Revision: 20904
http://sourceforge.net/p/jmol/code/20904
Author: hansonr
Date: 2015-12-23 21:59:40 +0000 (Wed, 23 Dec 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.4.1_2015.12.23b"
bug fix: JavaScript error reporting uses alert() instead of just setting the
error message
bug fix: PyMOL 1.8 PSE files cannot be read because of missing settings
code: more efficient loading of PyMOL .pse session files
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java
branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
branches/v14_4/Jmol/src/org/jmol/modelset/AtomCollection.java
branches/v14_4/Jmol/src/org/jmol/modelset/ModelLoader.java
branches/v14_4/Jmol/src/org/jmol/modelset/ModelSet.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptManager.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.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/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/script/ScriptManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified:
branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
2015-12-23 08:23:37 UTC (rev 20903)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
2015-12-23 21:59:40 UTC (rev 20904)
@@ -1,15 +1,13 @@
package org.jmol.adapter.readers.pymol;
+import java.util.Hashtable;
+import java.util.Map;
+
import javajs.api.GenericBinaryDocument;
import javajs.util.Lst;
import javajs.util.SB;
import org.jmol.util.Logger;
-
-import java.util.Hashtable;
-
-import java.util.Map;
-
import org.jmol.viewer.Viewer;
/**
@@ -98,6 +96,7 @@
PickleReader(GenericBinaryDocument doc, Viewer vwr) {
binaryDoc = doc;
this.vwr = vwr;
+ stack.ensureCapacity(1000);
}
private void log(String s) {
@@ -386,10 +385,11 @@
private Lst<Object> getObjects(int mark) {
int n = stack.size() - mark;
Lst<Object> args = new Lst<Object>();
- for (int j = 0; j < n; j++)
- args.addLast(null);
- for (int j = n, i = stack.size(); --i >= mark;)
- args.set(--j, stack.remove(i));
+ args.ensureCapacity(n);
+ for (int i = mark; i < stack.size(); ++i)
+ args.addLast(stack.get(i));
+ for (int i = stack.size(); --i >= mark;)
+ stack.remove(i);
return args;
}
@@ -417,8 +417,12 @@
switch (markCount) {
case 2:
thisSection = stack.get(i - 2);
- inMovie = "movie".equals(thisSection);
- inNames = "names".equals(thisSection);
+ // BH: Note that JavaScript string == object first converts object to
string, then checks.
+ // This can be very slow if the object is complex.
+ if (thisSection instanceof String) {
+ inMovie = "movie".equals(thisSection);
+ inNames = "names".equals(thisSection);
+ }
break;
default:
break;
Modified: branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java
2015-12-23 08:23:37 UTC (rev 20903)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java
2015-12-23 21:59:40 UTC (rev 20904)
@@ -3,6 +3,8 @@
import java.util.Hashtable;
import java.util.Map;
+import javajs.util.P3;
+
import org.jmol.util.Logger;
/**
@@ -471,7 +473,7 @@
final static int offscreen_rendering_for_antialiasing = 695;
final static int offscreen_rendering_multiplier = 696;
final static int opaque_background = 435;
- final static int ortho = 23;
+ final static int orthoscopic = 23;
final static int overlay = 61;
final static int overlay_lines = 311;
final static int pdb_conect_all = 329;
@@ -6243,30 +6245,137 @@
moreColors.put(id, Integer.valueOf(value));
}
- public static float getDefaultSetting(int i, int pymolVersion) {
+ /**
+ * All settings that Jmol uses should go here
+ *
+ * @param i
+ * @param pymolVersion
+ * @return setting or 0
+ */
+ static float getDefaultSetting(int i, int pymolVersion) {
switch (i) {
- case label_size:
- return 14;
+ case sphere_color:
case cartoon_color:
case ellipsoid_color:
case ribbon_color:
case line_color:
+ case dot_color:
case stick_color:
+ case surface_color:
+ case dash_color:
+ case mesh_color:
+ case cartoon_putty_quality:
case label_distance_digits:
case label_angle_digits:
case label_dihedral_digits:
+ case two_sided_lighting:
return -1;
case ray_pixel_scale:
case ellipsoid_scale:
+ case sphere_scale:
+ case mesh_width:
+ case cartoon_ladder_mode:
+ case clamp_colors:
+ case frame:
+ case state:
+ case depth_cue:
+ case fog:
+ case cartoon_round_helices:
+ case cartoon_fancy_helices:
+ case label_digits:
+ case ribbon_sampling:
return 1;
- default:
- Logger.info("PyMOL " + pymolVersion + " does not have setting " + i);
- //$FALL-THROUGH$
+ case sphere_transparency:
case ellipsoid_transparency:
case ribbon_transparency:
case nonbonded_transparency:
+ case cartoon_transparency:
+ case stick_transparency:
+ case transparency:
+ case bg_rgb:
+ case cartoon_cylindrical_helices:
+ case surface_mode:
+ case surface_solvent:
+ case all_states:
+ case valence:
+ case cgo_transparency:
+ case cartoon_putty_transform:
+ case orthoscopic:
+ case ribbon_radius:
+ case ribbon_smooth:
+ case sphere_solvent:
+ case surface_carve_cutoff:
return 0;
+ case cartoon_loop_radius:
+ return 0.2F;
+ case cartoon_rect_length:
+ return 1.4F;
+ case nonbonded_size:
+ return 0.25F;
+ case fog_start:
+ return 0.45f;
+ case label_size:
+ return 14;
+ case label_color:
+ return -6;
+ case label_font_id:
+ return 5;
+ case transparency_mode:
+ case cartoon_putty_range:
+ case cartoon_tube_cap:
+ return 2;
+ case cartoon_nucleic_acid_mode:
+ case cartoon_putty_scale_max:
+ return 4;
+ case cartoon_putty_radius:
+ return 0.4f;
+ case cartoon_putty_scale_min:
+ return 0.6f;
+ case cartoon_putty_scale_power:
+ return 1.5f;
+ case cartoon_tube_radius:
+ return 0.5f;
+ case solvent_radius:
+ return 1.4f;
+ case dash_width:
+ return 2.5f;
+ case line_width:
+ return 1.49f;
+ case ribbon_width:
+ return 3;
+ case field_of_view:
+ return 20;
+ case movie_fps:
+ return 30;
+ case stick_radius:
+ return 0.25f;
+ default:
+ Logger.error("PyMOL " + pymolVersion + " default float setting not
found: " + i);
+ return 0;
}
}
+ static P3 getDefaultSettingPt(int i, int pymolVersion, P3 pt) {
+ switch (i) {
+ case label_position:
+ pt.set(0, 0, 0.75f);
+ break;
+ default:
+ Logger.error("PyMOL " + pymolVersion + " default point setting not
found: " + i);
+ break;
+ }
+ return pt;
+ }
+
+ static String getDefaultSettingS(int i, int pymolVersion) {
+ switch (i) {
+ case surface_carve_selection:
+ break;
+ default:
+ Logger.info("PyMOL " + pymolVersion + " does not have String setting " +
i);
+ break;
+ }
+ return "";
+ }
+
}
Modified:
branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2015-12-23 08:23:37 UTC (rev 20903)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2015-12-23 21:59:40 UTC (rev 20904)
@@ -183,7 +183,7 @@
sourcePNGJ = false;
if (doCache)
bsBytesExcluded = new BS();
- logging = false;
+ //logging = true; // specifically for Pickle
super.initializeReader();
}
@@ -272,8 +272,9 @@
pymolVersion, haveScenes, baseAtomIndex, baseModelIndex, doCache,
filePath);
// just log and display some information here
-
- logging = (vwr.getLogFileName().length() > 0);
+ String logFile = vwr.getLogFileName();
+ logging = (logFile.length() > 0);
+ Logger.info(logging ? "PyMOL file data streaming to " + logFile : "To view
raw PyMOL file data, use 'set logFile \"some_filename\" ");
Lst<Object> names = getMapList(map, "names");
for (Map.Entry<String, Object> e : map.entrySet()) {
String name = e.getKey();
@@ -332,11 +333,11 @@
// resize frame
if (!isStateScript && doResize) {
int width = 0, height = 0;
- try {
- width = intAt(getMapList(map, "main"), 0);
- height = intAt(getMapList(map, "main"), 1);
- } catch (Exception e) {
- // ignore
+ Lst<Object> main = getMapList(map, "main");
+ if (main != null) {
+ // not all PSE files have this
+ width = intAt(main, 0);
+ height = intAt(main, 1);
}
String note;
if (width > 0 && height > 0) {
@@ -493,7 +494,7 @@
Lst<Object> setting = (Lst<Object>) mySettings.get(j);
int uid = (id << 10) + intAt(setting, 0);
uniqueSettings.put(Integer.valueOf(uid), setting);
- Logger.info("PyMOL unique setting " + id + " " + setting);
+ //System.out.println("PyMOL unique setting " + id + " " + setting);
}
}
}
@@ -514,7 +515,7 @@
for (int i = colors.size(); --i >= 0;) {
Lst<Object> c = listAt(colors, i);
PyMOL.addColor((Integer) c.get(1), isClamped ?
PyMOLScene.colorSettingClamped(c)
- : PyMOLScene.colorSetting(c));
+ : PyMOLScene.getColorPt(c.get(2)));
}
}
@@ -899,13 +900,15 @@
Lst<Object> coords = listAt(state, 2);
Lst<Object> labelPositions = listAt(state, 8);
- if (iState == 0 || !isTrajectory)
+ if (iState == 0 || !isTrajectory) {
+ pymolScene.ensureCapacity(n);
for (int idx = 0; idx < n; idx++) {
P3 a = addAtom(pymolAtoms, intAt(idxToAtm, idx), idx, coords,
labelPositions, bsAtoms, iState);
if (a != null)
trajectoryStep[trajectoryPtr++] = a;
}
+ }
addBonds(bonds);
addMolStructures();
atoms = asc.atoms;
@@ -940,9 +943,10 @@
* @return list of bonds
*/
private Lst<Bond> getBondList(Lst<Object> bonds) {
- Lst<Bond> bondList = new Lst<Bond>();
int asSingle = (pymolScene.booleanSetting(PyMOL.valence) ? 0 :
JmolAdapter.ORDER_PYMOL_SINGLE);
int n = bonds.size();
+ Lst<Bond> bondList = new Lst<Bond>();
+ bondList.ensureCapacity(n);
for (int i = 0; i < n; i++) {
Lst<Object> b = listAt(bonds, i);
int order = intAt(b, 2);
@@ -1081,7 +1085,7 @@
atom.radius = 1;
atom.partialCharge = floatAt(a, 17);
int formalCharge = intAt(a, 18);
-
+
BS bsReps = getBsReps(listAt(a, 20));
int intReps = (bsReps == null ? intAt(a, 20) : 0); // Pymol 1.8
int atomColor = intAt(a, 21);
@@ -1096,7 +1100,8 @@
atom.vib = V3.new3(uniqueID, cartoonType, Float.NaN);
if (a.size() > 46) {
float[] data = PyMOLScene.floatsAt(a, 41, new float[8], 6);
- asc.setAnisoBorU(atom, data, 12);
+ if (data[0] != 0)
+ asc.setAnisoBorU(atom, data, 12);
}
//if (uniqueID > 0)
//pymolScene.setUnique(uniqueID, atom);
Modified: branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2015-12-23 08:23:37 UTC (rev 20903)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2015-12-23 21:59:40 UTC (rev 20904)
@@ -212,10 +212,9 @@
this.stateCount = stateCount;
}
- @SuppressWarnings("unchecked")
PyMOLScene(PymolAtomReader reader, Viewer vwr, Lst<Object> settings,
- Map<Integer, Lst<Object>> uniqueSettings, int pymolVersion,
- boolean haveScenes, int baseAtomIndex, int baseModelIndex,
+ Map<Integer, Lst<Object>> uniqueSettings, int pymolVersion,
+ boolean haveScenes, int baseAtomIndex, int baseModelIndex,
boolean doCache, String filePath) {
this.reader = reader;
this.vwr = vwr;
@@ -229,11 +228,33 @@
this.surfaceInfoName = filePath + "##JmolSurfaceInfo##";
setVersionSettings();
settings.trimToSize();
- bgRgb = colorSetting(listAt(settings, PyMOL.bg_rgb));
- pointAt((Lst<Object>) listAt(settings, PyMOL.label_position).get(2),
- 0, labelPosition0);
+ bgRgb = colorSetting(PyMOL.bg_rgb);
+ labelPosition0 = pointSetting(PyMOL.label_position);
}
+ @SuppressWarnings("unchecked")
+ private int colorSetting(int i) {
+ Lst<Object> pos = listAt(settings, i);
+ Object o = (pos == null || pos.size() != 3 ? null : pos.get(2));
+ if (o == null)
+ return (int) PyMOL.getDefaultSetting(i, pymolVersion);
+ return (o instanceof Integer ? ((Integer) o).intValue() : CU
+ .colorPtToFFRGB(pointAt((Lst<Object>) o, 0, ptTemp)));
+ }
+
+ @SuppressWarnings("unchecked")
+ private P3 pointSetting(int i) {
+ P3 pt = new P3();
+ Lst<Object> pos = listAt(settings, i);
+ if (pos != null && pos.size() == 3)
+ return pointAt((Lst<Object>) pos.get(2), 0, pt);
+ return PyMOL.getDefaultSettingPt(i, pymolVersion, pt);
+ }
+
+ void ensureCapacity(int n) {
+ atomColorList.ensureCapacity(atomColorList.size() + n);
+ }
+
void setReaderObjectInfo(String name, int type, String groupName, boolean
isHidden,
Lst<Object> listObjSettings,
Lst<Object> listStateSettings, String ext) {
@@ -634,7 +655,7 @@
@SuppressWarnings("unchecked")
static int getColorPt(Object o) {
- return (o instanceof Integer ? ((Integer) o).intValue() : CU
+ return (o == null ? 0 : o instanceof Integer ? ((Integer) o).intValue() :
CU
.colorPtToFFRGB(pointAt((Lst<Object>) o, 0, ptTemp)));
}
@@ -642,10 +663,6 @@
return ((Number) list.get(i)).intValue();
}
- static int colorSetting(Lst<Object> c) {
- return getColorPt(c.get(2));
- }
-
void setReaderObjects() {
clearReaderData();
finalizeObjects();
@@ -723,7 +740,7 @@
for (int j = 0; j < 8; j++)
pymolView[pt++] = floatAt(view, i++);
- boolean isOrtho = booleanSetting(PyMOL.ortho); // 23
+ boolean isOrtho = booleanSetting(PyMOL.orthoscopic); // 23
float fov = floatSetting(PyMOL.field_of_view); // 152
pymolView[pt++] = (isOrtho ? fov : -fov);
@@ -735,12 +752,10 @@
@SuppressWarnings("unchecked")
float globalSetting(int i) {
- try {
- Lst<Object> setting = (Lst<Object>) settings.get(i);
+ Lst<Object> setting = (Lst<Object>) settings.get(i);
+ if (setting != null && setting.size() == 3)
return ((Number) setting.get(2)).floatValue();
- } catch (Exception e) {
- return PyMOL.getDefaultSetting(i, pymolVersion);
- }
+ return PyMOL.getDefaultSetting(i, pymolVersion);
}
/**
@@ -947,21 +962,17 @@
}
float floatSetting(int i) {
- try {
- Lst<Object> setting = getSetting(i);
+ Lst<Object> setting = getSetting(i);
+ if (setting != null && setting.size() == 3)
return ((Number) setting.get(2)).floatValue();
- } catch (Exception e) {
- return PyMOL.getDefaultSetting(i, pymolVersion);
- }
+ return PyMOL.getDefaultSetting(i, pymolVersion);
}
String stringSetting(int i) {
- try {
Lst<Object> setting = getSetting(i);
- return setting.get(2).toString();
- } catch (Exception e) {
- return null;
- }
+ if (setting != null && setting.size() == 3)
+ return setting.get(2).toString();
+ return PyMOL.getDefaultSettingS(i, pymolVersion);
}
@SuppressWarnings("unchecked")
@@ -1105,8 +1116,7 @@
}
static int colorSettingClamped(Lst<Object> c) {
- return (c.size() < 6 || intAt(c, 4) == 0 ? colorSetting(c) : getColorPt(c
- .get(5)));
+ return getColorPt(c.get(c.size() < 6 || intAt(c, 4) == 0 ? 2 : 5));
}
void setAtomColor(int atomColor) {
@@ -1685,11 +1695,11 @@
return defs;
}
- public boolean needSelections() {
+ boolean needSelections() {
return haveScenes || !htCarveSets.isEmpty();
}
- public void setUniqueBonds(BS bsBonds, boolean isSticks) {
+ void setUniqueBonds(BS bsBonds, boolean isSticks) {
if (isSticks) {
bsStickBonds.or(bsBonds);
bsStickBonds.andNot(bsLineBonds);
@@ -1734,7 +1744,7 @@
* @param argb
* @param trans
*/
- public void setBondParameters(Bond b, int modelIndex, float rad, float
pymolValence,
+ void setBondParameters(Bond b, int modelIndex, float rad, float pymolValence,
int argb, float trans) {
if (modelIndex >= 0 && b.atom1.mi != modelIndex)
return;
@@ -1755,7 +1765,7 @@
}
- public void addMesh(int tok, Lst<Object> obj, String objName, boolean isMep)
{
+ void addMesh(int tok, Lst<Object> obj, String objName, boolean isMep) {
JmolObject jo = addJmolObject(tok, null, obj);
setSceneObject(objName, -1);
int meshColor = (int) floatSetting(PyMOL.mesh_color);
@@ -1769,7 +1779,7 @@
jo.cacheID = surfaceInfoName;
}
- public JmolObject addIsosurface(String objectName) {
+ JmolObject addIsosurface(String objectName) {
JmolObject jo = addJmolObject(T.isosurface, null, objectName);
jo.cacheID = surfaceInfoName;
return jo;
Modified: branches/v14_4/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelset/AtomCollection.java
2015-12-23 08:23:37 UTC (rev 20903)
+++ branches/v14_4/Jmol/src/org/jmol/modelset/AtomCollection.java
2015-12-23 21:59:40 UTC (rev 20904)
@@ -2570,6 +2570,12 @@
atomTensors.remove(toDelete.get(i));
}
+
+ private int atomCapacity;
+ void setCapacity(int nAtoms) {
+ atomCapacity += nAtoms;
+ }
+
public void setAtomTensors(int atomIndex, Lst<Object> list) {
if (list == null || list.size() == 0)
return;
@@ -2590,6 +2596,16 @@
}
}
+ public void addTensor(Tensor t, String type) {
+ type = type.toLowerCase();
+ Lst<Object> tensors = atomTensors.get(type);
+ if (tensors == null) {
+ atomTensors.put(type, tensors = new Lst<Object>());
+ tensors.ensureCapacity(atomCapacity);
+ }
+ tensors.addLast(t);
+ }
+
private static Object[] getTensorList(Lst<Object> list) {
int pt = -1;
boolean haveTLS = false;
@@ -2637,14 +2653,6 @@
return null;
}
- public void addTensor(Tensor t, String type) {
- type = type.toLowerCase();
- Lst<Object> tensors = atomTensors.get(type);
- if (tensors == null)
- atomTensors.put(type, tensors = new Lst<Object>());
- tensors.addLast(t);
- }
-
public Lst<Object> getAllAtomTensors(String type) {
if (atomTensors == null)
return null;
Modified: branches/v14_4/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-12-23
08:23:37 UTC (rev 20903)
+++ branches/v14_4/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-12-23
21:59:40 UTC (rev 20904)
@@ -771,6 +771,7 @@
boolean addH = false;
boolean isLegacyHAddition = false;//vwr.getBoolean(T.legacyhaddition);
JmolAdapterAtomIterator iterAtom = adapter.getAtomIterator(asc);
+ ms.setCapacity(adapter.getAtomCount(asc));
int nRead = 0;
Model[] models = ms.am;
if (ms.mc > 0)
Modified: branches/v14_4/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelset/ModelSet.java 2015-12-23
08:23:37 UTC (rev 20903)
+++ branches/v14_4/Jmol/src/org/jmol/modelset/ModelSet.java 2015-12-23
21:59:40 UTC (rev 20904)
@@ -668,7 +668,7 @@
// full models are deleted for any model containing the specified atoms
includeAllRelatedFrames(bsModels);
- int nModelsDeleted = BSUtil.cardinalityOf(bsModels);
+ int nModelsDeleted = bsModels.cardinality();
if (nModelsDeleted == 0)
return null;
@@ -1310,14 +1310,14 @@
ptCenter.add(at[i]);
}
}
- if (nPoints > 0)
+ if (nPoints > 1)
ptCenter.scale(1.0f / nPoints);
return ptCenter;
}
public P3 getAverageAtomPoint() {
if (averageAtomPoint == null)
- (averageAtomPoint = new P3()).setT(getAtomSetCenter(vwr.getAllAtoms()));
+ averageAtomPoint = getAtomSetCenter(vwr.getAllAtoms());
return averageAtomPoint;
}
@@ -2710,7 +2710,7 @@
+ " pseudo-hbond calculation");
calcRasmolHydrogenBonds(bsA, bsB, null, false, Integer.MAX_VALUE, false,
bsHBonds);
- return -BSUtil.cardinalityOf(bsHBonds);
+ return -bsHBonds.cardinality();
}
Logger.info(haveHAtoms ? "Standard Hbond calculation"
: "Jmol pseudo-hbond calculation");
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptManager.java 2015-12-23
08:23:37 UTC (rev 20903)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptManager.java 2015-12-23
21:59:40 UTC (rev 20904)
@@ -540,7 +540,7 @@
try {
if (fileName.endsWith(".pse")) {
cmd = (isCached ? "" : "zap;") + "load SYNC " + PT.esc(fileName)
- + " filter 'DORESIZE'";
+ + (vwr.isApplet ? "" : " filter 'DORESIZE'");
return;
}
if (fileName.endsWith("jvxl")) {
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-23
08:23:37 UTC (rev 20903)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-23
21:59:40 UTC (rev 20904)
@@ -7,8 +7,15 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.1_2015.12.23"
+Jmol.___JmolVersion="14.4.1_2015.12.23b"
+bug fix: JavaScript error reporting uses alert() instead of just setting the
error message
+bug fix: PyMOL 1.8 PSE files cannot be read because of missing settings
+
+code: more efficient loading of PyMOL .pse session files
+
+JmolVersion="14.4.1_2015.12.23"
+
bug fix: PyMOL 1.8 PSE files cannot be read
bug fix: dots broken when colored none
bug fix: color cartoons red blue not saved in state
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
2015-12-23 08:23:37 UTC (rev 20903)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
2015-12-23 21:59:40 UTC (rev 20904)
@@ -1,15 +1,13 @@
package org.jmol.adapter.readers.pymol;
+import java.util.Hashtable;
+import java.util.Map;
+
import javajs.api.GenericBinaryDocument;
import javajs.util.Lst;
import javajs.util.SB;
import org.jmol.util.Logger;
-
-import java.util.Hashtable;
-
-import java.util.Map;
-
import org.jmol.viewer.Viewer;
/**
@@ -98,6 +96,7 @@
PickleReader(GenericBinaryDocument doc, Viewer vwr) {
binaryDoc = doc;
this.vwr = vwr;
+ stack.ensureCapacity(1000);
}
private void log(String s) {
@@ -386,10 +385,11 @@
private Lst<Object> getObjects(int mark) {
int n = stack.size() - mark;
Lst<Object> args = new Lst<Object>();
- for (int j = 0; j < n; j++)
- args.addLast(null);
- for (int j = n, i = stack.size(); --i >= mark;)
- args.set(--j, stack.remove(i));
+ args.ensureCapacity(n);
+ for (int i = mark; i < stack.size(); ++i)
+ args.addLast(stack.get(i));
+ for (int i = stack.size(); --i >= mark;)
+ stack.remove(i);
return args;
}
@@ -417,8 +417,12 @@
switch (markCount) {
case 2:
thisSection = stack.get(i - 2);
- inMovie = "movie".equals(thisSection);
- inNames = "names".equals(thisSection);
+ // BH: Note that JavaScript string == object first converts object to
string, then checks.
+ // This can be very slow if the object is complex.
+ if (thisSection instanceof String) {
+ inMovie = "movie".equals(thisSection);
+ inNames = "names".equals(thisSection);
+ }
break;
default:
break;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java 2015-12-23
08:23:37 UTC (rev 20903)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java 2015-12-23
21:59:40 UTC (rev 20904)
@@ -3,6 +3,8 @@
import java.util.Hashtable;
import java.util.Map;
+import javajs.util.P3;
+
import org.jmol.util.Logger;
/**
@@ -471,7 +473,7 @@
final static int offscreen_rendering_for_antialiasing = 695;
final static int offscreen_rendering_multiplier = 696;
final static int opaque_background = 435;
- final static int ortho = 23;
+ final static int orthoscopic = 23;
final static int overlay = 61;
final static int overlay_lines = 311;
final static int pdb_conect_all = 329;
@@ -6243,30 +6245,137 @@
moreColors.put(id, Integer.valueOf(value));
}
- public static float getDefaultSetting(int i, int pymolVersion) {
+ /**
+ * All settings that Jmol uses should go here
+ *
+ * @param i
+ * @param pymolVersion
+ * @return setting or 0
+ */
+ static float getDefaultSetting(int i, int pymolVersion) {
switch (i) {
- case label_size:
- return 14;
+ case sphere_color:
case cartoon_color:
case ellipsoid_color:
case ribbon_color:
case line_color:
+ case dot_color:
case stick_color:
+ case surface_color:
+ case dash_color:
+ case mesh_color:
+ case cartoon_putty_quality:
case label_distance_digits:
case label_angle_digits:
case label_dihedral_digits:
+ case two_sided_lighting:
return -1;
case ray_pixel_scale:
case ellipsoid_scale:
+ case sphere_scale:
+ case mesh_width:
+ case cartoon_ladder_mode:
+ case clamp_colors:
+ case frame:
+ case state:
+ case depth_cue:
+ case fog:
+ case cartoon_round_helices:
+ case cartoon_fancy_helices:
+ case label_digits:
+ case ribbon_sampling:
return 1;
- default:
- Logger.info("PyMOL " + pymolVersion + " does not have setting " + i);
- //$FALL-THROUGH$
+ case sphere_transparency:
case ellipsoid_transparency:
case ribbon_transparency:
case nonbonded_transparency:
+ case cartoon_transparency:
+ case stick_transparency:
+ case transparency:
+ case bg_rgb:
+ case cartoon_cylindrical_helices:
+ case surface_mode:
+ case surface_solvent:
+ case all_states:
+ case valence:
+ case cgo_transparency:
+ case cartoon_putty_transform:
+ case orthoscopic:
+ case ribbon_radius:
+ case ribbon_smooth:
+ case sphere_solvent:
+ case surface_carve_cutoff:
return 0;
+ case cartoon_loop_radius:
+ return 0.2F;
+ case cartoon_rect_length:
+ return 1.4F;
+ case nonbonded_size:
+ return 0.25F;
+ case fog_start:
+ return 0.45f;
+ case label_size:
+ return 14;
+ case label_color:
+ return -6;
+ case label_font_id:
+ return 5;
+ case transparency_mode:
+ case cartoon_putty_range:
+ case cartoon_tube_cap:
+ return 2;
+ case cartoon_nucleic_acid_mode:
+ case cartoon_putty_scale_max:
+ return 4;
+ case cartoon_putty_radius:
+ return 0.4f;
+ case cartoon_putty_scale_min:
+ return 0.6f;
+ case cartoon_putty_scale_power:
+ return 1.5f;
+ case cartoon_tube_radius:
+ return 0.5f;
+ case solvent_radius:
+ return 1.4f;
+ case dash_width:
+ return 2.5f;
+ case line_width:
+ return 1.49f;
+ case ribbon_width:
+ return 3;
+ case field_of_view:
+ return 20;
+ case movie_fps:
+ return 30;
+ case stick_radius:
+ return 0.25f;
+ default:
+ Logger.error("PyMOL " + pymolVersion + " default float setting not
found: " + i);
+ return 0;
}
}
+ static P3 getDefaultSettingPt(int i, int pymolVersion, P3 pt) {
+ switch (i) {
+ case label_position:
+ pt.set(0, 0, 0.75f);
+ break;
+ default:
+ Logger.error("PyMOL " + pymolVersion + " default point setting not
found: " + i);
+ break;
+ }
+ return pt;
+ }
+
+ static String getDefaultSettingS(int i, int pymolVersion) {
+ switch (i) {
+ case surface_carve_selection:
+ break;
+ default:
+ Logger.info("PyMOL " + pymolVersion + " does not have String setting " +
i);
+ break;
+ }
+ return "";
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2015-12-23 08:23:37 UTC (rev 20903)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2015-12-23 21:59:40 UTC (rev 20904)
@@ -183,7 +183,7 @@
sourcePNGJ = false;
if (doCache)
bsBytesExcluded = new BS();
- logging = false;
+ //logging = true; // specifically for Pickle
super.initializeReader();
}
@@ -333,12 +333,11 @@
// resize frame
if (!isStateScript && doResize) {
int width = 0, height = 0;
- try {
+ Lst<Object> main = getMapList(map, "main");
+ if (main != null) {
// not all PSE files have this
- width = intAt(getMapList(map, "main"), 0);
- height = intAt(getMapList(map, "main"), 1);
- } catch (Exception e) {
- // ignore
+ width = intAt(main, 0);
+ height = intAt(main, 1);
}
String note;
if (width > 0 && height > 0) {
@@ -495,7 +494,7 @@
Lst<Object> setting = (Lst<Object>) mySettings.get(j);
int uid = (id << 10) + intAt(setting, 0);
uniqueSettings.put(Integer.valueOf(uid), setting);
- Logger.info("PyMOL unique setting " + id + " " + setting);
+ //System.out.println("PyMOL unique setting " + id + " " + setting);
}
}
}
@@ -516,7 +515,7 @@
for (int i = colors.size(); --i >= 0;) {
Lst<Object> c = listAt(colors, i);
PyMOL.addColor((Integer) c.get(1), isClamped ?
PyMOLScene.colorSettingClamped(c)
- : PyMOLScene.colorSetting(c));
+ : PyMOLScene.getColorPt(c.get(2)));
}
}
@@ -901,13 +900,15 @@
Lst<Object> coords = listAt(state, 2);
Lst<Object> labelPositions = listAt(state, 8);
- if (iState == 0 || !isTrajectory)
+ if (iState == 0 || !isTrajectory) {
+ pymolScene.ensureCapacity(n);
for (int idx = 0; idx < n; idx++) {
P3 a = addAtom(pymolAtoms, intAt(idxToAtm, idx), idx, coords,
labelPositions, bsAtoms, iState);
if (a != null)
trajectoryStep[trajectoryPtr++] = a;
}
+ }
addBonds(bonds);
addMolStructures();
atoms = asc.atoms;
@@ -942,9 +943,10 @@
* @return list of bonds
*/
private Lst<Bond> getBondList(Lst<Object> bonds) {
- Lst<Bond> bondList = new Lst<Bond>();
int asSingle = (pymolScene.booleanSetting(PyMOL.valence) ? 0 :
JmolAdapter.ORDER_PYMOL_SINGLE);
int n = bonds.size();
+ Lst<Bond> bondList = new Lst<Bond>();
+ bondList.ensureCapacity(n);
for (int i = 0; i < n; i++) {
Lst<Object> b = listAt(bonds, i);
int order = intAt(b, 2);
@@ -1098,7 +1100,8 @@
atom.vib = V3.new3(uniqueID, cartoonType, Float.NaN);
if (a.size() > 46) {
float[] data = PyMOLScene.floatsAt(a, 41, new float[8], 6);
- asc.setAnisoBorU(atom, data, 12);
+ if (data[0] != 0)
+ asc.setAnisoBorU(atom, data, 12);
}
//if (uniqueID > 0)
//pymolScene.setUnique(uniqueID, atom);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2015-12-23 08:23:37 UTC (rev 20903)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2015-12-23 21:59:40 UTC (rev 20904)
@@ -212,10 +212,9 @@
this.stateCount = stateCount;
}
- @SuppressWarnings("unchecked")
PyMOLScene(PymolAtomReader reader, Viewer vwr, Lst<Object> settings,
- Map<Integer, Lst<Object>> uniqueSettings, int pymolVersion,
- boolean haveScenes, int baseAtomIndex, int baseModelIndex,
+ Map<Integer, Lst<Object>> uniqueSettings, int pymolVersion,
+ boolean haveScenes, int baseAtomIndex, int baseModelIndex,
boolean doCache, String filePath) {
this.reader = reader;
this.vwr = vwr;
@@ -229,11 +228,33 @@
this.surfaceInfoName = filePath + "##JmolSurfaceInfo##";
setVersionSettings();
settings.trimToSize();
- bgRgb = colorSetting(listAt(settings, PyMOL.bg_rgb));
- pointAt((Lst<Object>) listAt(settings, PyMOL.label_position).get(2),
- 0, labelPosition0);
+ bgRgb = colorSetting(PyMOL.bg_rgb);
+ labelPosition0 = pointSetting(PyMOL.label_position);
}
+ @SuppressWarnings("unchecked")
+ private int colorSetting(int i) {
+ Lst<Object> pos = listAt(settings, i);
+ Object o = (pos == null || pos.size() != 3 ? null : pos.get(2));
+ if (o == null)
+ return (int) PyMOL.getDefaultSetting(i, pymolVersion);
+ return (o instanceof Integer ? ((Integer) o).intValue() : CU
+ .colorPtToFFRGB(pointAt((Lst<Object>) o, 0, ptTemp)));
+ }
+
+ @SuppressWarnings("unchecked")
+ private P3 pointSetting(int i) {
+ P3 pt = new P3();
+ Lst<Object> pos = listAt(settings, i);
+ if (pos != null && pos.size() == 3)
+ return pointAt((Lst<Object>) pos.get(2), 0, pt);
+ return PyMOL.getDefaultSettingPt(i, pymolVersion, pt);
+ }
+
+ void ensureCapacity(int n) {
+ atomColorList.ensureCapacity(atomColorList.size() + n);
+ }
+
void setReaderObjectInfo(String name, int type, String groupName, boolean
isHidden,
Lst<Object> listObjSettings,
Lst<Object> listStateSettings, String ext) {
@@ -634,7 +655,7 @@
@SuppressWarnings("unchecked")
static int getColorPt(Object o) {
- return (o instanceof Integer ? ((Integer) o).intValue() : CU
+ return (o == null ? 0 : o instanceof Integer ? ((Integer) o).intValue() :
CU
.colorPtToFFRGB(pointAt((Lst<Object>) o, 0, ptTemp)));
}
@@ -642,10 +663,6 @@
return ((Number) list.get(i)).intValue();
}
- static int colorSetting(Lst<Object> c) {
- return getColorPt(c.get(2));
- }
-
void setReaderObjects() {
clearReaderData();
finalizeObjects();
@@ -723,7 +740,7 @@
for (int j = 0; j < 8; j++)
pymolView[pt++] = floatAt(view, i++);
- boolean isOrtho = booleanSetting(PyMOL.ortho); // 23
+ boolean isOrtho = booleanSetting(PyMOL.orthoscopic); // 23
float fov = floatSetting(PyMOL.field_of_view); // 152
pymolView[pt++] = (isOrtho ? fov : -fov);
@@ -735,12 +752,10 @@
@SuppressWarnings("unchecked")
float globalSetting(int i) {
- try {
- Lst<Object> setting = (Lst<Object>) settings.get(i);
+ Lst<Object> setting = (Lst<Object>) settings.get(i);
+ if (setting != null && setting.size() == 3)
return ((Number) setting.get(2)).floatValue();
- } catch (Exception e) {
- return PyMOL.getDefaultSetting(i, pymolVersion);
- }
+ return PyMOL.getDefaultSetting(i, pymolVersion);
}
/**
@@ -947,21 +962,17 @@
}
float floatSetting(int i) {
- try {
- Lst<Object> setting = getSetting(i);
+ Lst<Object> setting = getSetting(i);
+ if (setting != null && setting.size() == 3)
return ((Number) setting.get(2)).floatValue();
- } catch (Exception e) {
- return PyMOL.getDefaultSetting(i, pymolVersion);
- }
+ return PyMOL.getDefaultSetting(i, pymolVersion);
}
String stringSetting(int i) {
- try {
Lst<Object> setting = getSetting(i);
- return setting.get(2).toString();
- } catch (Exception e) {
- return null;
- }
+ if (setting != null && setting.size() == 3)
+ return setting.get(2).toString();
+ return PyMOL.getDefaultSettingS(i, pymolVersion);
}
@SuppressWarnings("unchecked")
@@ -1105,8 +1116,7 @@
}
static int colorSettingClamped(Lst<Object> c) {
- return (c.size() < 6 || intAt(c, 4) == 0 ? colorSetting(c) : getColorPt(c
- .get(5)));
+ return getColorPt(c.get(c.size() < 6 || intAt(c, 4) == 0 ? 2 : 5));
}
void setAtomColor(int atomColor) {
@@ -1685,11 +1695,11 @@
return defs;
}
- public boolean needSelections() {
+ boolean needSelections() {
return haveScenes || !htCarveSets.isEmpty();
}
- public void setUniqueBonds(BS bsBonds, boolean isSticks) {
+ void setUniqueBonds(BS bsBonds, boolean isSticks) {
if (isSticks) {
bsStickBonds.or(bsBonds);
bsStickBonds.andNot(bsLineBonds);
@@ -1734,7 +1744,7 @@
* @param argb
* @param trans
*/
- public void setBondParameters(Bond b, int modelIndex, float rad, float
pymolValence,
+ void setBondParameters(Bond b, int modelIndex, float rad, float pymolValence,
int argb, float trans) {
if (modelIndex >= 0 && b.atom1.mi != modelIndex)
return;
@@ -1755,7 +1765,7 @@
}
- public void addMesh(int tok, Lst<Object> obj, String objName, boolean isMep)
{
+ void addMesh(int tok, Lst<Object> obj, String objName, boolean isMep) {
JmolObject jo = addJmolObject(tok, null, obj);
setSceneObject(objName, -1);
int meshColor = (int) floatSetting(PyMOL.mesh_color);
@@ -1769,7 +1779,7 @@
jo.cacheID = surfaceInfoName;
}
- public JmolObject addIsosurface(String objectName) {
+ JmolObject addIsosurface(String objectName) {
JmolObject jo = addJmolObject(T.isosurface, null, objectName);
jo.cacheID = surfaceInfoName;
return jo;
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-12-23
08:23:37 UTC (rev 20903)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-12-23
21:59:40 UTC (rev 20904)
@@ -2570,6 +2570,12 @@
atomTensors.remove(toDelete.get(i));
}
+
+ private int atomCapacity;
+ void setCapacity(int nAtoms) {
+ atomCapacity += nAtoms;
+ }
+
public void setAtomTensors(int atomIndex, Lst<Object> list) {
if (list == null || list.size() == 0)
return;
@@ -2590,6 +2596,16 @@
}
}
+ public void addTensor(Tensor t, String type) {
+ type = type.toLowerCase();
+ Lst<Object> tensors = atomTensors.get(type);
+ if (tensors == null) {
+ atomTensors.put(type, tensors = new Lst<Object>());
+ tensors.ensureCapacity(atomCapacity);
+ }
+ tensors.addLast(t);
+ }
+
private static Object[] getTensorList(Lst<Object> list) {
int pt = -1;
boolean haveTLS = false;
@@ -2637,14 +2653,6 @@
return null;
}
- public void addTensor(Tensor t, String type) {
- type = type.toLowerCase();
- Lst<Object> tensors = atomTensors.get(type);
- if (tensors == null)
- atomTensors.put(type, tensors = new Lst<Object>());
- tensors.addLast(t);
- }
-
public Lst<Object> getAllAtomTensors(String type) {
if (atomTensors == null)
return null;
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-12-23 08:23:37 UTC
(rev 20903)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-12-23 21:59:40 UTC
(rev 20904)
@@ -771,6 +771,7 @@
boolean addH = false;
boolean isLegacyHAddition = false;//vwr.getBoolean(T.legacyhaddition);
JmolAdapterAtomIterator iterAtom = adapter.getAtomIterator(asc);
+ ms.setCapacity(adapter.getAtomCount(asc));
int nRead = 0;
Model[] models = ms.am;
if (ms.mc > 0)
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-12-23 08:23:37 UTC
(rev 20903)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-12-23 21:59:40 UTC
(rev 20904)
@@ -4057,5 +4057,6 @@
}
return (asMap ? map : lst);
}
+
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptManager.java 2015-12-23 08:23:37 UTC
(rev 20903)
+++ trunk/Jmol/src/org/jmol/script/ScriptManager.java 2015-12-23 21:59:40 UTC
(rev 20904)
@@ -540,7 +540,7 @@
try {
if (fileName.endsWith(".pse")) {
cmd = (isCached ? "" : "zap;") + "load SYNC " + PT.esc(fileName)
- + " filter 'DORESIZE'";
+ + (vwr.isApplet ? "" : " filter 'DORESIZE'");
return;
}
if (fileName.endsWith("jvxl")) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-23 08:23:37 UTC
(rev 20903)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-23 21:59:40 UTC
(rev 20904)
@@ -62,8 +62,21 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.1_2015.12.23"
+Jmol.___JmolVersion="14.5.1_2015.12.23b"
+bug fix: JavaScript error reporting uses alert() instead of just setting the
error message
+
+code: more efficient loading of PyMOL .pse session files
+
+Jmol.___JmolVersion="14.5.1_2015.12.23b"
+
+bug fix: JavaScript error reporting uses alert() instead of just setting the
error message
+bug fix: PyMOL 1.8 PSE files cannot be read because of missing settings
+
+code: more efficient loading of PyMOL .pse session files
+
+JmolVersion="14.5.1_2015.12.23"
+
bug fix: PyMOL 1.8 PSE files cannot be read
bug fix: dots broken when colored none
bug fix: color cartoons red blue not saved in state
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-12-23 08:23:37 UTC (rev
20903)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-12-23 21:59:40 UTC (rev
20904)
@@ -99,7 +99,6 @@
import org.jmol.modelset.Atom;
import org.jmol.modelset.AtomCollection;
import org.jmol.modelset.Bond;
-import org.jmol.modelset.Group;
import org.jmol.modelset.LabelToken;
import org.jmol.modelset.Measurement;
import org.jmol.modelset.MeasurementData;
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