Revision: 21201
http://sourceforge.net/p/jmol/code/21201
Author: hansonr
Date: 2016-08-10 12:57:12 +0000 (Wed, 10 Aug 2016)
Log Message:
-----------
PyMOL reader upgrade
Modified Paths:
--------------
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
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
Modified: branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2016-08-10 07:00:36 UTC (rev 21200)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2016-08-10 12:57:12 UTC (rev 21201)
@@ -315,8 +315,8 @@
Lst<Object> mep = (Lst<Object>) info;
sID = mep.get(mep.size() - 2).toString();
String mapID = mep.get(mep.size() - 1).toString();
- float min = PyMOLScene.floatAt(PyMOLScene.listAt(mep, 3), 0);
- float max = PyMOLScene.floatAt(PyMOLScene.listAt(mep, 3), 2);
+ float min = PyMOLReader.floatAt(PyMOLReader.listAt(mep, 3), 0);
+ float max = PyMOLReader.floatAt(PyMOLReader.listAt(mep, 3), 2);
sb = new SB();
sb.append(";isosurface ID ").append(PT.esc(sID)).append(" map
").append(PT.esc(cacheID)).append(" ")
.append(PT.esc(mapID)).append(
@@ -336,15 +336,15 @@
.append(m.getModelNumberDotted(modelIndex))
.append(" color ").append(Escape.escapeColor(argb)).append("
").append(PT.esc(cacheID)).append(" ")
.append(PT.esc(sID)).append(" mesh nofill frontonly");
- float within = PyMOLScene.floatAt(PyMOLScene.listAt(PyMOLScene.listAt(
+ float within = PyMOLReader.floatAt(PyMOLReader.listAt(PyMOLReader.listAt(
mesh, 2), 0), 11);
- Lst<Object> list = PyMOLScene.listAt(PyMOLScene.listAt(PyMOLScene
+ Lst<Object> list = PyMOLReader.listAt(PyMOLReader.listAt(PyMOLReader
.listAt(mesh, 2), 0), 12);
if (within > 0) {
P3 pt = new P3();
sb.append(";isosurface slab within ").appendF(within).append(" [ ");
for (int j = list.size() - 3; j >= 0; j -= 3) {
- PyMOLScene.pointAt(list, j, pt);
+ PyMOLReader.pointAt(list, j, pt);
sb.append(Escape.eP(pt));
}
sb.append(" ]");
Modified:
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2016-08-10 07:00:36 UTC (rev 21200)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2016-08-10 12:57:12 UTC (rev 21201)
@@ -45,6 +45,7 @@
import javajs.util.AU;
import javajs.util.BC;
+import javajs.util.CU;
import javajs.util.P3;
import javajs.util.PT;
import javajs.util.V3;
@@ -515,6 +516,8 @@
return max;
}
+ private final P3 ptTemp = new P3();
+
/**
* Add new colors from the main "colors" map object.
* Not 100% clear how color clamping works.
@@ -528,8 +531,8 @@
// note, we are ignoring lookup-table colors
for (int i = colors.size(); --i >= 0;) {
Lst<Object> c = listAt(colors, i);
- PyMOL.addColor((Integer) c.get(1), isClamped ?
PyMOLScene.colorSettingClamped(c)
- : PyMOLScene.getColorPt(c.get(2)));
+ PyMOL.addColor((Integer) c.get(1), isClamped ? colorSettingClamped(c,
ptTemp)
+ : getColorPt(c.get(2), ptTemp));
}
}
@@ -1326,11 +1329,16 @@
* list of atom details
* @param apt
* array pointer into pymolAtoms
+ * @param atomArray
+ * @param vArray
+ * @param lexStr
* @param icoord
* array pointer into coords (/3)
* @param coords
* coordinates array
+ * @param coordArray
* @param labelPositions
+ * @param labelArray
* @param bsState
* this state -- Jmol atomIndex
* @param iState
@@ -1409,7 +1417,7 @@
bonded = (intAt(a, 25) != 0);
uniqueID = (a.size() > 40 && intAt(a, 40) == 1 ? intAt(a, 32) : -1);
if (a.size() > 46)
- anisou = PyMOLScene.floatsAt(a, 41, new float[8], 6);
+ anisou = floatsAt(a, 41, new float[8], 6);
}
String insCode = (resi.length() > 3 ? resi.substring(3) : " ");
@@ -1686,13 +1694,12 @@
private void processSelectionsAndScenes(Map<String, Object> map) {
if (!pymolScene.needSelections())
return;
- Map<String, Lst<Object>> htObjNames = PyMOLScene.listToMap(getMapList(
+ Map<String, Lst<Object>> htObjNames = listToMap(getMapList(
map, "names"));
if (haveScenes) {
Map<String, Object> scenes = (Map<String, Object>) map.get("scene_dict");
finalizeSceneData();
- Map<String, Lst<Object>> htSecrets = PyMOLScene
- .listToMap(getMapList(map, "selector_secrets"));
+ Map<String, Lst<Object>> htSecrets = listToMap(getMapList(map,
"selector_secrets"));
for (int i = 0; i < sceneOrder.size(); i++) {
String name = stringAt(sceneOrder, i);
Lst<Object> thisScene = getMapList(scenes, name);
@@ -1737,12 +1744,53 @@
// generally useful static methods
- private static int intAt(Lst<Object> list, int i) {
+ static int intAt(Lst<Object> list, int i) {
// PyMOL 1.7.5 may simply have a null list for a setting
return (list == null ? -1 : ((Number) list.get(i)).intValue());
}
- private static String stringAt(Lst<Object> list, int i) {
+ static P3 pointAt(Lst<Object> list, int i, P3 pt) {
+ pt.set(floatAt(list, i++), floatAt(list, i++), floatAt(list, i));
+ return pt;
+ }
+
+ static float[] floatsAt(Lst<Object> a, int pt, float[] data, int len) {
+ if (a == null)
+ return null;
+ for (int i = 0; i < len; i++)
+ data[i] = floatAt(a, pt++);
+ return data;
+ }
+
+ static float floatAt(Lst<Object> list, int i) {
+ return (list == null ? 0 : ((Number) list.get(i)).floatValue());
+ }
+
+ @SuppressWarnings("unchecked")
+ static Lst<Object> listAt(Lst<Object> list, int i) {
+ if (list == null || i >= list.size())
+ return null;
+ Object o = list.get(i);
+ return (o instanceof Lst<?> ? (Lst<Object>) o : null);
+ }
+
+ /**
+ * return a map of lists of the type: [ [name1,...], [name2,...], ...]
+ *
+ * @param list
+ * @return Hashtable
+ */
+ static Map<String, Lst<Object>> listToMap(Lst<Object> list) {
+ Hashtable<String, Lst<Object>> map = new Hashtable<String, Lst<Object>>();
+ for (int i = list.size(); --i >= 0;) {
+ Lst<Object> item = listAt(list, i);
+ if (item != null && item.size() > 0)
+ map.put(stringAt(item, 0), item);
+ }
+ return map;
+ }
+
+ static String stringAt(Lst<Object> list, int i) {
if (!AU.isAB(list.get(i)))
System.out.println("??");
byte[] a = (byte[]) list.get(i);
@@ -1757,7 +1805,17 @@
}
}
+ static int colorSettingClamped(Lst<Object> c, P3 ptTemp) {
+ return getColorPt(c.get(c.size() < 6 || intAt(c, 4) == 0 ? 2 : 5), ptTemp);
+ }
+
@SuppressWarnings("unchecked")
+ static int getColorPt(Object o, P3 ptTemp) {
+ return (o == null ? 0 : o instanceof Integer ? ((Integer) o).intValue() :
CU
+ .colorPtToFFRGB(PyMOLReader.pointAt((Lst<Object>) o, 0, ptTemp)));
+ }
+
+ @SuppressWarnings("unchecked")
private static Lst<Object> getMapList(Map<String, Object> map, String key) {
return (Lst<Object>) map.get(key);
}
@@ -1774,14 +1832,6 @@
return bsReps;
}
- private float floatAt(Lst<Object> a, int i) {
- return PyMOLScene.floatAt(a, i);
- }
-
- private Lst<Object> listAt(Lst<Object> list, int i) {
- return PyMOLScene.listAt(list, i);
- }
-
/// PymolAtomReader interface
@Override
@@ -1809,6 +1859,4 @@
return atoms[iPrev].chainID != atoms[i].chainID;
}
-
-
}
Modified: branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2016-08-10 07:00:36 UTC (rev 21200)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2016-08-10 12:57:12 UTC (rev 21201)
@@ -234,20 +234,20 @@
@SuppressWarnings("unchecked")
private int colorSetting(int i) {
- Lst<Object> pos = listAt(settings, i);
+ Lst<Object> pos = PyMOLReader.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)));
+ .colorPtToFFRGB(PyMOLReader.pointAt((Lst<Object>) o, 0, ptTemp)));
}
@SuppressWarnings("unchecked")
private P3 pointSetting(int i) {
P3 pt = new P3();
- Lst<Object> pos = listAt(settings, i);
+ Lst<Object> pos = PyMOLReader.listAt(settings, i);
if (pos != null && pos.size() == 3)
- return pointAt((Lst<Object>) pos.get(2), 0, pt);
+ return PyMOLReader.pointAt((Lst<Object>) pos.get(2), 0, pt);
return PyMOL.getDefaultSettingPt(i, pymolVersion, pt);
}
@@ -260,7 +260,7 @@
Lst<Object> listStateSettings, String ext) {
objectName = name;
objectHidden = isHidden;
- objectNameID = (objectName == null ? null : PyMOLScene.fixName(objectName
+ objectNameID = (objectName == null ? null : fixName(objectName
+ ext));
objectSettings = new Hashtable<Integer, Lst<Object>>();
stateSettings = new Hashtable<Integer, Lst<Object>>();
@@ -285,7 +285,7 @@
}
@SuppressWarnings("unchecked")
- private static void listToSettings(Lst<Object> list,
+ private void listToSettings(Lst<Object> list,
Map<Integer, Lst<Object>> objectSettings) {
if (list != null && list.size() != 0) {
// if (debugging)
@@ -329,7 +329,7 @@
labelPosition = new P3();
try {
Lst<Object> setting = getObjectSetting(PyMOL.label_position);
- pointAt(listAt(setting, 2), 0, labelPosition);
+ PyMOLReader.pointAt(PyMOLReader.listAt(setting, 2), 0, labelPosition);
} catch (Exception e) {
// no problem.
}
@@ -404,7 +404,7 @@
smap.put("pymolFrame", frame);
smap.put("generator", this);
smap.put("name", name);
- Lst<Object> view = listAt(thisScene, 0);
+ Lst<Object> view = PyMOLReader.listAt(thisScene, 0);
if (view != null)
smap.put("pymolView", getPymolView(view, false));
@@ -421,23 +421,23 @@
Object[] reps = new Object[PyMOL.REP_LIST.length];
for (int j = PyMOL.REP_LIST.length; --j >= 0;) {
Lst<Object> list = htObjNames.get(sname + PyMOL.REP_LIST[j]);
- Lst<Object> data = listAt(list, 5);
+ Lst<Object> data = PyMOLReader.listAt(list, 5);
if (data != null && data.size() > 0)
- reps[j] = listToMap(data);
+ reps[j] = PyMOLReader.listToMap(data);
}
smap.put("moleculeReps", reps);
// there's no real point in getting
// get all colors from selector_secrets
sname = "_!c_" + name + "_";
- Lst<Object> colorection = listAt(thisScene, 3);
+ Lst<Object> colorection = PyMOLReader.listAt(thisScene, 3);
int n = colorection.size();
// [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);
+ int color = PyMOLReader.intAt(colorection, j);
Lst<Object> c = htSecrets.get(sname + color);
if (c != null && c.size() > 1)
colors[i++] = new Object[] { Integer.valueOf(color), c.get(1) };
@@ -512,7 +512,7 @@
String id = selection.get(0).toString();
id = "_" + (id.equals("sele") ? id : "sele_" + id);
PyMOLGroup g = getGroup(id);
- getSelectionAtoms(listAt(selection, 5), 0, g.bsAtoms);
+ getSelectionAtoms(PyMOLReader.listAt(selection, 5), 0, g.bsAtoms);
}
/**
@@ -526,7 +526,7 @@
private BS getSelectionAtoms(Lst<Object> molecules, int istate, BS bs) {
if (molecules != null)
for (int j = molecules.size(); --j >= 0;)
- selectAllAtoms(listAt(molecules, j), istate, bs);
+ selectAllAtoms(PyMOLReader.listAt(molecules, j), istate, bs);
return bs;
}
@@ -538,9 +538,9 @@
* @param bs
*/
private void selectAllAtoms(Lst<Object> obj, int istate, BS bs) {
- String name = (String) obj.get(0);
+ String name = PyMOLReader.stringAt(obj, 0);
setSceneObject(name, istate);
- Lst<Object> atomList = listAt(obj, 1);
+ Lst<Object> atomList = PyMOLReader.listAt(obj, 1);
int k0 = (istate == 0 ? 1 : istate);
int k1 = (istate == 0 ? stateCount : istate);
for (int k = k0; k <= k1; k++) {
@@ -570,7 +570,7 @@
if (name.equals("all"))
continue;
Lst<Object> list = (Lst<Object>) e.getValue();
- int tok = (intAt(list, 0) == 1 ? T.display : T.hide);
+ int tok = (PyMOLReader.intAt(list, 0) == 1 ? T.display : T.hide);
if (tok == T.hide)
htHiddenObjects.put(name, Boolean.TRUE);
switch (getObjectType(name)) {
@@ -607,7 +607,7 @@
MeasurementData[] mdList = htMeasures.get(name);
if (mdList != null)
addMeasurements(mdList, mdList[0].points.size(), null,
- getBS(listAt(list, 2)), intAt(list, 3), null, true);
+ getBS(PyMOLReader.listAt(list, 2)), PyMOLReader.intAt(list,
3), null, true);
}
info += "_*";
break;
@@ -654,27 +654,17 @@
private BS getBS(Lst<Object> list) {
BS bs = new BS();
for (int i = list.size(); --i >= 0;)
- bs.set(intAt(list, i));
+ bs.set(PyMOLReader.intAt(list, i));
return bs;
}
private void getBsAtoms(Lst<Object> list, int[] atomMap, BS bs) {
for (int i = list.size(); --i >= 0;)
- bs.set(atomMap[intAt(list, i)]);
+ bs.set(atomMap[PyMOLReader.intAt(list, i)]);
}
- private final static P3 ptTemp = new P3();
+ private final P3 ptTemp = new P3();
- @SuppressWarnings("unchecked")
- static int getColorPt(Object o) {
- return (o == null ? 0 : o instanceof Integer ? ((Integer) o).intValue() :
CU
- .colorPtToFFRGB(pointAt((Lst<Object>) o, 0, ptTemp)));
- }
-
- static int intAt(Lst<Object> list, int i) {
- return ((Number) list.get(i)).intValue();
- }
-
void setReaderObjects() {
clearReaderData();
finalizeObjects();
@@ -735,22 +725,22 @@
int i = 0;
// x-axis
for (int j = 0; j < 3; j++)
- pymolView[pt++] = floatAt(view, i++);
+ pymolView[pt++] = PyMOLReader.floatAt(view, i++);
if (isViewObj)
i++;
// y-axis
for (int j = 0; j < 3; j++)
- pymolView[pt++] = floatAt(view, i++);
+ pymolView[pt++] = PyMOLReader.floatAt(view, i++);
if (isViewObj)
i++;
// z-axis (not used)
for (int j = 0; j < 3; j++)
- pymolView[pt++] = floatAt(view, i++);
+ pymolView[pt++] = PyMOLReader.floatAt(view, i++);
if (isViewObj)
i += 5;
// xTrans, yTrans, -distanceToCenter, center(x,y,z), distanceToSlab,
distanceToDepth
for (int j = 0; j < 8; j++)
- pymolView[pt++] = floatAt(view, i++);
+ pymolView[pt++] = PyMOLReader.floatAt(view, i++);
boolean isOrtho = booleanSetting(PyMOL.orthoscopic); // 23
float fov = floatSetting(PyMOL.field_of_view); // 152
@@ -829,7 +819,7 @@
if (htCarveSets.isEmpty())
return;
for (Entry<String, BS> e: htCarveSets.entrySet())
- getSelectionAtoms(listAt(htObjNames.get(e.getKey()), 5), 0,
e.getValue());
+ getSelectionAtoms(PyMOLReader.listAt(htObjNames.get(e.getKey()), 5), 0,
e.getValue());
}
private void setGroupVisibilities() {
@@ -851,7 +841,7 @@
htDefinedAtoms.put(getJmolName(name), bs);
}
- private static String getJmolName(String name) {
+ private String getJmolName(String name) {
return "__" + fixName(name);
}
@@ -958,7 +948,7 @@
|| (setting = uniqueSettings.get(Integer.valueOf((id << 10) + key)))
== null)
return pt;
pt = new P3();
- pointAt((Lst<Object>) setting.get(2), 0, pt);
+ PyMOLReader.pointAt((Lst<Object>) setting.get(2), 0, pt);
Logger.info("Pymol unique setting for " + id + ": " + key + " = " + pt);
return pt;
}
@@ -998,32 +988,7 @@
return setting;
}
- static P3 pointAt(Lst<Object> list, int i, P3 pt) {
- pt.set(floatAt(list, i++), floatAt(list, i++), floatAt(list, i));
- return pt;
- }
-
- static float floatAt(Lst<Object> list, int i) {
- return (list == null ? 0 : ((Number) list.get(i)).floatValue());
- }
-
- static float[] floatsAt(Lst<Object> a, int pt, float[] data, int len) {
- if (a == null)
- return null;
- for (int i = 0; i < len; i++)
- data[i] = floatAt(a, pt++);
- return data;
- }
-
- @SuppressWarnings("unchecked")
- static Lst<Object> listAt(Lst<Object> list, int i) {
- if (list == null || i >= list.size())
- return null;
- Object o = list.get(i);
- return (o instanceof Lst<?> ? (Lst<Object>) o : null);
- }
-
- static float[] setLabelPosition(P3 offset, float[] labelPos) {
+ float[] setLabelPosition(P3 offset, float[] labelPos) {
labelPos[0] = 1;
labelPos[1] = offset.x;
labelPos[2] = offset.y;
@@ -1069,8 +1034,8 @@
if (isNew) {
Lst<Object> points = new Lst<Object>();
for (int i = 0; i < nCoord; i++, p += 3)
- points.addLast(pointAt(list, p, new Point3fi()));
- offset = floatsAt(listAt(offsets, index), 0, new float[7], 7);
+ points.addLast(PyMOLReader.pointAt(list, p, new Point3fi()));
+ offset = PyMOLReader.floatsAt(PyMOLReader.listAt(offsets, index), 0,
new float[7], 7);
if (offset == null)
offset = setLabelPosition(labelPosition, new float[7]);
md = mdList[index] = vwr.newMeasurementData(objectNameID + "_"
@@ -1126,10 +1091,6 @@
return C.getColixTranslucent3(colix, translucency > 0, translucency);
}
- static int colorSettingClamped(Lst<Object> c) {
- return getColorPt(c.get(c.size() < 6 || intAt(c, 4) == 0 ? 2 : 5));
- }
-
void setAtomColor(int atomColor) {
atomColorList.addLast(Integer.valueOf(getColix(atomColor, 0)));
}
@@ -1145,7 +1106,7 @@
frameObj = null;
}
- private static String fixName(String name) {
+ private String fixName(String name) {
char[] chars = name.toLowerCase().toCharArray();
for (int i = chars.length; --i >= 0;)
if (!PT.isLetterOrDigit(chars[i]))
@@ -1678,22 +1639,6 @@
return bs;
}
- /**
- * return a map of lists of the type: [ [name1,...], [name2,...], ...]
- *
- * @param list
- * @return Hashtable
- */
- static Map<String, Lst<Object>> listToMap(Lst<Object> list) {
- Hashtable<String, Lst<Object>> map = new Hashtable<String, Lst<Object>>();
- for (int i = list.size(); --i >= 0;) {
- Lst<Object> item = PyMOLScene.listAt(list, i);
- if (item != null && item.size() > 0)
- map.put(PyMOLReader.bytesToString(item.get(0)), item);
- }
- return map;
- }
-
Map<String, Object> setAtomDefs() {
setGroupVisibilities();
Map<String, Object> defs = new Hashtable<String, Object>();
@@ -1781,7 +1726,7 @@
setSceneObject(objName, -1);
int meshColor = (int) floatSetting(PyMOL.mesh_color);
if (meshColor < 0)
- meshColor = intAt(listAt(obj, 0), 2);
+ meshColor = PyMOLReader.intAt(PyMOLReader.listAt(obj, 0), 2);
if (!isMep) {
jo.setSize(meshWidth);
jo.argb = PyMOL.getRGB(meshColor);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2016-08-10 07:00:36 UTC (rev 21200)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2016-08-10 12:57:12 UTC (rev 21201)
@@ -315,8 +315,8 @@
Lst<Object> mep = (Lst<Object>) info;
sID = mep.get(mep.size() - 2).toString();
String mapID = mep.get(mep.size() - 1).toString();
- float min = PyMOLScene.floatAt(PyMOLScene.listAt(mep, 3), 0);
- float max = PyMOLScene.floatAt(PyMOLScene.listAt(mep, 3), 2);
+ float min = PyMOLReader.floatAt(PyMOLReader.listAt(mep, 3), 0);
+ float max = PyMOLReader.floatAt(PyMOLReader.listAt(mep, 3), 2);
sb = new SB();
sb.append(";isosurface ID ").append(PT.esc(sID)).append(" map
").append(PT.esc(cacheID)).append(" ")
.append(PT.esc(mapID)).append(
@@ -336,15 +336,15 @@
.append(m.getModelNumberDotted(modelIndex))
.append(" color ").append(Escape.escapeColor(argb)).append("
").append(PT.esc(cacheID)).append(" ")
.append(PT.esc(sID)).append(" mesh nofill frontonly");
- float within = PyMOLScene.floatAt(PyMOLScene.listAt(PyMOLScene.listAt(
+ float within = PyMOLReader.floatAt(PyMOLReader.listAt(PyMOLReader.listAt(
mesh, 2), 0), 11);
- Lst<Object> list = PyMOLScene.listAt(PyMOLScene.listAt(PyMOLScene
+ Lst<Object> list = PyMOLReader.listAt(PyMOLReader.listAt(PyMOLReader
.listAt(mesh, 2), 0), 12);
if (within > 0) {
P3 pt = new P3();
sb.append(";isosurface slab within ").appendF(within).append(" [ ");
for (int j = list.size() - 3; j >= 0; j -= 3) {
- PyMOLScene.pointAt(list, j, pt);
+ PyMOLReader.pointAt(list, j, pt);
sb.append(Escape.eP(pt));
}
sb.append(" ]");
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2016-08-10 07:00:36 UTC (rev 21200)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2016-08-10 12:57:12 UTC (rev 21201)
@@ -45,6 +45,7 @@
import javajs.util.AU;
import javajs.util.BC;
+import javajs.util.CU;
import javajs.util.P3;
import javajs.util.PT;
import javajs.util.V3;
@@ -515,6 +516,8 @@
return max;
}
+ private final P3 ptTemp = new P3();
+
/**
* Add new colors from the main "colors" map object.
* Not 100% clear how color clamping works.
@@ -528,8 +531,8 @@
// note, we are ignoring lookup-table colors
for (int i = colors.size(); --i >= 0;) {
Lst<Object> c = listAt(colors, i);
- PyMOL.addColor((Integer) c.get(1), isClamped ?
PyMOLScene.colorSettingClamped(c)
- : PyMOLScene.getColorPt(c.get(2)));
+ PyMOL.addColor((Integer) c.get(1), isClamped ? colorSettingClamped(c,
ptTemp)
+ : getColorPt(c.get(2), ptTemp));
}
}
@@ -1326,11 +1329,16 @@
* list of atom details
* @param apt
* array pointer into pymolAtoms
+ * @param atomArray
+ * @param vArray
+ * @param lexStr
* @param icoord
* array pointer into coords (/3)
* @param coords
* coordinates array
+ * @param coordArray
* @param labelPositions
+ * @param labelArray
* @param bsState
* this state -- Jmol atomIndex
* @param iState
@@ -1409,7 +1417,7 @@
bonded = (intAt(a, 25) != 0);
uniqueID = (a.size() > 40 && intAt(a, 40) == 1 ? intAt(a, 32) : -1);
if (a.size() > 46)
- anisou = PyMOLScene.floatsAt(a, 41, new float[8], 6);
+ anisou = floatsAt(a, 41, new float[8], 6);
}
String insCode = (resi.length() > 3 ? resi.substring(3) : " ");
@@ -1686,13 +1694,12 @@
private void processSelectionsAndScenes(Map<String, Object> map) {
if (!pymolScene.needSelections())
return;
- Map<String, Lst<Object>> htObjNames = PyMOLScene.listToMap(getMapList(
+ Map<String, Lst<Object>> htObjNames = listToMap(getMapList(
map, "names"));
if (haveScenes) {
Map<String, Object> scenes = (Map<String, Object>) map.get("scene_dict");
finalizeSceneData();
- Map<String, Lst<Object>> htSecrets = PyMOLScene
- .listToMap(getMapList(map, "selector_secrets"));
+ Map<String, Lst<Object>> htSecrets = listToMap(getMapList(map,
"selector_secrets"));
for (int i = 0; i < sceneOrder.size(); i++) {
String name = stringAt(sceneOrder, i);
Lst<Object> thisScene = getMapList(scenes, name);
@@ -1737,12 +1744,53 @@
// generally useful static methods
- private static int intAt(Lst<Object> list, int i) {
+ static int intAt(Lst<Object> list, int i) {
// PyMOL 1.7.5 may simply have a null list for a setting
return (list == null ? -1 : ((Number) list.get(i)).intValue());
}
- private static String stringAt(Lst<Object> list, int i) {
+ static P3 pointAt(Lst<Object> list, int i, P3 pt) {
+ pt.set(floatAt(list, i++), floatAt(list, i++), floatAt(list, i));
+ return pt;
+ }
+
+ static float[] floatsAt(Lst<Object> a, int pt, float[] data, int len) {
+ if (a == null)
+ return null;
+ for (int i = 0; i < len; i++)
+ data[i] = floatAt(a, pt++);
+ return data;
+ }
+
+ static float floatAt(Lst<Object> list, int i) {
+ return (list == null ? 0 : ((Number) list.get(i)).floatValue());
+ }
+
+ @SuppressWarnings("unchecked")
+ static Lst<Object> listAt(Lst<Object> list, int i) {
+ if (list == null || i >= list.size())
+ return null;
+ Object o = list.get(i);
+ return (o instanceof Lst<?> ? (Lst<Object>) o : null);
+ }
+
+ /**
+ * return a map of lists of the type: [ [name1,...], [name2,...], ...]
+ *
+ * @param list
+ * @return Hashtable
+ */
+ static Map<String, Lst<Object>> listToMap(Lst<Object> list) {
+ Hashtable<String, Lst<Object>> map = new Hashtable<String, Lst<Object>>();
+ for (int i = list.size(); --i >= 0;) {
+ Lst<Object> item = listAt(list, i);
+ if (item != null && item.size() > 0)
+ map.put(stringAt(item, 0), item);
+ }
+ return map;
+ }
+
+ static String stringAt(Lst<Object> list, int i) {
if (!AU.isAB(list.get(i)))
System.out.println("??");
byte[] a = (byte[]) list.get(i);
@@ -1757,7 +1805,17 @@
}
}
+ static int colorSettingClamped(Lst<Object> c, P3 ptTemp) {
+ return getColorPt(c.get(c.size() < 6 || intAt(c, 4) == 0 ? 2 : 5), ptTemp);
+ }
+
@SuppressWarnings("unchecked")
+ static int getColorPt(Object o, P3 ptTemp) {
+ return (o == null ? 0 : o instanceof Integer ? ((Integer) o).intValue() :
CU
+ .colorPtToFFRGB(PyMOLReader.pointAt((Lst<Object>) o, 0, ptTemp)));
+ }
+
+ @SuppressWarnings("unchecked")
private static Lst<Object> getMapList(Map<String, Object> map, String key) {
return (Lst<Object>) map.get(key);
}
@@ -1774,14 +1832,6 @@
return bsReps;
}
- private float floatAt(Lst<Object> a, int i) {
- return PyMOLScene.floatAt(a, i);
- }
-
- private Lst<Object> listAt(Lst<Object> list, int i) {
- return PyMOLScene.listAt(list, i);
- }
-
/// PymolAtomReader interface
@Override
@@ -1809,6 +1859,4 @@
return atoms[iPrev].chainID != atoms[i].chainID;
}
-
-
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2016-08-10 07:00:36 UTC (rev 21200)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2016-08-10 12:57:12 UTC (rev 21201)
@@ -234,20 +234,20 @@
@SuppressWarnings("unchecked")
private int colorSetting(int i) {
- Lst<Object> pos = listAt(settings, i);
+ Lst<Object> pos = PyMOLReader.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)));
+ .colorPtToFFRGB(PyMOLReader.pointAt((Lst<Object>) o, 0, ptTemp)));
}
@SuppressWarnings("unchecked")
private P3 pointSetting(int i) {
P3 pt = new P3();
- Lst<Object> pos = listAt(settings, i);
+ Lst<Object> pos = PyMOLReader.listAt(settings, i);
if (pos != null && pos.size() == 3)
- return pointAt((Lst<Object>) pos.get(2), 0, pt);
+ return PyMOLReader.pointAt((Lst<Object>) pos.get(2), 0, pt);
return PyMOL.getDefaultSettingPt(i, pymolVersion, pt);
}
@@ -260,7 +260,7 @@
Lst<Object> listStateSettings, String ext) {
objectName = name;
objectHidden = isHidden;
- objectNameID = (objectName == null ? null : PyMOLScene.fixName(objectName
+ objectNameID = (objectName == null ? null : fixName(objectName
+ ext));
objectSettings = new Hashtable<Integer, Lst<Object>>();
stateSettings = new Hashtable<Integer, Lst<Object>>();
@@ -285,7 +285,7 @@
}
@SuppressWarnings("unchecked")
- private static void listToSettings(Lst<Object> list,
+ private void listToSettings(Lst<Object> list,
Map<Integer, Lst<Object>> objectSettings) {
if (list != null && list.size() != 0) {
// if (debugging)
@@ -329,7 +329,7 @@
labelPosition = new P3();
try {
Lst<Object> setting = getObjectSetting(PyMOL.label_position);
- pointAt(listAt(setting, 2), 0, labelPosition);
+ PyMOLReader.pointAt(PyMOLReader.listAt(setting, 2), 0, labelPosition);
} catch (Exception e) {
// no problem.
}
@@ -404,7 +404,7 @@
smap.put("pymolFrame", frame);
smap.put("generator", this);
smap.put("name", name);
- Lst<Object> view = listAt(thisScene, 0);
+ Lst<Object> view = PyMOLReader.listAt(thisScene, 0);
if (view != null)
smap.put("pymolView", getPymolView(view, false));
@@ -421,23 +421,23 @@
Object[] reps = new Object[PyMOL.REP_LIST.length];
for (int j = PyMOL.REP_LIST.length; --j >= 0;) {
Lst<Object> list = htObjNames.get(sname + PyMOL.REP_LIST[j]);
- Lst<Object> data = listAt(list, 5);
+ Lst<Object> data = PyMOLReader.listAt(list, 5);
if (data != null && data.size() > 0)
- reps[j] = listToMap(data);
+ reps[j] = PyMOLReader.listToMap(data);
}
smap.put("moleculeReps", reps);
// there's no real point in getting
// get all colors from selector_secrets
sname = "_!c_" + name + "_";
- Lst<Object> colorection = listAt(thisScene, 3);
+ Lst<Object> colorection = PyMOLReader.listAt(thisScene, 3);
int n = colorection.size();
// [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);
+ int color = PyMOLReader.intAt(colorection, j);
Lst<Object> c = htSecrets.get(sname + color);
if (c != null && c.size() > 1)
colors[i++] = new Object[] { Integer.valueOf(color), c.get(1) };
@@ -512,7 +512,7 @@
String id = selection.get(0).toString();
id = "_" + (id.equals("sele") ? id : "sele_" + id);
PyMOLGroup g = getGroup(id);
- getSelectionAtoms(listAt(selection, 5), 0, g.bsAtoms);
+ getSelectionAtoms(PyMOLReader.listAt(selection, 5), 0, g.bsAtoms);
}
/**
@@ -526,7 +526,7 @@
private BS getSelectionAtoms(Lst<Object> molecules, int istate, BS bs) {
if (molecules != null)
for (int j = molecules.size(); --j >= 0;)
- selectAllAtoms(listAt(molecules, j), istate, bs);
+ selectAllAtoms(PyMOLReader.listAt(molecules, j), istate, bs);
return bs;
}
@@ -538,9 +538,9 @@
* @param bs
*/
private void selectAllAtoms(Lst<Object> obj, int istate, BS bs) {
- String name = (String) obj.get(0);
+ String name = PyMOLReader.stringAt(obj, 0);
setSceneObject(name, istate);
- Lst<Object> atomList = listAt(obj, 1);
+ Lst<Object> atomList = PyMOLReader.listAt(obj, 1);
int k0 = (istate == 0 ? 1 : istate);
int k1 = (istate == 0 ? stateCount : istate);
for (int k = k0; k <= k1; k++) {
@@ -570,7 +570,7 @@
if (name.equals("all"))
continue;
Lst<Object> list = (Lst<Object>) e.getValue();
- int tok = (intAt(list, 0) == 1 ? T.display : T.hide);
+ int tok = (PyMOLReader.intAt(list, 0) == 1 ? T.display : T.hide);
if (tok == T.hide)
htHiddenObjects.put(name, Boolean.TRUE);
switch (getObjectType(name)) {
@@ -607,7 +607,7 @@
MeasurementData[] mdList = htMeasures.get(name);
if (mdList != null)
addMeasurements(mdList, mdList[0].points.size(), null,
- getBS(listAt(list, 2)), intAt(list, 3), null, true);
+ getBS(PyMOLReader.listAt(list, 2)), PyMOLReader.intAt(list,
3), null, true);
}
info += "_*";
break;
@@ -654,27 +654,17 @@
private BS getBS(Lst<Object> list) {
BS bs = new BS();
for (int i = list.size(); --i >= 0;)
- bs.set(intAt(list, i));
+ bs.set(PyMOLReader.intAt(list, i));
return bs;
}
private void getBsAtoms(Lst<Object> list, int[] atomMap, BS bs) {
for (int i = list.size(); --i >= 0;)
- bs.set(atomMap[intAt(list, i)]);
+ bs.set(atomMap[PyMOLReader.intAt(list, i)]);
}
- private final static P3 ptTemp = new P3();
+ private final P3 ptTemp = new P3();
- @SuppressWarnings("unchecked")
- static int getColorPt(Object o) {
- return (o == null ? 0 : o instanceof Integer ? ((Integer) o).intValue() :
CU
- .colorPtToFFRGB(pointAt((Lst<Object>) o, 0, ptTemp)));
- }
-
- static int intAt(Lst<Object> list, int i) {
- return ((Number) list.get(i)).intValue();
- }
-
void setReaderObjects() {
clearReaderData();
finalizeObjects();
@@ -735,22 +725,22 @@
int i = 0;
// x-axis
for (int j = 0; j < 3; j++)
- pymolView[pt++] = floatAt(view, i++);
+ pymolView[pt++] = PyMOLReader.floatAt(view, i++);
if (isViewObj)
i++;
// y-axis
for (int j = 0; j < 3; j++)
- pymolView[pt++] = floatAt(view, i++);
+ pymolView[pt++] = PyMOLReader.floatAt(view, i++);
if (isViewObj)
i++;
// z-axis (not used)
for (int j = 0; j < 3; j++)
- pymolView[pt++] = floatAt(view, i++);
+ pymolView[pt++] = PyMOLReader.floatAt(view, i++);
if (isViewObj)
i += 5;
// xTrans, yTrans, -distanceToCenter, center(x,y,z), distanceToSlab,
distanceToDepth
for (int j = 0; j < 8; j++)
- pymolView[pt++] = floatAt(view, i++);
+ pymolView[pt++] = PyMOLReader.floatAt(view, i++);
boolean isOrtho = booleanSetting(PyMOL.orthoscopic); // 23
float fov = floatSetting(PyMOL.field_of_view); // 152
@@ -829,7 +819,7 @@
if (htCarveSets.isEmpty())
return;
for (Entry<String, BS> e: htCarveSets.entrySet())
- getSelectionAtoms(listAt(htObjNames.get(e.getKey()), 5), 0,
e.getValue());
+ getSelectionAtoms(PyMOLReader.listAt(htObjNames.get(e.getKey()), 5), 0,
e.getValue());
}
private void setGroupVisibilities() {
@@ -851,7 +841,7 @@
htDefinedAtoms.put(getJmolName(name), bs);
}
- private static String getJmolName(String name) {
+ private String getJmolName(String name) {
return "__" + fixName(name);
}
@@ -958,7 +948,7 @@
|| (setting = uniqueSettings.get(Integer.valueOf((id << 10) + key)))
== null)
return pt;
pt = new P3();
- pointAt((Lst<Object>) setting.get(2), 0, pt);
+ PyMOLReader.pointAt((Lst<Object>) setting.get(2), 0, pt);
Logger.info("Pymol unique setting for " + id + ": " + key + " = " + pt);
return pt;
}
@@ -998,32 +988,7 @@
return setting;
}
- static P3 pointAt(Lst<Object> list, int i, P3 pt) {
- pt.set(floatAt(list, i++), floatAt(list, i++), floatAt(list, i));
- return pt;
- }
-
- static float floatAt(Lst<Object> list, int i) {
- return (list == null ? 0 : ((Number) list.get(i)).floatValue());
- }
-
- static float[] floatsAt(Lst<Object> a, int pt, float[] data, int len) {
- if (a == null)
- return null;
- for (int i = 0; i < len; i++)
- data[i] = floatAt(a, pt++);
- return data;
- }
-
- @SuppressWarnings("unchecked")
- static Lst<Object> listAt(Lst<Object> list, int i) {
- if (list == null || i >= list.size())
- return null;
- Object o = list.get(i);
- return (o instanceof Lst<?> ? (Lst<Object>) o : null);
- }
-
- static float[] setLabelPosition(P3 offset, float[] labelPos) {
+ float[] setLabelPosition(P3 offset, float[] labelPos) {
labelPos[0] = 1;
labelPos[1] = offset.x;
labelPos[2] = offset.y;
@@ -1069,8 +1034,8 @@
if (isNew) {
Lst<Object> points = new Lst<Object>();
for (int i = 0; i < nCoord; i++, p += 3)
- points.addLast(pointAt(list, p, new Point3fi()));
- offset = floatsAt(listAt(offsets, index), 0, new float[7], 7);
+ points.addLast(PyMOLReader.pointAt(list, p, new Point3fi()));
+ offset = PyMOLReader.floatsAt(PyMOLReader.listAt(offsets, index), 0,
new float[7], 7);
if (offset == null)
offset = setLabelPosition(labelPosition, new float[7]);
md = mdList[index] = vwr.newMeasurementData(objectNameID + "_"
@@ -1126,10 +1091,6 @@
return C.getColixTranslucent3(colix, translucency > 0, translucency);
}
- static int colorSettingClamped(Lst<Object> c) {
- return getColorPt(c.get(c.size() < 6 || intAt(c, 4) == 0 ? 2 : 5));
- }
-
void setAtomColor(int atomColor) {
atomColorList.addLast(Integer.valueOf(getColix(atomColor, 0)));
}
@@ -1145,7 +1106,7 @@
frameObj = null;
}
- private static String fixName(String name) {
+ private String fixName(String name) {
char[] chars = name.toLowerCase().toCharArray();
for (int i = chars.length; --i >= 0;)
if (!PT.isLetterOrDigit(chars[i]))
@@ -1678,22 +1639,6 @@
return bs;
}
- /**
- * return a map of lists of the type: [ [name1,...], [name2,...], ...]
- *
- * @param list
- * @return Hashtable
- */
- static Map<String, Lst<Object>> listToMap(Lst<Object> list) {
- Hashtable<String, Lst<Object>> map = new Hashtable<String, Lst<Object>>();
- for (int i = list.size(); --i >= 0;) {
- Lst<Object> item = PyMOLScene.listAt(list, i);
- if (item != null && item.size() > 0)
- map.put(PyMOLReader.bytesToString(item.get(0)), item);
- }
- return map;
- }
-
Map<String, Object> setAtomDefs() {
setGroupVisibilities();
Map<String, Object> defs = new Hashtable<String, Object>();
@@ -1781,7 +1726,7 @@
setSceneObject(objName, -1);
int meshColor = (int) floatSetting(PyMOL.mesh_color);
if (meshColor < 0)
- meshColor = intAt(listAt(obj, 0), 2);
+ meshColor = PyMOLReader.intAt(PyMOLReader.listAt(obj, 0), 2);
if (!isMep) {
jo.setSize(meshWidth);
jo.argb = PyMOL.getRGB(meshColor);
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
