Revision: 18403
http://sourceforge.net/p/jmol/code/18403
Author: hansonr
Date: 2013-07-02 10:11:41 +0000 (Tue, 02 Jul 2013)
Log Message:
-----------
___JmolVersion="13.1.19_dev_2013.07.02"
new feature: ellipsoid OPTIONS "xxxx"
-- "xxxx" is a quoted string of options separated by semicolon:
"arcs;arrows;axes;ball;dots;fill;wireframe"
with optional "no" in front of each
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlVaspReader.java
trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/shapespecial/Ellipsoid.java
trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
trunk/Jmol/src/org/jmol/util/Parser.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlVaspReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlVaspReader.java
2013-07-02 07:17:11 UTC (rev 18402)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlVaspReader.java
2013-07-02 10:11:41 UTC (rev 18403)
@@ -125,7 +125,7 @@
if ("varray".equals(localName)) {
name = atts.get("name");
- if (name != null && Parser.isOneOf(name, "basis;positions;forces"))
+ if (name != null && Parser.isOneOf(name, ";basis;positions;forces;"))
data = new SB();
return;
}
Modified: trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
2013-07-02 07:17:11 UTC (rev 18402)
+++ trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
2013-07-02 10:11:41 UTC (rev 18403)
@@ -36,6 +36,7 @@
import org.jmol.util.Normix;
import org.jmol.util.P3;
import org.jmol.util.P3i;
+import org.jmol.util.Parser;
import org.jmol.util.V3;
import org.jmol.modelset.Atom;
import org.jmol.render.ShapeRenderer;
@@ -48,10 +49,20 @@
private Ellipsoids ellipsoids;
- private boolean drawDots, drawArcs, drawAxes, drawFill, drawBall, drawArrows;
+ private boolean[] bGlobals = new boolean[7];
+ private boolean[] bOptions = new boolean[7];
+ private final String[] OPTS = new String[] { "dots", "arcs", "axes", "fill",
"ball", "arrows", "wireframe" };
+ private final static int OPT_DOTS = 0;
+ private final static int OPT_ARCS = 1;
+ private final static int OPT_AXES = 2;
+ private final static int OPT_FILL = 3;
+ private final static int OPT_BALL = 4;
+ private final static int OPT_ARROWS = 5;
+ private final static int OPT_WIREFRAME = 6;
+ private static final int OPT_COUNT = 7;
+
private boolean fillArc;
private boolean isSet;
- private boolean wireframeOnly;
private int diameter, diameter0;
private int dotCount, dotScale;
@@ -89,6 +100,7 @@
private final static float toRadians = (float) Math.PI/180f;
private final static float[] cossin = new float[36];
+
static {
for (int i = 5, pt = 0; i <= 90; i += 5) {
cossin[pt++] = (float) Math.cos(i * toRadians);
@@ -115,16 +127,40 @@
}
private boolean setGlobals() {
- wireframeOnly = (viewer.getBoolean(T.wireframerotation) &&
viewer.getInMotion(true));
- drawAxes = viewer.getBooleanProperty("ellipsoidAxes");
- drawArcs = viewer.getBooleanProperty("ellipsoidArcs");
- drawArrows = viewer.getBooleanProperty("ellipsoidArrows");
- drawBall = viewer.getBooleanProperty("ellipsoidBall") && !wireframeOnly;
- drawDots = viewer.getBooleanProperty("ellipsoidDots") && !wireframeOnly;
- drawFill = viewer.getBooleanProperty("ellipsoidFill") && !wireframeOnly;
- fillArc = drawFill && !drawBall;
+ bGlobals[OPT_ARCS] = viewer.getBooleanProperty("ellipsoidArcs");
+ bGlobals[OPT_ARROWS] = viewer.getBooleanProperty("ellipsoidArrows");
+ bGlobals[OPT_AXES] = viewer.getBooleanProperty("ellipsoidAxes");
+ bGlobals[OPT_BALL] = viewer.getBooleanProperty("ellipsoidBall");
+ bGlobals[OPT_DOTS] = viewer.getBooleanProperty("ellipsoidDots");
+ bGlobals[OPT_FILL] = viewer.getBooleanProperty("ellipsoidFill");
+ bGlobals[OPT_WIREFRAME] = (viewer.getBoolean(T.wireframerotation) &&
viewer.getInMotion(true));
diameter0 = Math.round (((Float)
viewer.getParameter("ellipsoidAxisDiameter"))
- .floatValue() * 1000);
+ .floatValue() * 1000);
+ Matrix4f m4 = viewer.getMatrixtransform();
+ mat.setRow(0, m4.m00, m4.m01, m4.m02);
+ mat.setRow(1, m4.m10, m4.m11, m4.m12);
+ mat.setRow(2, m4.m20, m4.m21, m4.m22);
+ matScreenToCartesian.invertM(mat);
+ setLogic();
+ return true;
+ }
+
+ private void setOptions(String options) {
+ for (int i = 0; i < OPT_COUNT; i++)
+ bOptions[i] = bGlobals[i];
+ if (options != null) {
+ options = ";" + options + ";";
+ for (int i = 0; i < OPT_COUNT; i++) {
+ if (Parser.isOneOf(OPTS[i], options))
+ bOptions[i] = true;
+ else if (Parser.isOneOf("no" + OPTS[i], options))
+ bOptions[i] = false;
+ }
+ }
+ setLogic();
+ }
+
+ private void setLogic() {
//perspectiveOn = viewer.getPerspectiveDepth();
/* general logic:
*
@@ -137,31 +173,28 @@
* filling for ARCS
*/
- if (drawBall)
- drawDots = false;
- if (!drawDots && !drawArcs && !drawBall)
- drawAxes = true;
- if (drawDots) {
- drawArcs = false;
- drawFill = false;
+ bOptions[OPT_DOTS] &= !bOptions[OPT_WIREFRAME];
+ bOptions[OPT_BALL] &= !bOptions[OPT_WIREFRAME];
+ bOptions[OPT_FILL] &= !bOptions[OPT_WIREFRAME];
+ fillArc = bOptions[OPT_FILL] && !bOptions[OPT_BALL];
+
+ if (bOptions[OPT_BALL])
+ bOptions[OPT_DOTS] = false;
+ if (!bOptions[OPT_DOTS] && !bOptions[OPT_ARCS] && !bOptions[OPT_BALL])
+ bOptions[OPT_AXES] = true;
+ if (bOptions[OPT_DOTS]) {
+ bOptions[OPT_ARCS] = false;
+ bOptions[OPT_FILL] = false;
dotScale = viewer.getInt(T.dotscale);
}
- if (drawDots) {
+ if (bOptions[OPT_DOTS]) {
dotCount = ((Integer) viewer.getParameter("ellipsoidDotCount"))
.intValue();
if (coords == null || coords.length != dotCount * 3)
coords = new int[dotCount * 3];
}
-
- Matrix4f m4 = viewer.getMatrixtransform();
- mat.setRow(0, m4.m00, m4.m01, m4.m02);
- mat.setRow(1, m4.m10, m4.m11, m4.m12);
- mat.setRow(2, m4.m20, m4.m21, m4.m22);
- matScreenToCartesian.invertM(mat);
- return true;
}
-
private boolean renderEllipsoids(Map<?, Ellipsoid> ht, boolean isSimple) {
boolean needTranslucent = false;
Iterator<Ellipsoid> e = ht.values().iterator();
@@ -205,31 +238,32 @@
if (g3d.isClippedXY(dx + dx, s0.x, s0.y))
return;
eigenSignMask = e.tensor.eigenSignMask;
- diameter = (int) viewer.scaleToScreen(s0.z, wireframeOnly ? 1 : diameter0);
+ setOptions(e.options);
+ diameter = (int) viewer.scaleToScreen(s0.z, bOptions[OPT_WIREFRAME] ? 1 :
diameter0);
if (e.tensor.isIsotropic) {
renderBall();
return;
}
- if (drawBall) {
+ if (bOptions[OPT_BALL]) {
renderBall();
- if (drawArcs || drawAxes) {
+ if (bOptions[OPT_ARCS] || bOptions[OPT_AXES]) {
g3d.setColix(viewer.getColixBackgroundContrast());
//setAxes(atom, 1.0f);
- if (drawAxes)
+ if (bOptions[OPT_AXES])
renderAxes();
- if (drawArcs)
+ if (bOptions[OPT_ARCS])
renderArcs();
g3d.setColix(colix);
}
} else {
- if (drawAxes)
+ if (bOptions[OPT_AXES])
renderAxes();
- if (drawArcs)
+ if (bOptions[OPT_ARCS])
renderArcs();
}
- if (drawDots)
+ if (bOptions[OPT_DOTS])
renderDots();
- if (drawArrows)
+ if (bOptions[OPT_ARROWS])
renderArrows();
}
@@ -350,7 +384,7 @@
}
private void renderAxes() {
- if (drawBall && drawFill) {
+ if (bOptions[OPT_BALL] && bOptions[OPT_FILL]) {
g3d.fillCylinder(GData.ENDCAPS_FLAT, diameter, s0,
selectedPoints[0]);
g3d.fillCylinder(GData.ENDCAPS_FLAT, diameter, s0,
@@ -372,7 +406,7 @@
// screens[5]);
// g3d.setColix(colix);
// } else {
- if (drawBall) {
+ if (bOptions[OPT_BALL]) {
g3d.fillCylinder(GData.ENDCAPS_FLAT, diameter, screens[32],
screens[33]);
g3d.fillCylinder(GData.ENDCAPS_FLAT, diameter, screens[34],
@@ -412,9 +446,9 @@
}
private void renderArcs() {
- if (g3d.drawEllipse(center, points[0], points[2], fillArc, wireframeOnly))
{
- g3d.drawEllipse(center, points[2], points[5], fillArc, wireframeOnly);
- g3d.drawEllipse(center, points[5], points[0], fillArc, wireframeOnly);
+ if (g3d.drawEllipse(center, points[0], points[2], fillArc,
bOptions[OPT_WIREFRAME])) {
+ g3d.drawEllipse(center, points[2], points[5], fillArc,
bOptions[OPT_WIREFRAME]);
+ g3d.drawEllipse(center, points[5], points[0], fillArc,
bOptions[OPT_WIREFRAME]);
return;
}
for (int i = 1; i < 8; i += 2) {
@@ -438,7 +472,7 @@
pt1.setT(points[ptA]);
s1.setT(screens[ptA]);
short normix = Normix.get2SidedNormix(v3, bsTemp);
- if (!fillArc && !wireframeOnly)
+ if (!fillArc && !bOptions[OPT_WIREFRAME])
screens[6].setT(s1);
for (int i = 0, pt = 0; i < 18; i++, pt += 2) {
pt2.scaleAdd2(cossin[pt] * d1, v1, center);
@@ -447,14 +481,14 @@
if (fillArc)
g3d.fillTriangle3CN(s0, colix, normix, s1, colix, normix, s2, colix,
normix);
- else if (wireframeOnly)
+ else if (bOptions[OPT_WIREFRAME])
g3d.fillCylinder(GData.ENDCAPS_FLAT, diameter, s1, s2);
else
screens[i + 7].setT(s2);
pt1.setT(pt2);
s1.setT(s2);
}
- if (!fillArc && !wireframeOnly)
+ if (!fillArc && !bOptions[OPT_WIREFRAME])
for (int i = 0; i < 18; i++) {
g3d.fillHermite(5, diameter, diameter, diameter,
screens[i == 0 ? i + 6 : i + 5],
@@ -469,7 +503,7 @@
int zMin = Integer.MAX_VALUE;
selectedOctant = -1;
iCutout = -1;
- if (drawFill) {
+ if (bOptions[OPT_FILL]) {
for (int i = 0; i < 8; i++) {
int ptA = octants[i * 3];
int ptB = octants[i * 3 + 1];
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-07-02 07:17:11 UTC
(rev 18402)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-07-02 10:11:41 UTC
(rev 18403)
@@ -9997,7 +9997,7 @@
.substring(0, 1);
if (type.equals("a") || type.equals("r"))
isDerivative = true;
- if (!Parser.isOneOf(type, "w;x;y;z;r;a")) // a absolute; r relative
+ if (!Parser.isOneOf(type, ";w;x;y;z;r;a;")) // a absolute; r relative
evalError("QUATERNION [w,x,y,z,a,r] [difference][2]", null);
type = "quaternion " + type + (isDerivative ? " difference" : "")
+ (isSecondDerivative ? "2" : "") + (isDraw ? " draw" : "");
@@ -10962,7 +10962,7 @@
break;
case 2:
applet = parameterAsString(1);
- if (applet.indexOf("jmolApplet") == 0 || Parser.isOneOf(applet,
"*;.;^")) {
+ if (applet.indexOf("jmolApplet") == 0 || Parser.isOneOf(applet,
";*;.;^;")) {
text = "ON";
if (!chk)
viewer.syncScript(text, applet, 0);
@@ -11651,6 +11651,20 @@
boolean checkMore = false;
boolean isSet = false;
setShapeProperty(JC.SHAPE_ELLIPSOIDS, "thisID", null);
+ // the first three options, ON, OFF, and (int)scalePercent
+ // were implemented long before the idea of customized
+ // ellipsoids was considered. "ON" will produce an ellipsoid
+ // with a standard radius, and "OFF" will reduce its scale to 0,
+ // effectively elliminating it.
+
+ // The new options SET and ID are much more powerful. In those,
+ // ON and OFF simply do that -- turn the ellipsoid on or off --
+ // and there are many more options.
+
+ // The SET type ellipsoids, introduced in Jmol 13.1.19 in 7/2013,
+ // are created by all readers that read ellipsoid (PDB/CIF) or
+ // tensor (Castep, MagRes) data.
+
switch (getToken(1).tok) {
case T.on:
mad = Integer.MAX_VALUE; // default for this type
@@ -11720,6 +11734,7 @@
checkLength(i + 1);
break;
}
+ // these next are for SET "XXX" or ID "XXX" syntax only
if (value == null)
switch (theTok) {
case T.on:
@@ -11745,6 +11760,9 @@
translucentLevel = getColorTrans(i, true);
i = iToken;
continue;
+ case T.options:
+ value = parameterAsString(++i);
+ break;
}
if (value == null)
error(ERROR_invalidArgument);
@@ -13368,7 +13386,7 @@
if (lckey.indexOf("label") == 0
&& Parser
.isOneOf(key.substring(5).toLowerCase(),
-
"front;group;atom;offset;offsetexact;pointer;alignment;toggle;scalereference"))
{
+
";front;group;atom;offset;offsetexact;pointer;alignment;toggle;scalereference;"))
{
if (setLabel(key.substring(5)))
return;
}
@@ -13775,10 +13793,10 @@
private boolean setUnits(String units, int tok) throws ScriptException {
if (tok == T.measurementunits && Parser.isOneOf(units.toLowerCase(),
- "angstroms;au;bohr;nanometers;nm;picometers;pm;vanderwaals;vdw")) {
+ ";angstroms;au;bohr;nanometers;nm;picometers;pm;vanderwaals;vdw;")) {
if (!chk)
viewer.setUnits(units, true);
- } else if (tok == T.energyunits && Parser.isOneOf(units.toLowerCase(),
"kcal;kj")) {
+ } else if (tok == T.energyunits && Parser.isOneOf(units.toLowerCase(),
";kcal;kj;")) {
if (!chk)
viewer.setUnits(units, false);
} else {
@@ -14199,7 +14217,7 @@
int tok = tokAt(index);
String type = optParameterAsString(index).toLowerCase();
if (slen == index + 1
- && Parser.isOneOf(type, "window;unitcell;molecular")) {
+ && Parser.isOneOf(type, ";window;unitcell;molecular;")) {
setBooleanProperty("axes" + type, true);
return;
}
@@ -14686,7 +14704,7 @@
if (!chk) {
viewer.setVibrationOff();
if (!isJS)
- viewer.delayScript(this, 100);
+ viewer.delayScript(this, 100);
}
pt++;
break;
@@ -14704,7 +14722,7 @@
break;
case T.scene:
val = SV.sValue(tokenAt(++pt, args)).toUpperCase();
- if (Parser.isOneOf(val, "PNG;PNGJ")) {
+ if (Parser.isOneOf(val, ";PNG;PNGJ;")) {
sceneType = val;
pt++;
}
@@ -14714,8 +14732,7 @@
break;
}
if (tok == T.image) {
- T t = T.getTokenFromName(SV.sValue(args[pt])
- .toLowerCase());
+ T t = T.getTokenFromName(SV.sValue(args[pt]).toLowerCase());
if (t != null)
type = SV.sValue(t).toUpperCase();
if (Parser.isOneOf(type, driverList.toUpperCase())) {
@@ -14750,16 +14767,16 @@
// if (isApplet)
// evalError(GT._("The {0} command is not available for the applet.",
// "WRITE CLIPBOARD"));
- } else if (Parser.isOneOf(val.toLowerCase(),
- "png;pngj;pngt;jpg;jpeg;jpg64;jpeg64")) {
- if (tokAtArray(pt + 1, args) == T.integer && tokAtArray(pt + 2, args)
== T.integer) {
+ } else if (Parser.isOneOf(val.toLowerCase(), JC.IMAGE_TYPES)) {
+ if (tokAtArray(pt + 1, args) == T.integer
+ && tokAtArray(pt + 2, args) == T.integer) {
width = SV.iValue(tokenAt(++pt, args));
height = SV.iValue(tokenAt(++pt, args));
}
if (tokAtArray(pt + 1, args) == T.integer)
quality = SV.iValue(tokenAt(++pt, args));
} else if (Parser.isOneOf(val.toLowerCase(),
- "xyz;xyzrn;xyzvib;mol;sdf;v2000;v3000;cd;pdb;pqr;cml")) {
+ ";xyz;xyzrn;xyzvib;mol;sdf;v2000;v3000;cd;pdb;pqr;cml;")) {
type = val.toUpperCase();
if (pt + 1 == argCount)
pt++;
@@ -14773,8 +14790,7 @@
// write isosurface t.jvxl
if (type.equals("(image)")
- && Parser.isOneOf(val.toUpperCase(),
- "GIF;JPG;JPG64;JPEG;JPEG64;PNG;PNGJ;PNGT;PPM")) {
+ && Parser.isOneOf(val.toLowerCase(), JC.IMAGE_OR_SCENE)) {
type = val.toUpperCase();
pt++;
}
@@ -14850,8 +14866,7 @@
if (type.equals("COORD"))
type = (fileName != null && fileName.indexOf(".") >= 0 ? fileName
.substring(fileName.lastIndexOf(".") + 1).toUpperCase() : "XYZ");
- isImage = Parser.isOneOf(type,
- "GIF;JPEG64;JPEG;JPG64;JPG;PPM;PNG;PNGJ;PNGT;SCENE");
+ isImage = Parser.isOneOf(type.toLowerCase(), JC.IMAGE_OR_SCENE);
if (scripts != null) {
if (type.equals("PNG"))
type = "PNGJ";
@@ -14865,7 +14880,7 @@
&& !Parser
.isOneOf(
type,
-
"SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;ISOSURFACE;MESH;PMESH;VAR;FILE;FUNCTION;CD;CML;XYZ;XYZRN;XYZVIB;MENU;MOL;PDB;PGRP;PQR;QUAT;RAMA;SDF;V2000;V3000;INLINE"))
+
";SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;ISOSURFACE;MESH;PMESH;VAR;FILE;FUNCTION;CD;CML;XYZ;XYZRN;XYZVIB;MENU;MOL;PDB;PGRP;PQR;QUAT;RAMA;SDF;V2000;V3000;INLINE;"))
errorStr2(
ERROR_writeWhat,
"COORDS|FILE|FUNCTIONS|HISTORY|IMAGE|INLINE|ISOSURFACE|JMOL|MENU|MO|POINTGROUP|QUATERNION
[w,x,y,z] [derivative]"
@@ -14883,8 +14898,8 @@
// todo -- there's no reason this data has to be done this way.
// we could send all of them out to file directly
fullPath[0] = fileName;
- data = viewer.generateOutputForExport(data,
- isCommand || fileName != null ? fullPath : null, width, height);
+ data = viewer.generateOutputForExport(data, isCommand
+ || fileName != null ? fullPath : null, width, height);
if (data == null || data.length() == 0)
return "";
if (!isCommand)
@@ -14947,8 +14962,9 @@
data = viewer.getFunctionCalls(null);
type = "TXT";
} else if (data == "VAR") {
- data = ((SV) getParameter(SV.sValue(tokenAt(
- isCommand ? 2 : 1, args)), T.variable)).asString();
+ data = ((SV) getParameter(
+ SV.sValue(tokenAt(isCommand ? 2 : 1, args)), T.variable))
+ .asString();
type = "TXT";
} else if (data == "SPT") {
if (isCoord) {
@@ -14976,13 +14992,12 @@
error(ERROR_noData);
type = "XJVXL";
} else if (data == "ISOSURFACE" || data == "MESH") {
- if ((data = getIsosurfaceJvxl(data == "MESH",
- JC.SHAPE_ISOSURFACE)) == null)
+ if ((data = getIsosurfaceJvxl(data == "MESH", JC.SHAPE_ISOSURFACE))
== null)
error(ERROR_noData);
type = (data.indexOf("<?xml") >= 0 ? "XJVXL" : "JVXL");
if (!isShow)
- showString((String) getShapeProperty(
- JC.SHAPE_ISOSURFACE, "jvxlFileInfo"));
+ showString((String) getShapeProperty(JC.SHAPE_ISOSURFACE,
+ "jvxlFileInfo"));
} else {
// image
len = -1;
@@ -15021,11 +15036,10 @@
if (doDefer)
msg = viewer.streamFileData(fileName, type, type2, 0, null);
else
- msg = viewer.createImageSet(fileName, type,
- (bytes instanceof String ? (String) bytes : null),
- (bytes instanceof byte[] ? (byte[]) bytes : null),
- scripts, quality,
- width, height, bsFrames, nVibes, fullPath);
+ msg = viewer.createImageSet(fileName, type,
+ (bytes instanceof String ? (String) bytes : null),
+ (bytes instanceof byte[] ? (byte[]) bytes : null), scripts,
+ quality, width, height, bsFrames, nVibes, fullPath);
}
if (!chk && msg != null) {
if (!msg.startsWith("OK"))
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-02
07:17:11 UTC (rev 18402)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-02
10:11:41 UTC (rev 18403)
@@ -1434,7 +1434,7 @@
else if (s.equalsIgnoreCase("minArray"))
asArray = (nBitSets >= 1);
else if (Parser.isOneOf(s.toLowerCase(),
- "nm;nanometers;pm;picometers;angstroms;ang;au"))
+ ";nm;nanometers;pm;picometers;angstroms;ang;au;"))
units = s.toLowerCase();
else
strFormat = nPoints + ":" + s;
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2013-07-02 07:17:11 UTC (rev
18402)
+++ trunk/Jmol/src/org/jmol/script/T.java 2013-07-02 10:11:41 UTC (rev
18403)
@@ -1220,6 +1220,7 @@
final static int once = misc | 246;
final static int only = misc | 248;
final static int opaque = misc | 250;
+ final static int options = misc | 251;
final static int orbital = misc | 252;
final static int orientation = misc | 253;
final static int origin = misc | 254; // 12.1.51
@@ -1914,6 +1915,7 @@
"omega", T.t(omega),
"only", T.t(only),
"opaque", T.t(opaque),
+ "options", T.t(options),
"partialCharge", T.t(partialcharge),
"phi", T.t(phi),
"plane", T.t(plane),
Modified: trunk/Jmol/src/org/jmol/shapespecial/Ellipsoid.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Ellipsoid.java 2013-07-02 07:17:11 UTC
(rev 18402)
+++ trunk/Jmol/src/org/jmol/shapespecial/Ellipsoid.java 2013-07-02 10:11:41 UTC
(rev 18403)
@@ -39,6 +39,7 @@
public boolean isValid;
public P3 center = P3.new3(0, 0, 0);
public Tensor tensor;
+ public String options;
boolean isOn = true;
String id;
Modified: trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2013-07-02
07:17:11 UTC (rev 18402)
+++ trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2013-07-02
10:11:41 UTC (rev 18403)
@@ -153,6 +153,9 @@
ellipsoidSelected.isOn = ((Boolean) value).booleanValue();
return;
}
+ if ("options" == propertyName) {
+ ellipsoidSelected.options = ((String) value).toLowerCase();
+ }
if ("points" == propertyName) {
//Object[] o = (Object[]) value;
//setPoints((P3[]) o[1], (BS) o[2]);
@@ -219,6 +222,20 @@
return;
}
+ if ("options" == propertyName) {
+ String options = ((String) value).toLowerCase().trim();
+ if (options.length() == 0)
+ options = null;
+ if (selectedAtoms != null)
+ bs = selectedAtoms;
+ if (options != null)
+ setSize(Integer.MAX_VALUE, bs);
+ for (Ellipsoid e : atomEllipsoids.values())
+ if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs, -1))
+ e.options = options;
+ return;
+ }
+
if ("color" == propertyName) {
short colix = C.getColixO(value);
byte pid = EnumPalette.pidOf(value);
@@ -315,6 +332,8 @@
sb.append(" ").append(Escape.eP(v1));
}
sb.append(" " + getColorCommandUnk("", ellipsoid.colix,
translucentAllowed));
+ if (ellipsoid.options != null)
+ sb.append(" options ").append(Escape.eS(ellipsoid.options));
if (!ellipsoid.isOn)
sb.append(" off");
sb.append(";\n");
@@ -338,7 +357,9 @@
int i = e2.tensor.atomIndex1;
//
BSUtil.setMapBitSet(temp, i, i, (isADP ? "Ellipsoids " + e2.percent
- : cmd + " scale " + e2.scale + (e2.isOn ? " ON" : " OFF")));
+ : cmd + " scale " + e2.scale
+ + (e2.options == null ? "" : " options " +
Escape.eS(e2.options))
+ + (e2.isOn ? " ON" : " OFF")));
if (e2.colix != C.INHERIT_ALL)
BSUtil.setMapBitSet(temp2, i, i, getColorCommand(cmd, e2.pid,
e2.colix, translucentAllowed));
Modified: trunk/Jmol/src/org/jmol/util/Parser.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Parser.java 2013-07-02 07:17:11 UTC (rev
18402)
+++ trunk/Jmol/src/org/jmol/util/Parser.java 2013-07-02 10:11:41 UTC (rev
18403)
@@ -586,7 +586,9 @@
}
public static boolean isOneOf(String key, String semiList) {
- return key.indexOf(";") < 0 && (';' + semiList + ';').indexOf(';' + key +
';') >= 0;
+ if (semiList.charAt(0) != ';')
+ semiList = ";" + semiList + ";";
+ return key.indexOf(";") < 0 && (semiList).indexOf(';' + key + ';') >= 0;
}
public static String getQuotedAttribute(String info, String name) {
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2013-07-02 07:17:11 UTC (rev
18402)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2013-07-02 10:11:41 UTC (rev
18403)
@@ -122,7 +122,7 @@
public final static String SCRIPT_EDITOR_IGNORE = "\1## EDITOR_IGNORE ##";
- public final static String LOAD_ATOM_DATA_TYPES =
"xyz;vxyz;vibration;temperature;occupancy;partialcharge";
+ public final static String LOAD_ATOM_DATA_TYPES =
";xyz;vxyz;vibration;temperature;occupancy;partialcharge;";
public final static float radiansPerDegree = (float) (Math.PI / 180);
@@ -1541,6 +1541,9 @@
public final static String binaryExtensions = ";pse=PyMOL;";// PyMOL
public static final String SCRIPT_COMPLETED = "Script completed";
+ public static final String JPEG_EXTENSIONS = ";jpg;jpeg;jpg64;jpeg64;";
+ public final static String IMAGE_TYPES = JPEG_EXTENSIONS +
"gif;ppm;png;pngj;pngt;";
+ public static final String IMAGE_OR_SCENE = IMAGE_TYPES + "scene;";
public final static int getShapeVisibilityFlag(int shapeID) {
return (4 << shapeID);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-02 07:17:11 UTC
(rev 18402)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-02 10:11:41 UTC
(rev 18403)
@@ -9,8 +9,13 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.19_dev_2013.07.01"
+___JmolVersion="13.1.19_dev_2013.07.02"
+new feature: ellipsoid OPTIONS "xxxx"
+ -- "xxxx" is a quoted string of options separated by semicolon:
+ "arcs;arrows;axes;ball;dots;fill;wireframe"
+ with optional "no" in front of each
+
new feature: {xxx}.tensor(type,what)
-- type = "temp", "ms", "efg", etc.
-- what = "eigenvalues", "eigenvectors", "asymmetric", "symmetric", "trace",
"indices", and "type"
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-07-02 07:17:11 UTC
(rev 18402)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-07-02 10:11:41 UTC
(rev 18403)
@@ -2261,7 +2261,7 @@
JmolImageCreatorInterface c = null;
Object bytes = null;
type = type.toLowerCase();
- if (!Parser.isOneOf(type, "jpg;jpeg;jpg64;jpeg64"))
+ if (!Parser.isOneOf(type, JC.JPEG_EXTENSIONS))
try {
c = viewer.getImageCreator();
} catch (Error er) {
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