Revision: 20853
http://sourceforge.net/p/jmol/code/20853
Author: hansonr
Date: 2015-11-01 18:15:50 +0000 (Sun, 01 Nov 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.0_2015.11.01"
new feature: polyhedra ID xxx SCALE x.x
-- ID named polyhedra only
-- x.x is the scaling factor, initially 1
-- x.x < 0 does "explode" from {0 0 0} (for higher-order Brillouin zones, for
instance)
-- x.x > 0 does normal scaling
bug fix: slabbing should reset area and volume of isosurface
bug fix: meshSlicer may fail to add edge to sliced pmesh
FEATURE CHANGE: (Application only for now) PDB default for =xxxx
-- changed to
"pdb",
"http://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/%c2%c3/pdb%file.ent.gz";
-- will be complemented with file.ent for non-binary transfer, but that is
not implemented yet at RCSB
-- mmCIF counterpart not implemented yet.
-- not HTML5 because for that we need the option to remove .gz
new feature: set testflag3 TRUE gives random triangle effect to polyhedra
new feature: POLYHEDRON ID "xxx" OFFSET {3 3 3}
-- allows cartesian offset of named polyhedra
bug fix: bug fix: empty format crashes Jmol -- print "testing".format("")
bug fix: polyhedron volume will be incorrect if there is a
face triangle that has no edges visible (requires a six or more sided
face)
bug fix: nested if...{...if... } else {...} gives compiler syntax error:
if (i=1) {
print "i=1"
if (j=1)
print "j != 1"
} else { // } closes if (j=1) instead of if (i=1) {
print "i != 1"
}
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
trunk/Jmol/src/org/jmol/script/SV.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
trunk/Jmol/src/org/jmol/util/MeshSlicer.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/ShapeManager.java
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java 2015-10-30
12:08:02 UTC (rev 20852)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java 2015-11-01
18:15:50 UTC (rev 20853)
@@ -314,9 +314,10 @@
return true;
} else if (AU.isAS(value)) {
params.title = (String[]) value;
- for (int i = 0; i < params.title.length; i++)
- if (params.title[i].length() > 0)
- Logger.info(params.title[i]);
+ if (Logger.debugging)
+ for (int i = 0; i < params.title.length; i++)
+ if (params.title[i].length() > 0)
+ Logger.info(params.title[i]);
}
return true;
}
Modified: trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
2015-10-30 12:08:02 UTC (rev 20852)
+++ trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
2015-11-01 18:15:50 UTC (rev 20853)
@@ -35,6 +35,8 @@
import javajs.util.P3;
import javajs.util.P3i;
+import javajs.util.T3;
+import javajs.util.V3;
public class PolyhedraRenderer extends ShapeRenderer {
@@ -69,6 +71,7 @@
short[] colixes = ((Polyhedra) shape).colixes;
int iAtom = -1;
short colix;
+ float scale = 1;
if (p.id == null) {
iAtom = p.centralAtom.i;
colix = (colixes == null || iAtom >= colixes.length ? C.INHERIT_ALL
@@ -76,6 +79,7 @@
colix = C.getColixInherited(colix, p.centralAtom.colixAtom);
} else {
colix = p.colix;
+ scale = p.scale;
}
boolean needTranslucent = false;
if (C.renderPass2(colix)) {
@@ -83,7 +87,28 @@
} else if (!g3d.setC(colix)) {
return false;
}
- P3[] vertices = p.vertices;
+ T3[] vertices = p.vertices;
+ if (scale != 1) {
+ T3[] v = new T3[vertices.length];
+ if (scale < 0) {
+ // explode from {0 0 0}
+ V3 a = V3.newV(p.center);
+ a.scale(-scale - 1);
+ for (int i = v.length; --i >= 0;) {
+ V3 b = V3.newV(vertices[i]);
+ b.add(a);
+ v[i] = b;
+ }
+ } else {
+ // enlarge
+ for (int i = v.length; --i >= 0;) {
+ V3 a = V3.newVsub(vertices[i], p.center);
+ a.scaleAdd2(scale, a, p.center);
+ v[i] = a;
+ }
+ }
+ vertices = v;
+ }
if (screens3f == null || screens3f.length < vertices.length) {
screens3f = new P3[vertices.length];
for (int i = vertices.length; --i >= 0;)
Modified: trunk/Jmol/src/org/jmol/script/SV.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/SV.java 2015-10-30 12:08:02 UTC (rev
20852)
+++ trunk/Jmol/src/org/jmol/script/SV.java 2015-11-01 18:15:50 UTC (rev
20853)
@@ -1444,9 +1444,8 @@
/**
*
- * Script variables are pushed after cloning, because
- * the name comes with them when we do otherwise
- * they are not mutable anyway. We do want to have actual
+ * Script variables are pushed after cloning, because the name comes with
them
+ * when we do otherwise they are not mutable anyway. We do want to have
actual
* references to points, lists, and associative arrays
*
* @param value
@@ -1455,12 +1454,23 @@
* @return array
*/
public SV pushPop(SV value, SV mapKey) {
- if (mapKey != null ) {
+ if (mapKey != null) {
Map<String, SV> m = getMap();
if (value == null) {
- SV v;
- return (m == null || (v = m.remove(mapKey.asString())) == null ?
- newS("") : v);
+ SV v = null;
+ if (m == null) {
+ Lst<SV> lst = getList();
+ int len = lst.size();
+ int i = iValue(mapKey) - 1;
+ if (i < 0)
+ i += len;
+ if (i >= 0 && i < len) {
+ v = lst.remove(i);
+ }
+ } else {
+ v = m.remove(mapKey.asString());
+ }
+ return (v == null ? newS("") : v);
}
if (m != null)
m.put(mapKey.asString(), newI(0).setv(value));
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-10-30 12:08:02 UTC
(rev 20852)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-11-01 18:15:50 UTC
(rev 20853)
@@ -3192,6 +3192,7 @@
boolean onOffDelete = false;
boolean typeSeen = false;
boolean edgeParameterSeen = false;
+ float scale = Float.NaN;
// int lighting = T.nada; // never implemented; fullyLit does nothing
int nAtomSets = 0;
eval.sm.loadShape(JC.SHAPE_POLYHEDRA);
@@ -3209,6 +3210,9 @@
propertyValue = e.theToken.value;
needsGenerating = true;
break;
+ case T.scale:
+ scale = floatParameter(++i);
+ continue;
case T.unitcell:
if (id != null)
invArg();
@@ -3401,11 +3405,13 @@
if (!typeSeen && haveBonds)
setShapeProperty(JC.SHAPE_POLYHEDRA, "bonds", null);
setShapeProperty(JC.SHAPE_POLYHEDRA, "generate", null);
- } else if (!edgeParameterSeen && offset == null) {// && lighting == T.nada)
+ } else if (!edgeParameterSeen && offset == null && Float.isNaN(scale)) {//
&& lighting == T.nada)
error(ScriptError.ERROR_insufficientArguments);
}
if (offset != null)
setShapeProperty(JC.SHAPE_POLYHEDRA, "offset", offset);
+ if (!Float.isNaN(scale))
+ setShapeProperty(JC.SHAPE_POLYHEDRA, "scale", Float.valueOf(scale));
if (colorArgb[0] != Integer.MIN_VALUE)
setShapeProperty(JC.SHAPE_POLYHEDRA, "colorThis",
Integer.valueOf(colorArgb[0]));
Modified: trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-10-30 12:08:02 UTC
(rev 20852)
+++ trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-11-01 18:15:50 UTC
(rev 20853)
@@ -1125,6 +1125,7 @@
boolean isPmesh = (iShape == JC.SHAPE_PMESH);
boolean isPlot3d = (iShape == JC.SHAPE_PLOT3D);
boolean isLcaoCartoon = (iShape == JC.SHAPE_LCAOCARTOON);
+ boolean isSilent = (isLcaoCartoon || tokAt(1) == T.delete);
boolean surfaceObjectSeen = false;
boolean planeSeen = false;
boolean isMapped = false;
@@ -1185,6 +1186,10 @@
str = paramAsStr(i);
switch (eval.theTok) {
// settings only
+ case T.silent:
+ isSilent = true;
+ sbCommand.append(" silent");
+ continue;
case T.isosurfacepropertysmoothing:
smoothing = (getToken(++i).tok == T.on ? Boolean.TRUE
: eval.theTok == T.off ? Boolean.FALSE : null);
@@ -2732,7 +2737,7 @@
+ Escape.eBS(bsSelect) + " ")
+ cmd);
s = (String) getShapeProperty(iShape, "ID");
- if (s != null && !eval.tQuiet) {
+ if (s != null && !eval.tQuiet && !isSilent) {
cutoff = ((Float) getShapeProperty(iShape, "cutoff")).floatValue();
if (Float.isNaN(cutoff) && !Float.isNaN(sigma))
Logger.error("sigma not supported");
@@ -2759,7 +2764,7 @@
s += "\n" + svol;
}
}
- if (s != null)
+ if (s != null && !isSilent)
showString(s);
}
if (translucency != null)
@@ -2767,7 +2772,7 @@
setShapeProperty(iShape, "clear", null);
if (toCache)
setShapeProperty(iShape, "cache", null);
- if (iShape != JC.SHAPE_LCAOCARTOON && !isDisplay && !haveSlab)
+ if (!isSilent && !isDisplay && !haveSlab && eval.theTok != T.delete)
listIsosurface(iShape);
}
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-10-30 12:08:02 UTC
(rev 20852)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-11-01 18:15:50 UTC
(rev 20853)
@@ -162,6 +162,13 @@
return;
}
+ if ("scale" == propertyName) {
+ if (thisID != null)
+ scalePolyhedra(((Float) value).floatValue());
+ return;
+
+ }
+
if ("model" == propertyName) {
modelIndex = ((Integer) value).intValue();
return;
@@ -360,6 +367,12 @@
setPropAS(propertyName, value, bs);
}
+ private void scalePolyhedra(float scale) {
+ BS bs = findPolyBS(null);
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ polyhedrons[i].scale = scale;
+ }
+
private void offsetPolyhedra(P3 value) {
BS bs = findPolyBS(null);
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
@@ -723,15 +736,18 @@
* catalog. This uses the Point3i().toString() method.
*
* For these special cases, then, we define a reference point just behind
the plane
+ *
+ * Note that this is NOT AN OPTION for ID-named polyhedra (Jmol 14.5.0
10/31/2015)
*/
P3 ptRef = P3.newP(ptAve);
BS bsThroughCenter = new BS();
- for (int pt = 0, i = 0; i < ni; i++)
- for (int j = i + 1; j < nj; j++)
- for (int k = j + 1; k < vertexCount; k++, pt++)
- if (isPlanar(points[i], points[j], points[k], ptRef))
- bsThroughCenter.set(pt);
+ if (thisID == null)
+ for (int pt = 0, i = 0; i < ni; i++)
+ for (int j = i + 1; j < nj; j++)
+ for (int k = j + 1; k < vertexCount; k++, pt++)
+ if (isPlanar(points[i], points[j], points[k], ptRef))
+ bsThroughCenter.set(pt);
// this next check for distance allows for bond AND distance constraints
int[][] triangles = planesT;
P4 pTemp = new P4();
@@ -761,26 +777,27 @@
boolean isThroughCenter = bsThroughCenter.get(pt);
P3 rpt = (isThroughCenter ? randomPoint : ptAve);
V3 normal = new V3();
- boolean isWindingOK = Measure.getNormalFromCenter(rpt, points[i],
points[j],
- points[k], !isThroughCenter, normal, vAC);
+ boolean isWindingOK = Measure.getNormalFromCenter(rpt, points[i],
+ points[j], points[k], !isThroughCenter, normal, vAC);
// the standard face:
normals[triangleCount] = normal;
- triangles[triangleCount] = new int[] { isWindingOK ? i : j,
isWindingOK ? j : i,
- k, -7 };
- if (!checkFace(points, vertexCount, triangles, normals,
triangleCount, pTemp, nTemp,
- vAC, htNormMap, htEdgeMap, planarParam, bsTemp))
+ triangles[triangleCount] = new int[] { isWindingOK ? i : j,
+ isWindingOK ? j : i, k, -7 };
+ if (!checkFace(points, vertexCount, triangles, normals,
+ triangleCount, pTemp, nTemp, vAC, htNormMap, htEdgeMap,
+ planarParam, bsTemp))
continue;
if (isThroughCenter) {
bsCenterPlanes.set(triangleCount++);
} else if (collapsed) {
ptRef.setT(points[nPoints] = new P3());
points[nPoints].scaleAdd2(offset, normal, atomOrPt);
- addFacet(i, j, k, ptRef, points, normals, triangles,
triangleCount++, nPoints,
- isWindingOK, vAC);
- addFacet(k, i, j, ptRef, points, normals, triangles,
triangleCount++, nPoints,
- isWindingOK, vAC);
- addFacet(j, k, i, ptRef, points, normals, triangles,
triangleCount++, nPoints,
- isWindingOK, vAC);
+ addFacet(i, j, k, ptRef, points, normals, triangles,
+ triangleCount++, nPoints, isWindingOK, vAC);
+ addFacet(k, i, j, ptRef, points, normals, triangles,
+ triangleCount++, nPoints, isWindingOK, vAC);
+ addFacet(j, k, i, ptRef, points, normals, triangles,
+ triangleCount++, nPoints, isWindingOK, vAC);
nPoints++;
} else {
triangleCount++;
@@ -789,14 +806,16 @@
}
nPoints--;
if (Logger.debugging) {
- Logger
- .info("Polyhedron planeCount=" + triangleCount + " nPoints=" +
nPoints);
+ Logger.info("Polyhedron planeCount=" + triangleCount + " nPoints="
+ + nPoints);
for (int i = 0; i < triangleCount; i++)
- Logger.info("Polyhedron " + PT.toJSON("face[" +i + "]", triangles[i]));
+ Logger.info("Polyhedron " + PT.toJSON("face[" + i + "]",
triangles[i]));
}
//System.out.println(PT.toJSON(null, htEdgeMap));
- return new Polyhedron().set(thisID, modelIndex, atomOrPt, points, nPoints,
vertexCount,
- triangles, triangleCount, getFaces(triangles, triangleCount,
htNormMap), normals, bsCenterPlanes, collapsed, distanceRef);
+ return new Polyhedron().set(thisID, modelIndex, atomOrPt, points, nPoints,
+ vertexCount, triangles, triangleCount,
+ getFaces(triangles, triangleCount, htNormMap), normals, bsCenterPlanes,
+ collapsed, distanceRef);
}
/**
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-10-30
12:08:02 UTC (rev 20852)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-11-01
18:15:50 UTC (rev 20853)
@@ -32,7 +32,7 @@
Map<String, Object> info;
public String id;
- P3 center;
+ public P3 center;
public Atom centralAtom;
public P3[] vertices;
@@ -66,6 +66,8 @@
public int modelIndex = Integer.MIN_VALUE;
private P3 offset;
+
+ public float scale = 1;
Polyhedron() {
@@ -109,6 +111,8 @@
colixEdge = C.getColixS(info.get("colorEdge").asString());
if (info.containsKey("offset"))
offset = P3.newP(SV.ptValue(info.get("offset")));
+ if (info.containsKey("scale"))
+ scale = SV.fValue(info.get("scale"));
}
Lst<SV> lst = info.get("vertices").getList();
SV vc = info.get("vertexCount");
@@ -220,6 +224,8 @@
info.put("colorEdge", C.getHexCode(colixEdge == 0 ? colix : colixEdge));
if (offset != null)
info.put("offset", offset);
+ if (scale != 1)
+ info.put("scale", Float.valueOf(scale));
}
if (faces != null)
info.put("faces", faces);
Modified: trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2015-10-30
12:08:02 UTC (rev 20852)
+++ trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2015-11-01
18:15:50 UTC (rev 20853)
@@ -764,6 +764,8 @@
}
protected void slabPolygons(Object[] slabInfo) {
+ thisMesh.calculatedVolume = null;
+ thisMesh.calculatedArea = null;
thisMesh.getMeshSlicer().slabPolygons(slabInfo, false);
thisMesh.reinitializeLightingAndColor(vwr);
}
Modified: trunk/Jmol/src/org/jmol/util/MeshSlicer.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/MeshSlicer.java 2015-10-30 12:08:02 UTC
(rev 20852)
+++ trunk/Jmol/src/org/jmol/util/MeshSlicer.java 2015-11-01 18:15:50 UTC
(rev 20853)
@@ -583,7 +583,7 @@
if (iD == i2 && iE == i3) {
// cap but don't toss if tossing 23
doClear = !toss23;
- return false;
+ return !doClear; // was FALSE, but we need to recreate the edge
}
if (iD == i1 || iE == i1) {
// other is i2 or i3 -- along an edge
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-30 12:08:02 UTC
(rev 20852)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-01 18:15:50 UTC
(rev 20853)
@@ -62,8 +62,16 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.0_2015.10.30"
+Jmol.___JmolVersion="14.5.0_2015.11.01"
+new feature: polyhedra ID xxx SCALE x.x
+ -- ID named polyhedra only
+ -- x.x is the scaling factor, initially 1
+ -- x.x < 0 does "explode" from {0 0 0} (for higher-order Brillouin zones,
for instance)
+ -- x.x > 0 does normal scaling
+bug fix: slabbing should reset area and volume of isosurface
+bug fix: meshSlicer may fail to add edge to sliced pmesh
+
FEATURE CHANGE: (Application only for now) PDB default for =xxxx
-- changed to
"pdb",
"http://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/%c2%c3/pdb%file.ent.gz";
@@ -76,7 +84,7 @@
new feature: POLYHEDRON ID "xxx" OFFSET {3 3 3}
-- allows cartesian offset of named polyhedra
-bug fix: empty format crashes Jmol -- print "testing".format("")
+bug fix: bug fix: empty format crashes Jmol -- print "testing".format("")
bug fix: polyhedron volume will be incorrect if there is a
face triangle that has no edges visible (requires a six or more sided
face)
Modified: trunk/Jmol/src/org/jmol/viewer/ShapeManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ShapeManager.java 2015-10-30 12:08:02 UTC
(rev 20852)
+++ trunk/Jmol/src/org/jmol/viewer/ShapeManager.java 2015-11-01 18:15:50 UTC
(rev 20853)
@@ -217,6 +217,7 @@
JC.SHAPE_ECHO,
JC.SHAPE_CONTACT,
JC.SHAPE_ISOSURFACE,
+ JC.SHAPE_PMESH,
JC.SHAPE_DRAW,
JC.SHAPE_FRANK,
};
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