render();
gdata.endRendering();
gdata.snapshotAnaglyphChannelBytes();
- gdata.beginRendering(transformManager.getStereoRotationMatrix(false),
- isImageWrite);
+ beginRendering(false, isImageWrite);
render();
gdata.endRendering();
gdata.applyAnaglygh(transformManager.stereoMode,
@@ -6459,6 +6462,10 @@
private void setBooleanPropertyTok(String key, int tok, boolean value) {
boolean doRepaint = true;
switch (tok) {
+ case T.translucent:
+ // 13.1.17 false -> translucent objects are opaque among themselves
(Pymol transparency_mode 2)
+ global.translucent = value;
+ break;
case T.cartoonladders:
// 13.1.15
global.cartoonLadders = value;
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