Revision: 18317
http://sourceforge.net/p/jmol/code/18317
Author: hansonr
Date: 2013-06-10 02:47:10 +0000 (Mon, 10 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.17_dev_2013.06.08"
TODO: PyMOL uniqueAtomSettings for transparency
-- will require by-vertex translucent option
code: color/translucent/opaque clean up in ScriptEvaluator
bug fix: load :2-butanone fails
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-08 20:27:11 UTC (rev 18316)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-10 02:47:10 UTC (rev 18317)
@@ -787,18 +787,18 @@
}
private void setGroupVisibilities() {
- if (groups != null) {
- Collection<PyMOLGroup> list = groups.values();
- BS bsAll = new BS();
- for (PyMOLGroup g : list) {
- bsAll.or(g.bsAtoms);
- if (g.parent == null) // top
- setGroupVisible(g, true);
- else if (g.list.isEmpty()) // bottom
- g.addGroupAtoms(new BS());
- }
- defineAtoms("all", bsAll);
+ if (groups == null)
+ return;
+ Collection<PyMOLGroup> list = groups.values();
+ BS bsAll = new BS();
+ for (PyMOLGroup g : list) {
+ bsAll.or(g.bsAtoms);
+ if (g.parent == null) // top
+ setGroupVisible(g, true);
+ else if (g.list.isEmpty()) // bottom
+ g.addGroupAtoms(new BS());
}
+ defineAtoms("all", bsAll);
}
private void defineAtoms(String name, BS bs) {
Modified: trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
2013-06-08 20:27:11 UTC (rev 18316)
+++ trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
2013-06-10 02:47:10 UTC (rev 18317)
@@ -167,7 +167,7 @@
}
}
boolean tcover = g3d.getTranslucentCoverOnly();
- g3d.setTranslucentCoverOnly(imesh.frontOnly);
+ g3d.setTranslucentCoverOnly(imesh.frontOnly ||
!viewer.getBoolean(T.translucent));
thePlane = imesh.jvxlData.jvxlPlane;
vertexValues = imesh.vertexValues;
boolean isOK;
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-08 20:27:11 UTC
(rev 18316)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-10 02:47:10 UTC
(rev 18317)
@@ -7545,13 +7545,19 @@
return matches;
}
+ /**
+ *
+ * @param index 0 is this is the hbond command
+ *
+ * @throws ScriptException
+ */
private void connect(int index) throws ScriptException {
final float[] distances = new float[2];
BS[] atomSets = new BS[2];
atomSets[0] = atomSets[1] = viewer.getSelectionSet(false);
float radius = Float.NaN;
- int color = Integer.MIN_VALUE;
+ colorArgb[0] = Integer.MIN_VALUE;
int distanceCount = 0;
int bondOrder = JmolEdge.BOND_ORDER_NULL;
int bo;
@@ -7559,7 +7565,6 @@
boolean isDelete = false;
boolean haveType = false;
boolean haveOperation = false;
- String translucency = null;
float translucentLevel = Float.MAX_VALUE;
boolean isColorOrRadius = false;
int nAtomSets = 0;
@@ -7634,19 +7639,11 @@
addGroup = true;
break;
case T.color:
- int tok = tokAt(i + 1);
- if (tok != T.translucent && tok != T.opaque)
- ptColor = i + 1;
- continue;
case T.translucent:
case T.opaque:
- if (translucency != null)
- error(ERROR_invalidArgument);
isColorOrRadius = true;
- translucency = parameterAsString(i);
- if (theTok == T.translucent && isFloatParameter(i + 1))
- translucentLevel = getTranslucentLevel(++i);
- ptColor = i + 1;
+ translucentLevel = getColorTrans(i);
+ i = iToken;
break;
case T.pdb:
boolean isAuto = (tokAt(2) == T.auto);
@@ -7671,8 +7668,7 @@
break;
case T.struts:
if (!isColorOrRadius) {
- color = 0xFFFFFF;
- translucency = "translucent";
+ colorArgb[0] = 0xFFFFFF;
translucentLevel = 0.5f;
radius = viewer.getFloat(T.strutdefaultradius);
isColorOrRadius = true;
@@ -7682,16 +7678,16 @@
haveOperation = true;
//$FALL-THROUGH$
case T.identifier:
+ if (isColorParam(i)) {
+ ptColor = -i;
+ break;
+ }
+ //$FALL-THROUGH$
case T.aromatic:
case T.hbond:
if (i > 0) {
- if (ptColor == i)
- break;
+ // not hbond command
// I know -- should have required the COLOR keyword
- if (isColorParam(i)) {
- ptColor = -i;
- break;
- }
}
String cmd = parameterAsString(i);
if ((bo = getBondOrderFromString(cmd)) == JmolEdge.BOND_ORDER_NULL) {
@@ -7742,9 +7738,9 @@
// now check for color -- -i means we've already checked
if (i > 0) {
if (ptColor == -i || ptColor == i && isColorParam(i)) {
- color = getArgbParam(i);
+ isColorOrRadius = true;
+ colorArgb[0] = getArgbParam(i);
i = iToken;
- isColorOrRadius = true;
} else if (ptColor == i) {
error(ERROR_invalidArgument);
}
@@ -7758,8 +7754,7 @@
distances[1] = distances[0];
distances[0] = JC.DEFAULT_MIN_CONNECT_DISTANCE;
}
- if (translucency != null || !Float.isNaN(radius)
- || color != Integer.MIN_VALUE) {
+ if (isColorOrRadius) {
if (!haveType)
bondOrder = JmolEdge.BOND_ORDER_ANY;
if (!haveOperation)
@@ -7798,17 +7793,7 @@
viewer.selectBonds(bsBonds);
if (!Float.isNaN(radius))
setShapeSizeBs(JC.SHAPE_STICKS, Math.round(radius * 2000), null);
- if (color != Integer.MIN_VALUE)
- setShapePropertyBs(JC.SHAPE_STICKS, "color", Integer
- .valueOf(color), bsBonds);
- if (translucency != null) {
- if (translucentLevel == Float.MAX_VALUE)
- translucentLevel = viewer.getFloat(T.defaulttranslucent);
- setShapeProperty(JC.SHAPE_STICKS, "translucentLevel", Float
- .valueOf(translucentLevel));
- setShapePropertyBs(JC.SHAPE_STICKS, "translucency",
- translucency, bsBonds);
- }
+ finalizeObject(JC.SHAPE_STICKS, colorArgb[0], translucentLevel, 0,
false, null, 0, bsBonds);
viewer.selectBonds(null);
}
if (!(tQuiet || scriptLevel > scriptReportingLevel))
@@ -8184,10 +8169,10 @@
prefix = "vertex";
} else {
bs = atomExpressionAt(index);
- // don't allow isosurface partial translucency (yet)
prefix = "atom";
}
- translucentLevel = Float.MIN_VALUE;
+ // don't allow isosurface partial translucency (yet)
+ //translucentLevel = Float.MIN_VALUE;
getToken(index = iToken + 1);
break;
}
@@ -11623,6 +11608,7 @@
private void ellipsoid() throws ScriptException {
int mad = 0;
int i = 1;
+ float translucentLevel = Float.MAX_VALUE;
switch (getToken(1).tok) {
case T.on:
mad = 50;
@@ -11648,7 +11634,7 @@
while (++i < slen) {
String key = parameterAsString(i);
Object value = null;
- switch (tokAt(i)) {
+ switch (getToken(i).tok) {
case T.dollarsign:
key = "points";
Object[] data = new Object[3];
@@ -11678,31 +11664,11 @@
i = iToken;
break;
case T.color:
- float translucentLevel = Float.NaN;
- if (tokAt(i) == T.color)
- i++;
- if ((theTok = tokAt(i)) == T.translucent) {
- value = "translucent";
- if (isFloatParameter(++i))
- translucentLevel = getTranslucentLevel(i++);
- else
- translucentLevel = viewer.getFloat(T.defaulttranslucent);
- } else if (theTok == T.opaque) {
- value = "opaque";
- i++;
- }
- if (isColorParam(i)) {
- setShapeProperty(JC.SHAPE_ELLIPSOIDS, "color", Integer
- .valueOf(getArgbParam(i)));
- i = iToken;
- }
- if (value == null)
- continue;
- if (!Float.isNaN(translucentLevel))
- setShapeProperty(JC.SHAPE_ELLIPSOIDS,
- "translucentLevel", Float.valueOf(translucentLevel));
- key = "translucency";
- break;
+ case T.translucent:
+ case T.opaque:
+ translucentLevel = getColorTrans(i);
+ i = iToken;
+ continue;
case T.delete:
value = Boolean.TRUE;
checkLength(3);
@@ -11726,6 +11692,7 @@
setShapeProperty(JC.SHAPE_ELLIPSOIDS, key.toLowerCase(),
value);
}
+ finalizeObject(JC.SHAPE_ELLIPSOIDS, colorArgb[0], translucentLevel, 0,
false, null, 0, null);
setShapeProperty(JC.SHAPE_ELLIPSOIDS, "thisID", null);
return;
default:
@@ -15546,6 +15513,8 @@
return (String) getShapePropertyIndex(JC.SHAPE_MO, "showMO", ptMO);
}
+ private int[] colorArgb = new int[] {Integer.MIN_VALUE};
+
private void cgo() throws ScriptException {
sm.loadShape(JC.SHAPE_CGO);
if (tokAt(1) == T.list && listIsosurface(JC.SHAPE_CGO))
@@ -15554,11 +15523,10 @@
String thisId = initIsosurface(JC.SHAPE_CGO);
boolean idSeen = (thisId != null);
boolean isWild = (idSeen && getShapeProperty(JC.SHAPE_CGO, "ID") == null);
- boolean isTranslucent = false;
boolean isInitialized = false;
JmolList<Object> data = null;
float translucentLevel = Float.MAX_VALUE;
- int colorArgb = Integer.MIN_VALUE;
+ colorArgb[0] = Integer.MIN_VALUE;
int intScale = 0;
for (int i = iToken; i < slen; ++i) {
String propertyName = null;
@@ -15588,24 +15556,8 @@
case T.color:
case T.translucent:
case T.opaque:
- if (theTok != T.color)
- --i;
- if (tokAt(i + 1) == T.translucent) {
- i++;
- isTranslucent = true;
- if (isFloatParameter(i + 1))
- translucentLevel = getTranslucentLevel(++i);
- } else if (tokAt(i + 1) == T.opaque) {
- i++;
- isTranslucent = true;
- translucentLevel = 0;
- }
- if (isColorParam(i + 1)) {
- colorArgb = getArgbParam(++i);
- i = iToken;
- } else if (!isTranslucent) {
- error(ERROR_invalidArgument);
- }
+ translucentLevel = getColorTrans(i);
+ i = iToken;
idSeen = true;
continue;
case T.id:
@@ -15637,22 +15589,56 @@
if (propertyName != null)
setShapeProperty(JC.SHAPE_CGO, propertyName, propertyValue);
}
- finalizeObject(JC.SHAPE_CGO, colorArgb, isTranslucent ? translucentLevel
- : Float.MAX_VALUE, intScale, data != null, data, iptDisplayProperty);
+ finalizeObject(JC.SHAPE_CGO, colorArgb[0], translucentLevel, intScale,
data != null, data, iptDisplayProperty, null);
}
-
+
+ /**
+ * Checks color, translucent, opaque parameters.
+ *
+ * @param i
+ * @return translucentLevel and sets iToken and colorArgb[0]
+ *
+ * @throws ScriptException
+ */
+ private float getColorTrans(int i) throws ScriptException {
+ float translucentLevel = Float.MAX_VALUE;
+ if (theTok != T.color)
+ --i;
+ switch (tokAt(i + 1)) {
+ case T.translucent:
+ i++;
+ translucentLevel = (isFloatParameter(i + 1) ? getTranslucentLevel(++i)
+ : viewer.getFloat(T.defaulttranslucent));
+ break;
+ case T.opaque:
+ i++;
+ translucentLevel = 0;
+ break;
+ }
+ if (isColorParam(i + 1)) {
+ colorArgb[0] = getArgbParam(++i);
+ i = iToken;
+ } else if (translucentLevel == Float.MAX_VALUE) {
+ error(ERROR_invalidArgument);
+ } else {
+ colorArgb[0] = Integer.MIN_VALUE;
+ }
+ i = iToken;
+ return translucentLevel;
+ }
+
private void finalizeObject(int shapeID, int colorArgb,
float translucentLevel, int intScale,
- boolean havePoints, Object data, int
iptDisplayProperty) throws ScriptException {
- if (havePoints) {
+ boolean doSet, Object data, int
iptDisplayProperty, BS bs) throws ScriptException {
+ if (doSet) {
setShapeProperty(shapeID, "set", data);
}
if (colorArgb != Integer.MIN_VALUE)
- setShapeProperty(shapeID, "color", Integer
- .valueOf(colorArgb));
+ setShapePropertyBs(shapeID, "color", Integer
+ .valueOf(colorArgb), bs);
if (translucentLevel != Float.MAX_VALUE)
setShapeTranslucency(shapeID, "", "translucent",
- translucentLevel, null);
+ translucentLevel, bs);
if (intScale != 0) {
setShapeProperty(shapeID, "scale", Integer
.valueOf(intScale));
@@ -15683,13 +15669,12 @@
boolean havePoints = false;
boolean isInitialized = false;
boolean isSavedState = false;
- boolean isTranslucent = false;
boolean isIntersect = false;
boolean isFrame = false;
P4 plane;
int tokIntersect = 0;
float translucentLevel = Float.MAX_VALUE;
- int colorArgb = Integer.MIN_VALUE;
+ colorArgb[0] = Integer.MIN_VALUE;
int intScale = 0;
String swidth = "";
int iptDisplayProperty = 0;
@@ -16084,25 +16069,9 @@
case T.color:
case T.translucent:
case T.opaque:
- if (theTok != T.color)
- --i;
- if (tokAt(i + 1) == T.translucent) {
- i++;
- isTranslucent = true;
- if (isFloatParameter(i + 1))
- translucentLevel = getTranslucentLevel(++i);
- } else if (tokAt(i + 1) == T.opaque) {
- i++;
- isTranslucent = true;
- translucentLevel = 0;
- }
- if (isColorParam(i + 1)) {
- colorArgb = getArgbParam(++i);
- i = iToken;
- } else if (!isTranslucent) {
- error(ERROR_invalidArgument);
- }
idSeen = true;
+ translucentLevel = getColorTrans(i);
+ i = iToken;
continue;
default:
if (!setMeshDisplayProperty(JC.SHAPE_DRAW, 0, theTok)) {
@@ -16130,8 +16099,8 @@
if (propertyName != null)
setShapeProperty(JC.SHAPE_DRAW, propertyName, propertyValue);
}
- finalizeObject(JC.SHAPE_DRAW, colorArgb, isTranslucent ? translucentLevel
: Float.MAX_VALUE,
- intScale, havePoints, connections, iptDisplayProperty);
+ finalizeObject(JC.SHAPE_DRAW, colorArgb[0], translucentLevel,
+ intScale, havePoints, connections, iptDisplayProperty, null);
}
private void polyhedra() throws ScriptException {
@@ -16156,9 +16125,8 @@
setShapeProperty(JC.SHAPE_POLYHEDRA, "init", null);
String setPropertyName = "centers";
String decimalPropertyName = "radius_";
- boolean isTranslucent = false;
float translucentLevel = Float.MAX_VALUE;
- int color = Integer.MIN_VALUE;
+ colorArgb[0] = Integer.MIN_VALUE;
for (int i = 1; i < slen; ++i) {
String propertyName = null;
Object propertyValue = null;
@@ -16247,24 +16215,8 @@
case T.color:
case T.translucent:
case T.opaque:
- isTranslucent = false;
- if (theTok != T.color)
- --i;
- if (tokAt(i + 1) == T.translucent) {
- i++;
- isTranslucent = true;
- if (isFloatParameter(i + 1))
- translucentLevel = getTranslucentLevel(++i);
- } else if (tokAt(i + 1) == T.opaque) {
- i++;
- isTranslucent = true;
- translucentLevel = 0;
- }
- if (isColorParam(i + 1)) {
- color = getArgbParam(i);
- i = iToken;
- } else if (!isTranslucent)
- error(ERROR_invalidArgument);
+ translucentLevel = getColorTrans(i);
+ i = iToken;
continue;
case T.collapsed:
case T.flat:
@@ -16288,7 +16240,7 @@
continue;
default:
if (isColorParam(i)) {
- color = getArgbParam(i);
+ colorArgb[0] = getArgbParam(i);
i = iToken;
continue;
}
@@ -16303,10 +16255,10 @@
error(ERROR_insufficientArguments);
if (needsGenerating)
setShapeProperty(JC.SHAPE_POLYHEDRA, "generate", null);
- if (color != Integer.MIN_VALUE)
+ if (colorArgb[0] != Integer.MIN_VALUE)
setShapeProperty(JC.SHAPE_POLYHEDRA, "colorThis", Integer
- .valueOf(color));
- if (isTranslucent)
+ .valueOf(colorArgb[0]));
+ if (translucentLevel != Float.MAX_VALUE)
setShapeTranslucency(JC.SHAPE_POLYHEDRA, "", "translucentThis",
translucentLevel, null);
if (lighting != 0)
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-08 20:27:11 UTC
(rev 18316)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-10 02:47:10 UTC
(rev 18317)
@@ -9,11 +9,13 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.17_dev_2013.06.07"
+___JmolVersion="13.1.17_dev_2013.06.08"
TODO: PyMOL uniqueAtomSettings for transparency
-- will require by-vertex translucent option
+code: color/translucent/opaque clean up in ScriptEvaluator
+bug fix: load :2-butanone fails
bug fix: PyMOL volume map data saved from PyMOL 1.6 has slightly different
data structure
bug fix: jvxl reader ignores jvxlVertexColorData
bug fix: ellipsoid rendering problems
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-08 20:27:11 UTC (rev
18316)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-10 02:47:10 UTC (rev
18317)
@@ -4554,7 +4554,12 @@
case ':': // PubChem
format = global.pubChemFormat;
String fl = f.toLowerCase();
- int fi = Parser.parseInt(f);
+ int fi = Integer.MIN_VALUE;
+ try {
+ fi = Integer.parseInt(f);
+ } catch (Exception e) {
+ //
+ }
if (fi != Integer.MIN_VALUE) {
f = "cid/" + fi;
} else {
@@ -5751,6 +5756,8 @@
return global.strutsMultiple;
case T.tracealpha:
return global.traceAlpha;
+ case T.translucent:
+ return global.translucent;
case T.twistedsheets:
return global.twistedSheets;
case T.vectorsymmetry:
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