Revision: 18301
http://sourceforge.net/p/jmol/code/18301
Author: hansonr
Date: 2013-06-06 20:59:04 +0000 (Thu, 06 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.16_a"
new feature: set defaults PyMOL
-- 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
new feature: restore SCENE "xxxx" nSec
new feature: Scene menu
-- PyMOL scene names, in order
new feature: added parameters to moveTo allows setting cameraDepth, cameraX,
and cameraY
new feature: moveTo <nseconds> PYMOL [18-element standard PyMOL view matrix]
-- used for PSE file loading
-- to be used also for scenes
[0-8] are 3x3 rotation matrix (row/column inverted)
[9,10] are x,y translations (y negative)
[11] is distance from camera to center (negative)
[12-14] are rotation center coords
[15-16] are slab and depth distance from camera (0 to ignore)
[17] is field of view; positive for orthographic projection
new feature: cache CLEAR
-- same as cache REMOVE ALL
new feature: load xxx.pse FILTER "DOCACHE"
-- specifically for editing large PSE files when included in a state
-- caches streamlined file that is still readable by PyMOL (needs testing!)
(no electron density map data, for instance -- see HupA_2.pse)
-- caches all isosurfaces, creating JVXL equivalents
-- should be followed with WRITE xxx.pngj or WRITE xxx.jmol or WRITE xxx.zip
-- for example:
before:
04/07/2013 07:46 AM 11,929,507 HupA_2.pse
$ zap;load SYNC "file:///C:/temp/downloads/HupA_2.pse" filter 'DOcache'
$ write t.zip
after:
Listing archive: t.zip
Physical Size = 395174
Date Time Attr Size Compressed Name
------------------- ----- ------------ ------------
------------------------
2013-05-17 06:46:36 ..... 1092432 219718 HupA_2.pse
2013-05-17 06:46:36 ..... 1473760 6589
isosurface_level2
2013-05-17 06:46:36 ..... 25495 11624 state.spt
2013-05-17 06:46:36 ..... 134 119
JmolManifest.txt
2013-05-17 06:46:36 ..... 0 2
Jmol_version_13.1.16_dev_2013.05.17__2013-05-15_07.09
2013-05-17 06:46:36 ..... 158082 156316 preview.png
------------------- ----- ------------ ------------
------------------------
2749903 394368 6 files, 0
folders
new feature: anim FRAMES [1, 3, 9, 9, 9, 3, 1]
-- arbitrary PyMOL-like model list
new feature: FRAME n
-- same as MODEL n, unless we have PyMOL-like frames
-- if have frames, then FRAME 2 goes to the second frame (model 3 in this
case)
-- MODEL n still always goes to a specific model.
-- all relative options -- FIRST LAST PREV NEXT -- refer to frames if there
are frames
even if the MODEL command is given.
new feature: pyMOL PSE state options: LOAD "FOO.PSE" state FILTER "xxxx"
-- [state not present; default] load all PyMOL states (one PyMOL state == one
Jmol model)
-- state = 0 (load only the current PyMOL state)
-- state > 0 (load just a specific PyMOL state)
-- FILTER "nosurface" -- load PyMOL file without surfaces
-- FILTER "
new feature: getProperty BONDINFO {atomset1} {atomset2}
new feature: measurements with IDs and radius/diameter:
-- measure ID "xxx" ...
-- measure ID "xxx" RADIUS x.y (or DIAMETER x.y)
-- renders as dots
new feature: set zoomHeight
-- FALSE by default
-- set TRUE for PyMOL-like resizing (scale only set by height adjustment)
new feature: isosurface color density (decimal)
- variable decimal point size
new feature: PyMOL CGOs as CGO command
- needs testing
- CGO ID "xxx" [ cgo data (float array) ]
- includes basic CGO methods
BEGIN
GL_POINTS
GL_LINES
GL_LINESTRIP
GL_TRIANGLE
GL_TRIANGLE_STRIP
GL_TRIANGLE_FAN
VERTEX
END
COLOR
NORMAL
SIMPLE_LINE
SAUSAGE
TRICOLOR_TRIANGLE
popup: added menu for MEP range -0.1 0.1
PyMOL: uniqueBondSettings working
PyMOL: better scene restore;
PyMOL: adds SASURFACE option (surface_solvent ON), with "carving"
(ProFusion_ABL.pse, scene F6)
PyMOL: abstraction of scene setting from reader
PyMOL: first phase of reader development complete (working with Jaime Prilusky)
-- 104 test models http://ispcsrv3.weizmann.ac.il/a2jmolb/browse
-- implementation of standard objects, including:
-- atoms with labels
-- bonds
-- standard PyMOL rendering, including:
-- lines
-- sticks
-- nonbonded (stars)
-- nb_spheres
-- cartoons of various types (not plank)
-- rockets
-- ribbon (backbone/trace)
-- putty (trace)
-- dots
-- measures
-- simple CGO objects
-- molecular surfaces
-- electron density as points and meshes
-- custom colors
-- fog and slab
-- morphing movies
-- JVXL caching of isosurfaces
PyMOL: measurement font/offsets enabled
-- adds measure ID "xxx" FONT scale face style
-- adds measure ID "xxx" OFFSET [mode, sx, sy, sz, ax, ay, az]
-- adds measure ID "xxx" OFFSET {sx, sy, sz}
PyMOL: perspective fix for translated center -- H115W.PinM.PSE
PyMOL: preliminary scene implementation
-- view only
-- use RESTORE ORIENTATION xxxxx
code: Text.java, Object2d.java moved from shapes to modelset
bug fix: COMPARE move of group saved in state may not be correct when restored
bug fix: write command doesn't accept parameter sequence IMAGE PNGJ ... (broken
in 13.1.14)
bug fix: load APPEND with PDB file loses structure (broken in 13.1.15)
bug fix: restore command broken
bug fix: JavaScript: adding SYNC
bug fix: antialiasing or resizing stray lines problem solved (introduced in
11.0, 08/2006!)
bug fix: "display add" by itself should not do anything
bug fix: Hall translation initialization problem
bug fix: JavaScript reading of old-style JVXL files
bug fix: Gaussian reader not splitting MO set by model
bug fix: polyhedron reading from state
bug fix: connect delete not saved in state
bug fix: rockets not working for alpha polymer (also in 13.0.16)
bug fix: GXL added to carbohydrates
bug fix: show state/anim turns "anim" into "animation"
bug fix: MoldenReader orbitals are not in energy order; use FILTER "NOSORT" to
prevent sorting by energy
bug fix: simultaneous spin/animation broken in 13.1.13
bug fix: MoldenReader fix for file blank lines and g,h,i orbitals - also for
13.0.16
bug fix: COMPARE does not allow nSeconds at beginning, as described in
documentation
bug fix: isosurface VOLUME/AREA SET n cannot return to full array reporting;
SET -1 added.
bug fix: isosurface VOLUME/AREA always returns an array, possibly of length 0
bug fix: isosurface molecular/solvent can give inappropriate inner surfaces
bug fix: show selected includes deleted atoms
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/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/render/RepaintManager.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/smiles/InvalidSmilesException.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 20:56:00 UTC (rev 18300)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2013-06-06 20:59:04 UTC (rev 18301)
@@ -60,7 +60,7 @@
private short[] colixes;
private Object[] colors;
- String objectNameID;
+ String jmolName;
int argb;
float translucency = 0;
boolean visible = true;
@@ -77,7 +77,7 @@
this.id = id;
this.bsAtoms = bsAtoms;
this.info = info;
- this.objectNameID = branchNameID;
+ this.jmolName = branchNameID;
}
/**
@@ -173,12 +173,9 @@
sm.viewer.setCurrentModelIndex(-1);
}
return;
- case T.group:
- // if we implement GROUP in Jmol, we need to do something here.
- return;
case T.scene:
- sm.viewer.saveScene(objectNameID, (Map<String, Object>) info);
- sm.viewer.saveOrientation(objectNameID,
+ sm.viewer.saveScene(jmolName, (Map<String, Object>) info);
+ sm.viewer.saveOrientation(jmolName,
(float[]) ((Map<String, Object>) info).get("pymolView"));
return;
case JC.SHAPE_LABELS:
@@ -234,7 +231,7 @@
sm.setShapePropertyBs(id, "measure", md, bsAtoms);
return;
case T.isosurface:
- sID = (bsAtoms == null ? (String) info : objectNameID);
+ sID = (bsAtoms == null ? (String) info : jmolName);
// when getting a scene, ignore creation of this surface
if (sm.getShapeIdFromObjectName(sID) >= 0) {
sm.viewer.setObjectProp(sID, T.display);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-06 20:56:00 UTC (rev 18300)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-06 20:59:04 UTC (rev 18301)
@@ -179,7 +179,7 @@
@Override
public void finalizeModelSet(int baseModelIndex, int baseAtomIndex) {
- pymolScene.setObjects(mepList, doCache, baseModelIndex, baseAtomIndex);
+ pymolScene.setReaderObjects(mepList, doCache, baseModelIndex,
baseAtomIndex);
if (haveMeasurements) {
appendLoadNote(viewer.getMeasurementInfoAsString());
@@ -271,7 +271,7 @@
try {
viewer.log(TextFormat.simpleReplace(list.toString(), "[", "\n["));
} catch (Throwable e) {
- e.printStackTrace();
+ //
}
}
}
@@ -364,7 +364,7 @@
}
for (int i = 1; i < n; i++)
processObject(listAt(names, i), false, 0);
- pymolScene.setObjectInfo(null, 0, null, false, null, null, null);
+ pymolScene.setReaderObjectInfo(null, 0, null, false, null, null, null);
// not currently generating selections
//processSelections();
@@ -380,9 +380,9 @@
}
processDefinitions();
- processSelections(map);
+ processSelectionsAndScenes(map);
// no need to render if this is a state script
- pymolScene.finalizeEverything();
+ pymolScene.finalizeVisibility();
if (!isStateScript) {
// same idea as for a Jmol state -- session reinitializes
viewer.initialize(true);
@@ -554,7 +554,7 @@
if (haveFrames && !haveCommands && !haveViews) {
// simple animation
isMovie = true;
- pymolScene.setObjectInfo(null, 0, null, false, null, null, null);
+ pymolScene.setReaderObjectInfo(null, 0, null, false, null, null, null);
pymolScene.setFrameObject(T.movie, movie);
} else {
//isMovie = true; for now, no scripted movies
@@ -622,7 +622,7 @@
execObject, 6));
if (" ".equals(parentGroupName))
parentGroupName = null;
- pymolScene.setObjectInfo(objectName, type, parentGroupName, isHidden,
listAt(objectHeader, 8), stateSettings, (moleculeOnly ? "_" + (iState + 1) :
""));
+ pymolScene.setReaderObjectInfo(objectName, type, parentGroupName,
isHidden, listAt(objectHeader, 8), stateSettings, (moleculeOnly ? "_" + (iState
+ 1) : ""));
BS bsAtoms = null;
boolean doExclude = (bsBytesExcluded != null);
String msg = null;
@@ -886,12 +886,12 @@
int n = bonds.size();
for (int i = 0; i < n; i++) {
JmolList<Object> b = listAt(bonds, i);
- int order = intAt(b, 2) | asSingle;
+ int order = intAt(b, 2);
if (order < 1 || order > 3)
order = 1;
int ia = intAt(b, 0);
int ib = intAt(b, 1);
- Bond bond = new Bond(ia, ib, order);
+ Bond bond = new Bond(ia, ib, order | asSingle);
bond.uniqueID = (b.size() > 6 && intAt(b, 6) != 0 ? intAt(b, 5) : -1);
bondList.addLast(bond);
}
@@ -1220,7 +1220,7 @@
* @param map
*/
@SuppressWarnings("unchecked")
- private void processSelections(Map<String, Object> map) {
+ private void processSelectionsAndScenes(Map<String, Object> map) {
if (!pymolScene.needSelections())
return;
Map<String, JmolList<Object>> htObjNames = PyMOLScene.listToMap(getMapList(
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-06 20:56:00 UTC (rev 18300)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-06 20:59:04 UTC (rev 18301)
@@ -30,7 +30,7 @@
/**
* A class to allow manipulation of scenes dissociated from file loading. A
* "scene" in this context is a distillation of PyMOL information into a
- * Hashtable for easier retrieval. This organization is:
+ * Hashtable for easier retrieval using RESTORE SCENE name.
*
*/
class PyMOLScene implements JmolSceneGenerator {
@@ -116,14 +116,17 @@
private int bgRgb;
private int surfaceMode;
private int surfaceColor;
+ private int sphereColor;
private int labelFontId;
private int labelColor;
+ private float cartoonTranslucency;
private float labelSize;
+ private float meshWidth;
+ private float nonbondedSize;
+ private float sphereScale;
private float sphereTranslucency;
- private float cartoonTranslucency;
private float stickTranslucency;
- private float nonBondedSize;
- private float sphereScale;
+ private float transparency;
private boolean cartoonLadderMode;
private boolean cartoonRockets;
private boolean haveNucleicLadder;
@@ -132,7 +135,7 @@
private String objectName;
private String objectNameID;
- private String objectSelectionName;
+ private String objectJmolName;
private int objectType;
private BS objectAtoms;
private boolean objectHidden;
@@ -180,7 +183,7 @@
0, labelPosition0);
}
- void setObjectInfo(String name, int type, String groupName, boolean isHidden,
+ void setReaderObjectInfo(String name, int type, String groupName, boolean
isHidden,
JmolList<Object> listObjSettings,
JmolList<Object> listStateSettings, String ext) {
objectName = name;
@@ -190,7 +193,7 @@
objectSettings = new Hashtable<Integer, JmolList<Object>>();
stateSettings = new Hashtable<Integer, JmolList<Object>>();
if (objectName != null) {
- objectSelectionName = getSelectionName(name);
+ objectJmolName = getJmolName(name);
if (groupName != null) {
htObjectGroups.put(objectName, groupName);
htObjectGroups.put(objectNameID, groupName);
@@ -223,8 +226,10 @@
}
private void getObjectSettings() {
- nonBondedSize = floatSetting(PyMOL.nonbonded_size);
+ transparency = floatSetting(PyMOL.transparency);
+ nonbondedSize = floatSetting(PyMOL.nonbonded_size);
sphereScale = floatSetting(PyMOL.sphere_scale);
+ sphereColor = (int) floatSetting(PyMOL.sphere_color);
cartoonTranslucency = floatSetting(PyMOL.cartoon_transparency);
stickTranslucency = floatSetting(PyMOL.stick_transparency);
sphereTranslucency = floatSetting(PyMOL.sphere_transparency);
@@ -233,6 +238,7 @@
surfaceMode = (int) floatSetting(PyMOL.surface_mode);
surfaceColor = (int) floatSetting(PyMOL.surface_color);
solventAccessible = booleanSetting(PyMOL.surface_solvent);
+ meshWidth = floatSetting(PyMOL.mesh_width);
String carveSet = stringSetting(PyMOL.surface_carve_selection).trim();
if (carveSet.length() == 0) {
bsCarve = null;
@@ -264,11 +270,49 @@
this.newChain = newChain;
this.radii = radii;
}
+
+ ////////////// scene-related methods //////////
+
+// From module/pymol/Viewing.py:
+//
+// DESCRIPTION
+//
+// "scene" makes it possible to save and restore multiple scenes
+// within a single session. A scene consists of the view, all object
+// activity information, all atom-wise visibility, color,
+// representations, and the global frame index.
+
/**
+ * Set scene object/state-specific global fields and
+ * settings based on the name and state or stored values
+ * from when the file was loaded.
+ *
+ * @param name
+ * @param istate
+ *
+ */
+ private void setSceneObject(String name, int istate) {
+ objectName = name;
+ objectType = getObjectType(name);
+ objectJmolName = getJmolName(name);
+ objectNameID = (istate == 0 && objectType != 0 ? getObjectID(name) :
objectJmolName + "_"
+ + istate);
+ objectAtoms = htObjectAtoms.get(name);
+ objectSettings = htObjectSettings.get(name);
+ stateSettings = htStateSettings.get(name+"_" + istate);
+ String groupName = htObjectGroups.get(name);
+ objectHidden = (htHiddenObjects.containsKey(name) || groupName != null
+ && !groups.get(groupName).visible);
+ getObjectSettings();
+ }
+
+ /**
+ * Build a scene at file reading time. We only implement frame-specific
+ * scenes. Creates a map of information that can be used later and
+ * will also be a reference to this instance of PyMOLScene, which is an
+ * implementation of JmolSceneGenerator.
*
- * frame scenes only here
- *
* @param name
* @param thisScene
* @param htObjNames
@@ -279,14 +323,6 @@
Map<String, JmolList<Object>> htObjNames,
Map<String, JmolList<Object>> htSecrets) {
Object frame = thisScene.get(2);
- // generator : this
- // name : scene name
- // pymolFrame : specified frame
- // pymolView : specified view [ 18-member array ]
- // visibilities: { name1: [visFlag, repOn, repVis, colorIndex],...}
- // moleculeReps: [ representation-based list of object lists]
- // colors: [colorIndex, object list]
- //
Map<String, Object> smap = new Hashtable<String, Object>();
smap.put("pymolFrame", frame);
smap.put("generator", this);
@@ -319,8 +355,9 @@
sname = "_!c_" + name + "_";
JmolList<Object> colorection = listAt(thisScene, 3);
int n = colorection.size();
- // I don't know what the idea of the pyList is that it is bivalued:
- // [3, 262, 0, 263, 4, 264, 26, 265, 27, 266, 28, 267]
+ // [color/selEntry,color/selEntry,color/selEntry.....]
+ // [3, 262, 0, 263, 4, 264, .....]
+ // see layer3/Selector.c SelectorColorectionApply
Object[] colors = new Object[n / 2];
for (int j = 0, i = 0; j < n; j += 2) {
int color = intAt(colorection, j);
@@ -329,11 +366,13 @@
colors[i++] = new Object[] { Integer.valueOf(color), c.get(1) };
}
smap.put("colors", colors);
- addJmolObject(T.scene, null, smap).objectNameID = name;
+ addJmolObject(T.scene, null, smap).jmolName = name;
}
/**
- * Generate the saved scene.
+ * Generate the saved scene using file settings preserved here and
+ * scene-specific information including frame, view, colors, visibilities,
+ * . Called by StateManager via implemented JmolSceneGenerator.
*
* @param scene
*
@@ -353,14 +392,23 @@
generateVisibilities((Map<String, Object>) scene.get("visibilities"));
generateColors((Object[]) scene.get("colors"));
generateShapes((Object[]) scene.get("moleculeReps"));
- finalizeEverything();
+ finalizeVisibility();
finalizeObjects();
} catch (Exception e) {
System.out.println("PyMOLScene exception " + e);
- e.printStackTrace();
+ if (!viewer.isApplet())
+ e.printStackTrace();
}
}
+ /**
+ * Set PyMOL "atom-wise" colors -- the colors that are defined
+ * initially as element colors but possibly set with the PyMOL 'color'
+ * command and are used when representation colors (cartoon, dots, etc.)
+ * are not defined (-1). This is the same as Jmol's inherited atom color.
+ *
+ * @param colors
+ */
@SuppressWarnings("unchecked")
private void generateColors(Object[] colors) {
if (colors == null)
@@ -376,6 +424,14 @@
}
}
+ /**
+ * Add selected atoms to a growing bit set.
+ *
+ * @param molecules
+ * @param istate
+ * @param bs
+ * @return bs for convenience
+ */
private BS getSelectionAtoms(JmolList<Object> molecules, int istate, BS bs) {
if (molecules != null)
for (int j = molecules.size(); --j >= 0;)
@@ -383,9 +439,16 @@
return bs;
}
+ /**
+ * Collect all the atoms specified by an object state into a bit set.
+ *
+ * @param obj
+ * @param istate 0 for "all states"
+ * @param bs
+ */
private void selectAllAtoms(JmolList<Object> obj, int istate, BS bs) {
String name = (String) obj.get(0);
- setObject(name, istate);
+ setSceneObject(name, istate);
JmolList<Object> atomList = listAt(obj, 1);
int k0 = (istate == 0 ? 1 : istate);
int k1 = (istate == 0 ? stateCount : istate);
@@ -397,6 +460,12 @@
}
}
+ /**
+ * Hide everything, then just make visible the sets of
+ * atoms specified in the visibility (i.e. "activity") list within
scene_dict.
+ *
+ * @param vis
+ */
@SuppressWarnings("unchecked")
private void generateVisibilities(Map<String, Object> vis) {
if (vis == null)
@@ -426,13 +495,13 @@
String name = e.getKey();
if (name.equals("all"))
continue;
- setObject(name, thisState);
+ setSceneObject(name, thisState);
if (objectHidden)
continue;
JmolList<Object> list = (JmolList<Object>) e.getValue();
int tok = (objectHidden ? T.hide : T.display);
bs = null;
- String info = objectSelectionName;
+ String info = objectJmolName;
switch (objectType) {
case 0: // doesn't have selected state
case PyMOL.OBJECT_GROUP:
@@ -457,26 +526,15 @@
// might need to set color here for these?
break;
}
- //addJmolObject(tok, null, objectNameID);
addJmolObject(tok, bs, info);
}
}
- private void setObject(String name, int istate) {
- objectName = name;
- objectType = getObjectType(name);
- objectSelectionName = getSelectionName(name);
- objectNameID = (istate == 0 && objectType != 0 ? getObjectID(name) :
objectSelectionName + "_"
- + istate);
- objectAtoms = htObjectAtoms.get(name);
- objectSettings = htObjectSettings.get(name);
- String groupName = htObjectGroups.get(objectName);
- objectHidden = (htHiddenObjects.containsKey(name) || groupName != null
- && !groups.get(groupName).visible);
- stateSettings = htStateSettings.get(objectName+"_" + istate);
- getObjectSettings();
- }
-
+ /**
+ * Create all Jmol shape objects.
+ *
+ * @param reps
+ */
@SuppressWarnings("unchecked")
private void generateShapes(Object[] reps) {
if (reps == null)
@@ -485,8 +543,7 @@
// through all molecules...
// for (int m = moleculeNames.size(); --m >= 0;) {
for (int m = 0; m < moleculeNames.size(); m++) {
- setObject(moleculeNames.get(m), thisState);
- getObjectSettings();
+ setSceneObject(moleculeNames.get(m), thisState);
if (objectHidden)
continue;
BS[] molReps = new BS[PyMOL.REP_JMOL_MAX];
@@ -531,7 +588,7 @@
return getColorPt(c.get(2));
}
- void setObjects(String mepList, boolean doCache, int baseModelIndex,
+ void setReaderObjects(String mepList, boolean doCache, int baseModelIndex,
int baseAtomIndex) {
this.baseModelIndex = baseModelIndex;
this.baseAtomIndex = baseAtomIndex;
@@ -545,7 +602,11 @@
}
}
+ /**
+ * Finally, we turn each JmolObject into its Jmol equivalent.
+ */
private void finalizeObjects() {
+ viewer.setStringProperty("defaults", "PyMOL");
for (int i = 0; i < jmolObjects.size(); i++) {
try {
JmolObject obj = jmolObjects.get(i);
@@ -553,18 +614,19 @@
obj.finalizeObject(this, viewer.modelSet, mepList, doCache);
} catch (Exception e) {
System.out.println(e);
- e.printStackTrace();
+ if (!viewer.isApplet())
+ e.printStackTrace();
}
}
finalizeUniqueBonds();
jmolObjects.clear();
}
- JmolObject getJmolObject(int id, BS bsAtoms, Object info) {
+ private JmolObject getJmolObject(int id, BS bsAtoms, Object info) {
return new JmolObject(id, objectNameID, bsAtoms, info);
}
- JmolObject addJmolObject(int id, BS bsAtoms, Object info) {
+ private JmolObject addJmolObject(int id, BS bsAtoms, Object info) {
return addObject(getJmolObject(id, bsAtoms, info));
}
@@ -575,7 +637,7 @@
* @param isViewObj
* @return 22-element array
*/
- float[] getPymolView(JmolList<Object> view, boolean isViewObj) {
+ private float[] getPymolView(JmolList<Object> view, boolean isViewObj) {
float[] pymolView = new float[21];
boolean depthCue = booleanSetting(PyMOL.depth_cue); // 84
boolean fog = booleanSetting(PyMOL.fog); // 88
@@ -623,7 +685,7 @@
}
/**
- * Create a heirarchical list of named groups as generally seen on the PyMOL
+ * Create a hierarchical list of named groups as generally seen on the PyMOL
* app's right-hand object menu.
*
* @param object
@@ -661,19 +723,15 @@
/**
* Create group JmolObjects, and set hierarchical visibilities
*/
- void finalizeEverything() {
- viewer.setStringProperty("measurementUnits", "ANGSTROMS");
- viewer.setBooleanProperty("zoomHeight", true);
+ void finalizeVisibility() {
setGroupVisibilities();
- if (groups != null) {
+ if (groups != null)
for (int i = jmolObjects.size(); --i >= 0;) {
JmolObject obj = jmolObjects.get(i);
- if (obj.objectNameID != null
- && occludedObjects.containsKey(obj.objectNameID))
+ if (obj.jmolName != null
+ && occludedObjects.containsKey(obj.jmolName))
obj.visible = false;
}
- addJmolObject(T.group, null, groups);
- }
if (!bsHidden.isEmpty())
addJmolObject(T.hidden, bsHidden, null);
}
@@ -701,13 +759,20 @@
}
private void defineAtoms(String name, BS bs) {
- htDefinedAtoms.put(getSelectionName(name), bs);
+ htDefinedAtoms.put(getJmolName(name), bs);
}
- private static String getSelectionName(String name) {
+ private static String getJmolName(String name) {
return "__" + fixName(name);
}
+ /**
+ * create all objects for a given molecule or scene
+ * @param reps
+ * @param allowSurface
+ * @param atomCount0 > 0 for a molecule; -1 for a scene
+ * @param atomCount
+ */
void createShapeObjects(BS[] reps, boolean allowSurface, int atomCount0,
int atomCount) {
if (atomCount >= 0) {
@@ -721,8 +786,7 @@
colixes[i] = (short) atomColorList.get(i).intValue();
jo.setColors(colixes, 0);
jo.setSize(0);
- jo = addJmolObject(JC.SHAPE_STICKS, objectAtoms,
- Float.valueOf(floatSetting(PyMOL.valence)));
+ jo = addJmolObject(JC.SHAPE_STICKS, objectAtoms, null);
jo.setSize(0);
}
createShapeObject(PyMOL.REP_LINES, reps[PyMOL.REP_LINES]);
@@ -817,6 +881,7 @@
}
JmolList<Object> getObjectSetting(int i) {
+ // why label_position only?
return objectSettings.get(Integer.valueOf(i));
}
@@ -913,9 +978,7 @@
color = (int) floatSetting(PyMOL.dash_color);
int c = PyMOL.getRGB(color);
short colix = C.getColix(c);
- int clabel = (int) floatSetting(PyMOL.label_color);
- if (clabel < 0)
- clabel = color;
+ int clabel = (labelColor < 0 ? color : labelColor);
if (isNew) {
mdList = new MeasurementData[n];
htMeasures.put(objectName, mdList);
@@ -1024,11 +1087,11 @@
BS setAtomMap(int[] atomMap, int atomCount0) {
htAtomMap.put(objectNameID, atomMap);
- BS bsAtoms = htDefinedAtoms.get(objectSelectionName);
+ BS bsAtoms = htDefinedAtoms.get(objectJmolName);
if (bsAtoms == null) {
bsAtoms = BS.newN(atomCount0 + atomMap.length);
Logger.info("PyMOL molecule " + objectName);
- htDefinedAtoms.put(objectSelectionName, bsAtoms);
+ htDefinedAtoms.put(objectJmolName, bsAtoms);
htObjectAtoms.put(objectName, bsAtoms);
moleculeNames.addLast(objectName);
}
@@ -1281,20 +1344,20 @@
if (bs.isEmpty())
return;
jo = addJmolObject(JC.SHAPE_STARS, bs, null);
- jo.rd = new RadiusData(null, floatSetting(PyMOL.nonbonded_size) / 2,
+ jo.rd = new RadiusData(null, nonbondedSize / 2,
RadiusData.EnumType.FACTOR, EnumVdw.AUTO);
break;
case PyMOL.REP_NBSPHERES:
case PyMOL.REP_SPHERES:
jo = addJmolObject(JC.SHAPE_BALLS, bs, null);
- f = floatSetting(PyMOL.sphere_color);
+ f = sphereColor;
if (f != -1)
jo.argb = PyMOL.getRGB((int) f);
jo.translucency = sphereTranslucency;
break;
case PyMOL.REP_DOTS:
jo = addJmolObject(JC.SHAPE_DOTS, bs, null);
- f = floatSetting(PyMOL.sphere_scale);
+ f = sphereScale;
jo.rd = new RadiusData(null, f, RadiusData.EnumType.FACTOR,
EnumVdw.AUTO);
break;
case PyMOL.REP_CARTOON:
@@ -1307,7 +1370,7 @@
case PyMOL.REP_MESH: // = 8;
jo = addJmolObject(T.isosurface, bs, null);
jo.setSize(floatSetting(PyMOL.solvent_radius));
- jo.translucency = floatSetting(PyMOL.transparency);
+ jo.translucency = transparency;
break;
case PyMOL.REP_SURFACE: // = 2;
float withinDistance = floatSetting(PyMOL.surface_carve_cutoff);
@@ -1316,7 +1379,7 @@
(surfaceMode == 3 || surfaceMode == 4) ? " only" : "",
bsCarve, Float.valueOf(withinDistance)});
jo.setSize(floatSetting(PyMOL.solvent_radius) * (solventAccessible ? -1
: 1));
- jo.translucency = floatSetting(PyMOL.transparency);
+ jo.translucency = transparency;
if (surfaceColor >= 0)
jo.argb = PyMOL.getRGB(surfaceColor);
break;
@@ -1504,7 +1567,7 @@
f = sphereScale;
break;
case PyMOL.nonbonded_size:
- f = nonBondedSize;
+ f = nonbondedSize;
break;
default:
return 0;
@@ -1583,12 +1646,12 @@
public void addMesh(int tok, JmolList<Object> obj, String objName, boolean
isMep) {
JmolObject jo = addJmolObject(tok, null, obj);
- setObject(objName, -1);
+ setSceneObject(objName, -1);
if (!isMep) {
- jo.setSize(floatSetting(PyMOL.mesh_width));
+ jo.setSize(meshWidth);
jo.argb = PyMOL.getRGB(intAt(listAt(obj, 0), 2));
}
- jo.translucency = floatSetting(PyMOL.transparency);
+ jo.translucency = transparency;
}
public void addIsosurface(String objectName) {
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-06-06 20:56:00 UTC (rev 18300)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-06-06 20:59:04 UTC (rev 18301)
@@ -238,13 +238,9 @@
}
finalizeReader();
} catch (Throwable e) {
- System.out.println(e);
- /**
- * @j2sNative
- */
- {
- e.printStackTrace();
- }
+ Logger.info("Reader error: " + e);
+ if (!viewer.isApplet())
+ e.printStackTrace();
setError(e);
}
if (reader != null)
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2013-06-06 20:56:00 UTC
(rev 18300)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2013-06-06 20:59:04 UTC
(rev 18301)
@@ -94,7 +94,6 @@
String structureID, int serialID, int strandCount,
char startChainID, int startSeqcode,
char endChainID, int endSeqcode, int istart, int
iend, BS bsAssigned) {
- System.out.println("biomodel " + type + " " + structureID + " " +
serialID + " " + istart + " " + iend);
for (int i = bioPolymerCount; --i >= 0; )
bioPolymers[i].addStructure(type, structureID, serialID, strandCount,
startChainID, startSeqcode,
endChainID, endSeqcode, istart, iend,
bsAssigned);
Modified: trunk/Jmol/src/org/jmol/render/RepaintManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/RepaintManager.java 2013-06-06 20:56:00 UTC
(rev 18300)
+++ trunk/Jmol/src/org/jmol/render/RepaintManager.java 2013-06-06 20:59:04 UTC
(rev 18301)
@@ -215,8 +215,9 @@
}
g3d.renderAllStrings(null);
} catch (Exception e) {
- e.printStackTrace();
- Logger.error("rendering error? ");
+ if (!viewer.isApplet())
+ e.printStackTrace();
+ Logger.error("rendering error? " + e);
}
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-06 20:56:00 UTC
(rev 18300)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-06 20:59:04 UTC
(rev 18301)
@@ -707,8 +707,9 @@
} catch (Exception ex) {
viewer.setStringProperty("_errormessage", "" + ex);
if (e.thisContext == null) {
- Logger.error("Error evaluating context");
- ex.printStackTrace();
+ Logger.error("Error evaluating context " + ex);
+ if (!viewer.isApplet())
+ ex.printStackTrace();
}
return false;
}
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2013-06-06 20:56:00 UTC (rev
18300)
+++ trunk/Jmol/src/org/jmol/script/T.java 2013-06-06 20:59:04 UTC (rev
18301)
@@ -328,7 +328,7 @@
final static int minimize = scriptCommand | 30;
//final static int model see mathfunc
//final static int measure see mathfunc
- final static int move = scriptCommand | 32;
+ public final static int move = scriptCommand | 32;
public final static int moveto = scriptCommand | 34;
public final static int navigate = scriptCommand | 35;
//final static int quaternion see mathfunc
Modified: trunk/Jmol/src/org/jmol/smiles/InvalidSmilesException.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/InvalidSmilesException.java 2013-06-06
20:56:00 UTC (rev 18300)
+++ trunk/Jmol/src/org/jmol/smiles/InvalidSmilesException.java 2013-06-06
20:59:04 UTC (rev 18301)
@@ -54,7 +54,7 @@
public InvalidSmilesException(String message) {
super(message);
lastError = message;
- printStackTrace();
+ //printStackTrace();
}
/**
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-06 20:56:00 UTC
(rev 18300)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-06 20:59:04 UTC
(rev 18301)
@@ -15,6 +15,10 @@
___JmolVersion="13.1.16_a"
+new feature: set defaults PyMOL
+ -- zoomHeight TRUE
+ -- measurementUnits ANGSTROMS
+
TODO: PyMOL uniqueAtomSettings should override scene color settings
TODO: PyMOL uniqueAtomSettings for all atom settings
@@ -166,6 +170,7 @@
code: Text.java, Object2d.java moved from shapes to modelset
+bug fix: COMPARE move of group saved in state may not be correct when restored
bug fix: write command doesn't accept parameter sequence IMAGE PNGJ ...
(broken in 13.1.14)
bug fix: load APPEND with PDB file loses structure (broken in 13.1.15)
bug fix: restore command broken
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-06-06 20:56:00 UTC
(rev 18300)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-06-06 20:59:04 UTC
(rev 18301)
@@ -180,6 +180,12 @@
viewer.setDefaultVdw("Rasmol");
}
+ public void setPyMOLDefaults() {
+ setCommonDefaults();
+ viewer.setStringProperty("measurementUnits", "ANGSTROMS");
+ viewer.setBooleanProperty("zoomHeight", true);
+ }
+
private static Object getNoCase(Map<String, Object> saved, String name) {
for (Entry<String, Object> e : saved.entrySet())
if (e.getKey().equalsIgnoreCase(name))
@@ -1514,6 +1520,7 @@
return sv;
}
+
///////// state serialization
}
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-06 20:56:00 UTC (rev
18300)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-06 20:59:04 UTC (rev
18301)
@@ -3277,6 +3277,8 @@
// atom coordinates may be moved here
// but this is not included as an atomMovedCallback
modelSet.setAtomData(type, name, coordinateData, isDefault);
+ if (type == AtomCollection.TAINT_COORD)
+ checkCoordinatesChanged();
refreshMeasures(true);
}
@@ -6006,7 +6008,7 @@
global.helpPath = value;
break;
case T.defaults:
- if (!value.equalsIgnoreCase("RasMol"))
+ if (!value.equalsIgnoreCase("RasMol") &&
!value.equalsIgnoreCase("PyMOL"))
value = "Jmol";
setDefaultsType(value);
break;
@@ -7475,6 +7477,10 @@
stateManager.setRasMolDefaults();
return;
}
+ if (type.equalsIgnoreCase("PyMOL")) {
+ stateManager.setPyMOLDefaults();
+ return;
+ }
setDefaults();
}
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