Revision: 20837
http://sourceforge.net/p/jmol/code/20837
Author: hansonr
Date: 2015-10-19 06:22:30 +0000 (Mon, 19 Oct 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.4.0_2015.10.18"
bug fix: Polyhedra can have missing triangle for hexagonal faces
bug fix: calculate symmetry can break Jmol if unit cell has been changed
bug fix: DRAW POLYGON front/back nature of winding was reversed.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/shape/Echo.java
trunk/Jmol/src/org/jmol/shape/Mesh.java
trunk/Jmol/src/org/jmol/shape/MeshCollection.java
trunk/Jmol/src/org/jmol/shape/Shape.java
trunk/Jmol/src/org/jmol/shapecgo/CGO.java
trunk/Jmol/src/org/jmol/shapespecial/Dipoles.java
trunk/Jmol/src/org/jmol/shapespecial/Draw.java
trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.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/shapesurface/IsosurfaceMesh.java
trunk/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java
trunk/Jmol/src/org/jmol/shapesurface/Pmesh.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/util/MeshCapper.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
Modified: trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
2015-10-17 23:45:49 UTC (rev 20836)
+++ trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
2015-10-19 06:22:30 UTC (rev 20837)
@@ -67,10 +67,11 @@
if (p.visibilityFlags == 0)
return false;
short[] colixes = ((Polyhedra) shape).colixes;
- int iAtom = p.centralAtom.i;
- short colix = (colixes == null || iAtom >= colixes.length ? C.INHERIT_ALL
+ int iAtom = (p.id == null ? p.centralAtom.i : -1);
+ short colix = (p.id != null ? p.colix : colixes == null || iAtom >=
colixes.length ? C.INHERIT_ALL
: colixes[iAtom]);
- colix = C.getColixInherited(colix, p.centralAtom.colixAtom);
+ if (p.centralAtom != null)
+ colix = C.getColixInherited(colix, p.centralAtom.colixAtom);
boolean needTranslucent = false;
if (C.renderPass2(colix)) {
needTranslucent = true;
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-10-17 23:45:49 UTC
(rev 20836)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-10-19 06:22:30 UTC
(rev 20837)
@@ -3197,6 +3197,7 @@
setShapeProperty(JC.SHAPE_POLYHEDRA, "init", Boolean.TRUE);
float translucentLevel = Float.MAX_VALUE;
int[] colorArgb = new int[] { Integer.MIN_VALUE };
+ String id = null;
for (int i = 1; i < slen; ++i) {
String propertyName = null;
Object propertyValue = null;
@@ -3266,6 +3267,15 @@
}
propertyValue = Float.valueOf(floatParameter(++i));
break;
+ case T.id:
+ if (i != 1)
+ invPO();
+ setShapeProperty(JC.SHAPE_POLYHEDRA, "id", stringParameter(++i));
+ setShapeProperty(JC.SHAPE_POLYHEDRA, "center", centerParameter(++i));
+ i = eval.iToken;
+ if (tokAt(++i) != T.to)
+ invPO();
+ //$FALL-THROUGH$
case T.to:
if (nAtomSets > 1)
invPO();
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-17 23:45:49 UTC
(rev 20836)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-19 06:22:30 UTC
(rev 20837)
@@ -1435,7 +1435,7 @@
*
* @param mp
* @param args
- * @param tok0
+ * @param tok0
* @param isAtomProperty
* @return true if no syntax problems
* @throws ScriptException
@@ -1452,7 +1452,9 @@
return mp.addXObj(vwr.extractProperty(args[0].value,
args[1].value.toString(), -1));
}
- String propertyName = (args.length > 0 ? SV.sValue(args[pt++]) : "");
+ BS bsSelect = (isAtomProperty && args.length == 1 && args[0].tok ==
T.bitset ? SV.bsSelectVar(args[0]) : null);
+ String pname = (bsSelect == null && args.length > 0 ?
SV.sValue(args[pt++]) : "");
+ String propertyName = pname;
String lc = propertyName.toLowerCase();
if (!isSelect && lc.indexOf("[select ") < 0)
propertyName = lc;
@@ -1464,9 +1466,48 @@
SV x = null;
if (isAtomProperty) {
x = mp.getX();
- if (x.tok != T.bitset) {
+ switch (x.tok) {
+ case T.bitset:
+ break;
+ case T.string:
+ String name = (String) x.value;
+ Object[] data = new Object[3];
+ int shapeID;
+ if (name.startsWith("$")) {
+ // "P4".getProperty....
+ name = name.substring(1);
+ shapeID = vwr.shm.getShapeIdFromObjectName(name);
+ if (shapeID >= 0) {
+ data[0] = name;
+ vwr.shm.getShapePropertyData(shapeID, "index", data);
+ if (data[1] != null && !pname.equals("index")) {
+ int index = ((Integer) data[1]).intValue();
+ data[1] = vwr.shm.getShapePropertyIndex(shapeID,
+ pname.intern(), index);
+ }
+ }
+ } else {
+ shapeID = JC.shapeTokenIndex(T.getTokFromName(name));
+ if (shapeID >= 0) {
+ // "isosurface".getProperty...
+ data[0] = pname;
+ data[1] = Integer.valueOf(-1);
+ vwr.shm.getShapePropertyData(shapeID, pname.intern(), data);
+ }
+ }
+ return (data[1] == null ? mp.addXStr("") : mp.addXObj(data[1]));
+ case T.varray:
+ if (bsSelect != null) {
+ Lst<SV> l0 = x.getList();
+ Lst<SV> lst = new Lst<SV>();
+ for (int i = bsSelect.nextSetBit(0); i >= 0; i =
bsSelect.nextSetBit(i + 1))
+ lst.addLast(l0.get(i));
+ return mp.addXList(lst);
+ }
+ //$FALL-THROUGH$
+ default:
if (isSelect)
- propertyName = "[SELECT " + propertyName + "]";
+ propertyName = "[SELECT " + propertyName + "]";
return mp.addXObj(vwr.extractProperty(x, propertyName, -1));
}
}
@@ -3121,9 +3162,9 @@
plane = e.getHklPlane(pt);
break;
case T.varray:
- if (last != 2)
+ pt = (last == 2 ? SV.ptValue(args[1]) : last == 1 ? P3.new3(Float.NaN,
0, 0) : null);
+ if (pt == null)
return false;
- pt = SV.ptValue(args[1]);
break;
}
if (last > 0 && plane == null && pt == null
@@ -3142,13 +3183,42 @@
if (pt != null) {
if (args[last].tok == T.varray) {
// within(dist, pt, [pt1, pt2, pt3...])
- Lst<SV> sv = args[2].getList();
+ Lst<SV> sv = args[last].getList();
Lst<T3> pts = new Lst<T3>();
Bspt bspt = new Bspt(3, 0);
- for (int i = sv.size(); --i >= 0;) {
+ CubeIterator iter;
+ if (Float.isNaN(pt.x)) {
+ // internal comparison
+ Point3fi p;
+ Point3fi[] pt3 = new Point3fi[sv.size()];
+ for (int i = pt3.length; --i >= 0;) {
+ p = new Point3fi();
+ p.setT(SV.ptValue(sv.get(i)));
+ p.i = i;
+ pt3[i] = p;
+ bspt.addTuple(p);
+ }
+ iter = bspt.allocateCubeIterator();
+ BS bsp = BSUtil.newBitSet2(0, sv.size());
+ for (int i = pt3.length; --i >= 0;) {
+ iter.initialize(p = pt3[i], distance, false);
+ float d2 = distance * distance;
+ int n = 0;
+ while (iter.hasMoreElements()) {
+ Point3fi pt2 = (Point3fi) iter.nextElement();
+ if (bsp.get(pt2.i) && pt2.distanceSquared(p) <= d2
+ && (++n > 1))
+ bsp.clear(pt2.i);
+ }
+ }
+ for (int i = bsp.nextSetBit(0); i >= 0; i = bsp.nextSetBit(i + 1))
+ pts.addLast(P3.newP(pt3[i]));
+ return mp.addXList(pts);
+
+ }
+ for (int i = sv.size(); --i >= 0;)
bspt.addTuple(SV.ptValue(sv.get(i)));
- }
- CubeIterator iter = bspt.allocateCubeIterator();
+ iter = bspt.allocateCubeIterator();
iter.initialize(pt, distance, false);
float d2 = distance * distance;
while (iter.hasMoreElements()) {
Modified: trunk/Jmol/src/org/jmol/shape/Echo.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Echo.java 2015-10-17 23:45:49 UTC (rev
20836)
+++ trunk/Jmol/src/org/jmol/shape/Echo.java 2015-10-19 06:22:30 UTC (rev
20837)
@@ -190,7 +190,7 @@
}
return false;
}
- return false;
+ return getPropShape(property, data);
}
@Override
Modified: trunk/Jmol/src/org/jmol/shape/Mesh.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Mesh.java 2015-10-17 23:45:49 UTC (rev
20836)
+++ trunk/Jmol/src/org/jmol/shape/Mesh.java 2015-10-19 06:22:30 UTC (rev
20837)
@@ -503,12 +503,20 @@
info.put("polygonCount", Integer.valueOf(pc));
info.put("haveQuads", Boolean.valueOf(haveQuads));
info.put("haveValues", Boolean.valueOf(vvs != null));
- if (vc > 0 && isAll)
- info.put("vertices", AU.arrayCopyPt(vs, vc));
- if (vvs != null && isAll)
- info.put("vertexValues", AU.arrayCopyF(vvs, vc));
- if (pc > 0 && isAll)
- info.put("polygons", AU.arrayCopyII(pis, pc));
+ if (isAll) {
+ if (vc > 0) {
+ info.put("vertices", AU.arrayCopyPt(vs, vc));
+ if (bsSlabDisplay != null)
+ info.put("bsVertices", getVisibleVBS());
+ }
+ if (vvs != null)
+ info.put("vertexValues", AU.arrayCopyF(vvs, vc));
+ if (pc > 0) {
+ info.put("polygons", AU.arrayCopyII(pis, pc));
+ if (bsSlabDisplay != null)
+ info.put("bsPolygons", bsSlabDisplay);
+ }
+ }
return info;
}
Modified: trunk/Jmol/src/org/jmol/shape/MeshCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/MeshCollection.java 2015-10-17 23:45:49 UTC
(rev 20836)
+++ trunk/Jmol/src/org/jmol/shape/MeshCollection.java 2015-10-19 06:22:30 UTC
(rev 20837)
@@ -379,6 +379,13 @@
@SuppressWarnings("unchecked")
protected boolean getPropDataMC(String property, Object[] data) {
+ if (property == "keys") {
+ Lst<String> keys = (data[1] instanceof Lst<?> ? (Lst<String>) data[1] :
new Lst<String>());
+ data[1] = keys;
+ keys.addLast("count");
+ keys.addLast("getCenter");
+ // will continue on to getPropertyIndex
+ }
if (property == "getNames") {
Map<String, T> map = (Map<String, T>) data[0];
boolean withDollar = ((Boolean) data[1]).booleanValue();
@@ -404,6 +411,11 @@
data[1] = list.get(0).thisID;
return true;
}
+ if (property == "index") {
+ Mesh m = getMesh((String) data[0]);
+ data[1] = Integer.valueOf(m == null ? -1 : m.index);
+ return true;
+ }
if (property == "getCenter") {
String id = (String) data[0];
int index = ((Integer) data[1]).intValue();
@@ -416,7 +428,7 @@
data[2] = m.vs[m.getVertexIndexFromNumber(index)];
return true;
}
- return false;
+ return getPropShape(property, data);
}
/**
@@ -445,8 +457,11 @@
return list;
}
- protected Object getPropMC(String property) {
- Mesh m;
+ protected Object getPropMC(String property, int index) {
+ Mesh m = currentMesh;
+ if (index >= 0
+ && (index >= meshCount || (m = meshes[index]) == null))
+ return null;
if (property == "count") {
int n = 0;
for (int i = 0; i < meshCount; i++)
@@ -454,26 +469,34 @@
n++;
return Integer.valueOf(n);
}
+ if (property == "bsVertices") {
+ if (m == null)
+ return null;
+ Lst<Object> lst = new Lst<Object>();
+ lst.addLast(m.vs);
+ lst.addLast(m.getVisibleVBS());
+ return lst;
+ }
if (property == "ID")
- return (currentMesh == null ? null : currentMesh.thisID);
+ return (m == null ? null : m.thisID);
if (property.startsWith("list")) {
- clean();
- SB sb = new SB();
+ clean();
+ SB sb = new SB();
int k = 0;
boolean isNamed = property.length() > 5;
- String id = (property.equals("list") ? null : isNamed ?
property.substring(5) : currentMesh == null ? null : currentMesh.thisID);
+ String id = (property.equals("list") ? null : isNamed ? property
+ .substring(5) : m == null ? null : m.thisID);
for (int i = 0; i < meshCount; i++) {
m = meshes[i];
if (id != null && !id.equalsIgnoreCase(m.thisID))
continue;
- sb.appendI((++k)).append(" id:" + m.thisID).append(
- "; model:" + vwr.getModelNumberDotted(m.modelIndex)).append(
- "; vertices:" + m.vc).append(
- "; polygons:" + m.pc)
+ sb.appendI((++k)).append(" id:" + m.thisID)
+ .append("; model:" + vwr.getModelNumberDotted(m.modelIndex))
+ .append("; vertices:" + m.vc).append("; polygons:" + m.pc)
.append("; visible:" + m.visible);
float[] range = (float[]) getProperty("dataRange", 0);
if (range != null)
- sb.append("; dataRange:").append(Escape.eAF(range));
+ sb.append("; dataRange:").append(Escape.eAF(range));
if (m.title != null) {
String s = "";
for (int j = 0; j < m.title.length; j++)
@@ -492,11 +515,11 @@
return sb.toString();
}
if (property == "vertices")
- return getVertices(currentMesh);
- if (property == "getInfo")
- return (currentMesh == null ? null : currentMesh.getInfo(false));
- if (property == "getData")
- return (currentMesh == null ? null : currentMesh.getInfo(true));
+ return getVertices(m);
+ if (property == "info")
+ return (m == null ? null : m.getInfo(false));
+ if (property == "data")
+ return (m == null ? null : m.getInfo(true));
return null;
}
Modified: trunk/Jmol/src/org/jmol/shape/Shape.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Shape.java 2015-10-17 23:45:49 UTC (rev
20836)
+++ trunk/Jmol/src/org/jmol/shape/Shape.java 2015-10-19 06:22:30 UTC (rev
20837)
@@ -212,17 +212,6 @@
// balls, dots, other atomshapes
}
- /**
- *
- * @param property
- * @param data
- * @return true if serviced
- */
- public boolean getPropertyData(String property, Object[] data) {
- return false;
- }
-
-
@SuppressWarnings("unchecked")
protected void setPropS(String propertyName, Object value, BS bsSelected) {
if (propertyName == "setProperties") {
@@ -250,6 +239,25 @@
/**
*
* @param property
+ * @param data
+ * @return true if serviced
+ */
+ public boolean getPropertyData(String property, Object[] data) {
+ return getPropShape(property, data);
+ }
+
+ protected boolean getPropShape(String property, Object[] data) {
+ if (data[1] instanceof Integer) {
+ int index = ((Integer) data[1]).intValue();
+ data[1] = getProperty(property, index);
+ return (data[1] != null);
+ }
+ return false;
+ }
+
+ /**
+ *
+ * @param property
* @param index
* @return true if serviced
*/
Modified: trunk/Jmol/src/org/jmol/shapecgo/CGO.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapecgo/CGO.java 2015-10-17 23:45:49 UTC (rev
20836)
+++ trunk/Jmol/src/org/jmol/shapecgo/CGO.java 2015-10-19 06:22:30 UTC (rev
20837)
@@ -108,7 +108,14 @@
}
@Override
+ @SuppressWarnings("unchecked")
public boolean getPropertyData(String property, Object[] data) {
+ if (property == "keys") {
+ Lst<String> keys = (data[1] instanceof Lst<?> ? (Lst<String>) data[1] :
new Lst<String>());
+ data[1] = keys;
+ keys.addLast("data");
+ // will continue on to getPropertyIndex
+ }
if (property == "data")
return CGOMesh.getData(data);
return getPropDataMC(property, data);
Modified: trunk/Jmol/src/org/jmol/shapespecial/Dipoles.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Dipoles.java 2015-10-17 23:45:49 UTC
(rev 20836)
+++ trunk/Jmol/src/org/jmol/shapespecial/Dipoles.java 2015-10-19 06:22:30 UTC
(rev 20837)
@@ -423,7 +423,7 @@
}
return false;
}
- return false;
+ return getPropShape(property, data);
}
@Override
Modified: trunk/Jmol/src/org/jmol/shapespecial/Draw.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Draw.java 2015-10-17 23:45:49 UTC
(rev 20836)
+++ trunk/Jmol/src/org/jmol/shapespecial/Draw.java 2015-10-19 06:22:30 UTC
(rev 20837)
@@ -478,8 +478,15 @@
}
}
+ @SuppressWarnings("unchecked")
@Override
public boolean getPropertyData(String property, Object[] data) {
+ if (property == "keys") {
+ Lst<String> keys = (data[1] instanceof Lst<?> ? (Lst<String>) data[1] :
new Lst<String>());
+ data[1] = keys;
+ keys.addLast("getSpinAxis");
+ // will continue on to super
+ }
if (property == "getCenter") {
String id = (String) data[0];
int index = ((Integer) data[1]).intValue();
@@ -498,11 +505,14 @@
@Override
public Object getProperty(String property, int index) {
+ DrawMesh m = this.thisMesh;
+ if (index >= 0 && (index >= meshCount || (m = (DrawMesh) meshes[index]) ==
null))
+ return null;
if (property == "command")
- return getCommand(thisMesh);
+ return getCommand(m);
if (property == "type")
- return Integer.valueOf(thisMesh == null ? EnumDrawType.NONE.id :
thisMesh.drawType.id);
- return getPropMC(property);
+ return Integer.valueOf(m == null ? EnumDrawType.NONE.id : m.drawType.id);
+ return getPropMC(property, index);
}
private T3 getSpinCenter(String axisID, int vertexIndex, int modelIndex) {
Modified: trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2015-10-17
23:45:49 UTC (rev 20836)
+++ trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2015-10-19
06:22:30 UTC (rev 20837)
@@ -117,7 +117,7 @@
if (property == "checkID") {
return (checkID((String) data[0]));
}
- return false;
+ return getPropShape(property, data);
}
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-10-17 23:45:49 UTC
(rev 20836)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-10-19 06:22:30 UTC
(rev 20837)
@@ -95,6 +95,8 @@
private boolean haveBitSetVertices;
private BS centers;
+ private String thisID;
+ private P3 center;
private BS bsVertices;
private BS bsVertexCount;
@@ -116,6 +118,8 @@
nVertices = 0;
nPoints = 0;
bsVertices = null;
+ thisID = null;
+ center = null;
useUnitCell = false;
centers = null;
info = null;
@@ -137,6 +141,16 @@
return;
}
+ if ("center" == propertyName) {
+ center = (P3) value;
+ return;
+ }
+
+ if ("id" == propertyName) {
+ thisID = (String) value;
+ return;
+ }
+
if ("collapsed" == propertyName) {
isCollapsed = ((Boolean) value).booleanValue();
return;
@@ -250,14 +264,28 @@
// but from Color we need to identify the centers.
bs = ("colorThis" == propertyName && iHaveCenterBitSet ? centers
: andBitSet(bs));
+ Object cvalue = ("colorPhase" == propertyName ? ((Object[]) value)[1]
+ : value);
short colixEdge = ("colorPhase" == propertyName ? C
.getColix(((Integer) ((Object[]) value)[0]).intValue())
: C.INHERIT_ALL);
- for (int i = polyhedronCount; --i >= 0;)
- if (bs.get(polyhedrons[i].centralAtom.i))
- polyhedrons[i].colixEdge = colixEdge;
- if ("colorPhase" == propertyName)
- value = ((Object[]) value)[1];
+ for (int i = polyhedronCount; --i >= 0;) {
+ Polyhedron p = polyhedrons[i];
+ if (thisID != null) {
+ if (thisID == p.id) {
+ p.colixEdge = colixEdge;
+ isActive = true;
+ p.colix = C.getColixO(value);
+ return;
+ }
+ } else {
+ if (bs.get(p.centralAtom.i))
+ p.colixEdge = colixEdge;
+ }
+ }
+ if (thisID != null)
+ return;
+ value = cvalue;
propertyName = "color";
//allow super
}
@@ -272,15 +300,15 @@
//allow super
}
-// if ("token" == propertyName) {
-// int tok = ((Integer) value).intValue();
-// Swit
-// if (tok == T.triangles && tok == T.notriangles) {
-// } else {
-// setLighting(tok == T.fullylit, bs);
-// }
-// return;
-// }
+ // if ("token" == propertyName) {
+ // int tok = ((Integer) value).intValue();
+ // Swit
+ // if (tok == T.triangles && tok == T.notriangles) {
+ // } else {
+ // setLighting(tok == T.fullylit, bs);
+ // }
+ // return;
+ // }
if ("radius" == propertyName) {
radius = ((Float) value).floatValue();
@@ -390,7 +418,7 @@
}
return false;
}
- return false;
+ return getPropShape(property, data);
}
@Override
@@ -445,51 +473,59 @@
}
}
- private int buildMode;
-
private void buildPolyhedra() {
- boolean useBondAlgorithm = radius == 0 || bondedOnly;
- buildMode = (info != null ? MODE_INFO : nPoints > 0 ? MODE_POINTS
- : haveBitSetVertices ? MODE_BITSET : useUnitCell ? MODE_UNITCELL
- : useBondAlgorithm ? MODE_BONDING : MODE_RADIUS);
- AtomIndexIterator iter = (buildMode == MODE_RADIUS ? ms
- .getSelectedAtomIterator(null, false, false, false, false) : null);
- for (int i = centers.nextSetBit(0); i >= 0; i = centers.nextSetBit(i + 1))
{
- Atom atom = atoms[i];
- Polyhedron p = null;
- switch (buildMode) {
- case MODE_BITSET:
- p = constructBitSetPolyhedron(atom);
- break;
- case MODE_UNITCELL:
- p = constructUnitCellPolygon(atom, useBondAlgorithm);
- break;
- case MODE_BONDING:
- p = constructBondsPolyhedron(atom, 0);
- break;
- case MODE_RADIUS:
- vwr.setIteratorForAtom(iter, i, radius);
- p = constructRadiusPolyhedron(atom, iter);
- break;
- case MODE_INFO:
- p = new Polyhedron().setInfo(info, vwr.ms.at);
- break;
- case MODE_POINTS:
- p = validatePolyhedron(atom, nPoints);
- break;
+ Polyhedron p = null;
+ if (center != null) {
+ p = validatePolyhedron(center, nPoints);
+ if (p != null)
+ addPolyhedron(p);
+ } else {
+ boolean useBondAlgorithm = radius == 0 || bondedOnly;
+ int buildMode = (info != null ? MODE_INFO : nPoints > 0 ? MODE_POINTS
+ : haveBitSetVertices ? MODE_BITSET : useUnitCell ? MODE_UNITCELL
+ : useBondAlgorithm ? MODE_BONDING : MODE_RADIUS);
+ AtomIndexIterator iter = (buildMode == MODE_RADIUS ? ms
+ .getSelectedAtomIterator(null, false, false, false, false) : null);
+ for (int i = centers.nextSetBit(0); i >= 0; i = centers.nextSetBit(i +
1)) {
+ Atom atom = atoms[i];
+ p = null;
+ switch (buildMode) {
+ case MODE_BITSET:
+ p = constructBitSetPolyhedron(atom);
+ break;
+ case MODE_UNITCELL:
+ p = constructUnitCellPolygon(atom, useBondAlgorithm);
+ break;
+ case MODE_BONDING:
+ p = constructBondsPolyhedron(atom, 0);
+ break;
+ case MODE_RADIUS:
+ vwr.setIteratorForAtom(iter, i, radius);
+ p = constructRadiusPolyhedron(atom, iter);
+ break;
+ case MODE_INFO:
+ p = new Polyhedron().setInfo(info, vwr.ms.at);
+ break;
+ case MODE_POINTS:
+ p = validatePolyhedron(atom, nPoints);
+ break;
+ }
+ if (p != null)
+ addPolyhedron(p);
+ if (haveBitSetVertices)
+ break;
}
- if (p != null) {
- if (polyhedronCount == polyhedrons.length)
- polyhedrons = (Polyhedron[]) AU.doubleLength(polyhedrons);
- polyhedrons[polyhedronCount++] = p;
- }
- if (haveBitSetVertices)
- break;
+ if (iter != null)
+ iter.release();
}
- if (iter != null)
- iter.release();
}
+ private void addPolyhedron(Polyhedron p) {
+ if (polyhedronCount == polyhedrons.length)
+ polyhedrons = (Polyhedron[]) AU.doubleLength(polyhedrons);
+ polyhedrons[polyhedronCount++] = p;
+ }
+
private Polyhedron constructBondsPolyhedron(Atom atom, int otherAtomCount) {
if (otherAtomCount == 0) {
Bond[] bonds = atom.bonds;
@@ -593,7 +629,7 @@
otherAtomCount));
}
- private Polyhedron validatePolyhedron(Atom centralAtom, int vertexCount) {
+ private Polyhedron validatePolyhedron(P3 atomOrPt, int vertexCount) {
P3[] points = otherAtoms;
boolean collapsed = isCollapsed;
int triangleCount = 0;
@@ -603,8 +639,8 @@
float planarParam = (Float.isNaN(this.planarParam) ? DEFAULT_PLANAR_PARAM
: this.planarParam);
- points[vertexCount] = centralAtom;
- P3 ptAve = P3.newP(centralAtom);
+ points[vertexCount] = atomOrPt;
+ P3 ptAve = P3.newP(atomOrPt);
for (int i = 0; i < vertexCount; i++)
ptAve.add(points[i]);
ptAve.scale(1f / (vertexCount + 1));
@@ -674,7 +710,7 @@
bsCenterPlanes.set(triangleCount++);
} else if (collapsed) {
ptRef.setT(points[nPoints] = new P3());
- points[nPoints].scaleAdd2(offset, normal, centralAtom);
+ 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,
@@ -695,7 +731,7 @@
Logger.info("Polyhedron " + PT.toJSON("face[" +i + "]", triangles[i]));
}
//System.out.println(PT.toJSON(null, htEdgeMap));
- return new Polyhedron().set(centralAtom, points, nPoints, vertexCount,
+ return new Polyhedron().set(thisID, atomOrPt, points, nPoints, vertexCount,
triangles, triangleCount, getFaces(triangles, triangleCount,
htNormMap), normals, bsCenterPlanes, collapsed, distanceRef);
}
@@ -777,6 +813,8 @@
}
V3 norm = normals[index];
Integer normix = Integer.valueOf(Normix.getNormixV(norm, bsTemp));
+ //if (normix != 629)
+ //return false;
Object[] o = htNormMap.get(normix);
//System.out.println(PT.toJSON(null, p1) + " " + normix);
if (o == null) {
@@ -837,6 +875,7 @@
String edge = normix + s + s1;
if (htEdgeMap.containsKey(edge))
return false;
+ // System.out.println(edge);
//reverse maps are in
String edge0 = normix + s1 + s;
Object o = htEdgeMap.get(edge0);
@@ -867,6 +906,8 @@
} else {
// set mask to exclude both of these.
int[] p10 = (int[]) ((Object[]) o)[0];
+ if (p10 == null)
+ return false; // already seen
int i0 = ((Integer) ((Object[]) o)[1]).intValue();
p10[3] = -((-p10[3]) ^ (1 << i0));
p1[3] = -((-p1[3]) ^ (1 << i));
@@ -879,6 +920,8 @@
}
}
// not supported for JavaScript faceList.removeObj(b);
+ htEdgeMap.put(edge, new Object[] {null});
+ htEdgeMap.put(edge0, new Object[] {null});
}
return true;
}
@@ -952,13 +995,17 @@
*/
for (int i = polyhedronCount; --i >= 0;) {
Polyhedron p = polyhedrons[i];
- if (ms.at[p.centralAtom.i].isDeleted())
- p.isValid = false;
- p.visibilityFlags = (p.visible && bsModels.get(p.centralAtom.mi)
- && !ms.isAtomHidden(p.centralAtom.i)
- && !ms.at[p.centralAtom.i].isDeleted() ? vf : 0);
- if (p.visibilityFlags != 0)
- setShapeVisibility(atoms[p.centralAtom.i], true);
+ if (p.id != null) {
+ p.visibilityFlags = (p.visible ? vf : 0);
+ } else {
+ if (ms.at[p.centralAtom.i].isDeleted())
+ p.isValid = false;
+ p.visibilityFlags = (p.visible && bsModels.get(p.centralAtom.mi)
+ && !ms.isAtomHidden(p.centralAtom.i)
+ && !ms.at[p.centralAtom.i].isDeleted() ? vf : 0);
+ if (p.visibilityFlags != 0)
+ setShapeVisibility(atoms[p.centralAtom.i], true);
+ }
}
}
@@ -977,7 +1024,7 @@
s.append(vwr.getAtomShapeState(this));
for (int i = 0; i < polyhedronCount; i++) {
Polyhedron p = polyhedrons[i];
- if (p.isValid && p.colixEdge != C.INHERIT_ALL
+ if (p.isValid && p.id == null && p.colixEdge != C.INHERIT_ALL
&& bsColixSet.get(p.centralAtom.i))
appendCmd(
s,
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-10-17
23:45:49 UTC (rev 20836)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-10-19
06:22:30 UTC (rev 20837)
@@ -48,14 +48,19 @@
public boolean isValid = true;
public short colixEdge = C.INHERIT_ALL;
public int visibilityFlags = 0;
+ P3 center;
+ public String id;
Polyhedron() {
}
- Polyhedron set(Atom centralAtom, P3[] points, int nPoints, int vertexCount,
+ Polyhedron set(String id, P3 atomOrPt, P3[] points, int nPoints, int
vertexCount,
int[][] triangles, int triangleCount, int[][] faces, V3[] normals, BS
bsFlat, boolean collapsed, float distanceRef) {
+
this.distanceRef = distanceRef;
- this.centralAtom = centralAtom;
+ centralAtom = (id == null ? (Atom) atomOrPt : null);
+ center = (centralAtom == null ? (P3) atomOrPt : null);
+ this.id = id;
this.nVertices = vertexCount;
this.vertices = new P3[nPoints + 1];
this.normals = new V3[triangleCount];
@@ -76,7 +81,11 @@
Polyhedron setInfo(Map<String, SV> info, Atom[] at) {
try {
collapsed = info.containsKey("collapsed");
- centralAtom = at[info.get("atomIndex").intValue];
+ center = (info.containsKey("center") ? P3.newP(SV.ptValue(info
+ .get("center"))) : null);
+ if (center == null) {
+ centralAtom = at[info.get("atomIndex").intValue];
+ }
Lst<SV> lst = info.get("vertices").getList();
SV vc = info.get("vertexCount");
if (vc == null) {
@@ -141,6 +150,7 @@
}
Map<String, Object> info;
+ public short colix;
Map<String, Object> getInfo(Viewer vwr, boolean isAll) {
if (isAll && this.info != null && !Logger.debugging)
@@ -151,8 +161,10 @@
info.put("modelIndex", Integer.valueOf(centralAtom.mi));
info.put("modelNumber", Integer.valueOf(centralAtom.getModelNumber()));
info.put("center", P3.newP(centralAtom));
- info.put("atomNumber", Integer.valueOf(centralAtom.getAtomNumber()));
- info.put("atomName", centralAtom.getInfo());
+ if (center == null) {
+ info.put("atomNumber", Integer.valueOf(centralAtom.getAtomNumber()));
+ info.put("atomName", centralAtom.getInfo());
+ }
info.put("element", centralAtom.getElementSymbol());
info.put("triangleCount", Integer.valueOf(triangles.length));
info.put("volume", getVolume());
@@ -193,7 +205,12 @@
info.put("triangles", AU.arrayCopyII(triangles, triangles.length));
}
info.put("vertexCount", Integer.valueOf(nVertices));
- info.put("atomIndex", Integer.valueOf(centralAtom.i));
+ if (center == null) {
+ info.put("atomIndex", Integer.valueOf(centralAtom.i));
+ } else {
+ info.put("id", id);
+ info.put("center", P3.newP(center));
+ }
info.put("vertices",
AU.arrayCopyPt(vertices, (isAll ? nVertices : vertices.length)));
int[] elemNos = new int[nVertices];
@@ -207,6 +224,8 @@
}
String getSymmetry(Viewer vwr, boolean withPointGroup) {
+ if (id != null)
+ return "";
info = null;
SmilesMatcherInterface sm = vwr.getSmilesMatcher();
try {
@@ -261,9 +280,10 @@
}
String getState(Viewer vwr) {
+ String ident = (id == null ? "({"+centralAtom.i+"})" : "ID " +
Escape.e(id));
return " polyhedron @{" + Escape.e(getInfo(vwr, false)) + "} "
+ (isFullyLit ? " fullyLit" : "") + ";"
- + (visible ? "" : "polyhedra ({"+centralAtom.i+"}) off;") + "\n";
+ + (visible ? "" : "polyhedra " + ident + " off;") + "\n";
}
public void move(M4 mat) {
@@ -289,4 +309,5 @@
}
return normixes;
}
+
}
Modified: trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2015-10-17
23:45:49 UTC (rev 20836)
+++ trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2015-10-19
06:22:30 UTC (rev 20837)
@@ -222,7 +222,7 @@
return;
String id = currentMesh.thisID;
int imodel = currentMesh.modelIndex;
- vwr.cachePut("cache://isosurface_" + id, getPropI("jvxlDataXml"));
+ vwr.cachePut("cache://isosurface_" + id, getPropI("jvxlDataXml", -1));
deleteMeshI(currentMesh.index);
setPropI("init", null, null);
setPropI("thisID", id, null);
@@ -782,18 +782,24 @@
sg.setJvxlData(jvxlData);
}
+
@SuppressWarnings("unchecked")
@Override
public boolean getPropertyData(String property, Object[] data) {
+ if (property == "keys") {
+ Lst<String> keys = (data[1] instanceof Lst<?> ? (Lst<String>) data[1] :
new Lst<String>());
+ data[1] = keys;
+ keys.addLast("info");
+ keys.addLast("data");
+ // will continue on to super
+ }
if (property == "colorEncoder") {
IsosurfaceMesh mesh = (IsosurfaceMesh) getMesh((String) data[0]);
- if (mesh == null || (data[1] = mesh.colorEncoder) == null)
- return false;
- return true;
+ return (mesh != null && (data[1] = mesh.colorEncoder) != null);
}
if (property == "intersectPlane") {
IsosurfaceMesh mesh = (IsosurfaceMesh) getMesh((String) data[0]);
- if (mesh == null)
+ if (mesh == null || data.length < 4)
return false;
data[3] = Integer.valueOf(mesh.modelIndex);
mesh.getMeshSlicer().getIntersection(0, (P4) data[1], null, (Lst<P3[]>)
data[2], null, null, null, false, false, T.plane, false);
@@ -847,13 +853,16 @@
@Override
public Object getProperty(String property, int index) {
- return getPropI(property);
+ return getPropI(property, index);
}
- protected Object getPropI(String property) {
- Object ret = getPropMC(property);
+ protected Object getPropI(String property, int index) {
+ IsosurfaceMesh thisMesh = this.thisMesh;
+ if (index >= 0 && (index >= meshCount || (thisMesh = isomeshes[index]) ==
null))
+ return null;
+ Object ret = getPropMC(property, index);
if (ret != null)
- return ret;
+ return ret;
if (property == "message") {
String s = "";
if (shapeID == JC.SHAPE_ISOSURFACE)
@@ -861,13 +870,13 @@
if (jvxlData.dataMin != Float.MAX_VALUE)
s += " min=" + jvxlData.dataMin + " max=" + jvxlData.dataMax;
s += "; " + JC.shapeClassBases[shapeID].toLowerCase() + " count: "
- + getPropMC("count");
- return s + getPropI("dataRangeStr") + jvxlData.msg;
+ + getPropMC("count", index);
+ return s + getPropI("dataRangeStr", index) + jvxlData.msg;
}
if (property == "dataRange")
- return getDataRange();
+ return getDataRange(thisMesh);
if (property == "dataRangeStr") {
- float[] dataRange = getDataRange();
+ float[] dataRange = getDataRange(thisMesh);
return (dataRange != null && dataRange[0] != Float.MAX_VALUE
&& dataRange[0] != dataRange[1] ? "\nisosurface"
+ " full data range " + dataRange[0] + " to " + dataRange[1]
@@ -881,9 +890,9 @@
if (property == "nSets")
return Integer.valueOf(thisMesh == null ? 0 : thisMesh.nSets);
if (property == "area") // could be Float or double[]
- return (thisMesh == null ? Float.valueOf(Float.NaN) :
calculateVolumeOrArea(true));
+ return (thisMesh == null ? Float.valueOf(Float.NaN) :
calculateVolumeOrArea(thisMesh, true));
if (property == "volume") // could be Float or double[]
- return (thisMesh == null ? Float.valueOf(Float.NaN) :
calculateVolumeOrArea(false));
+ return (thisMesh == null ? Float.valueOf(Float.NaN) :
calculateVolumeOrArea(thisMesh, false));
if (thisMesh == null)
return null;//"no current isosurface";
if (property == "cutoff")
@@ -899,7 +908,7 @@
jvxlData.slabInfo = null;
if (property == "jvxlMeshXml" || jvxlData.vertexDataOnly ||
thisMesh.bsSlabDisplay != null && thisMesh.bsSlabGhost == null) {
meshData = new MeshData();
- fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
+ fillMeshData(meshData, MeshData.MODE_GET_VERTICES, thisMesh);
meshData.polygonColorData = getPolygonColorData(meshData.pc,
meshData.pcs, (meshData.colorsExplicit ? meshData.pis : null),
meshData.bsSlabDisplay);
} else if (thisMesh.bsSlabGhost != null) {
jvxlData.slabInfo = thisMesh.slabOptions.toString();
@@ -915,7 +924,7 @@
}
if (property == "command") {
SB sb = new SB();
- Lst<Mesh> list = getMeshList(previousMeshID, false);
+ Lst<Mesh> list = getMeshList((index < 0 ? previousMeshID :
thisMesh.thisID), false);
for (int i = list.size(); --i >= 0;)
getMeshCommand(sb, i);
return sb.toString();
@@ -923,41 +932,34 @@
return null;
}
- private float[] getDataRange() {
- return (thisMesh == null || jvxlData.jvxlPlane != null
- && thisMesh.colorEncoder == null ? null : new float[] {
- jvxlData.mappedDataMin,
- jvxlData.mappedDataMax,
- (jvxlData.isColorReversed ? jvxlData.valueMappedToBlue
- : jvxlData.valueMappedToRed),
- (jvxlData.isColorReversed ? jvxlData.valueMappedToRed
- : jvxlData.valueMappedToBlue) });
+ private float[] getDataRange(IsosurfaceMesh mesh) {
+ return (mesh == null ? null : mesh.getDataRange());
}
- private Object calculateVolumeOrArea(boolean isArea) {
+ private Object calculateVolumeOrArea(IsosurfaceMesh mesh, boolean isArea) {
if (isArea) {
- if (thisMesh.calculatedArea != null)
- return thisMesh.calculatedArea;
+ if (mesh.calculatedArea != null)
+ return mesh.calculatedArea;
} else {
- if (thisMesh.calculatedVolume != null)
- return thisMesh.calculatedVolume;
+ if (mesh.calculatedVolume != null)
+ return mesh.calculatedVolume;
}
MeshData meshData = new MeshData();
- fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
- meshData.nSets = thisMesh.nSets;
- meshData.vertexSets = thisMesh.vertexSets;
- if (!isArea && thisMesh.jvxlData.colorDensity) {
- float f = thisMesh.jvxlData.voxelVolume;
- f *= (thisMesh.bsSlabDisplay == null ? thisMesh.vc :
thisMesh.bsSlabDisplay.cardinality());
- return thisMesh.calculatedVolume = Float.valueOf(f);
+ fillMeshData(meshData, MeshData.MODE_GET_VERTICES, mesh);
+ meshData.nSets = mesh.nSets;
+ meshData.vertexSets = mesh.vertexSets;
+ if (!isArea && mesh.jvxlData.colorDensity) {
+ float f = mesh.jvxlData.voxelVolume;
+ f *= (mesh.bsSlabDisplay == null ? mesh.vc :
mesh.bsSlabDisplay.cardinality());
+ return mesh.calculatedVolume = Float.valueOf(f);
}
- Object ret = MeshData.calculateVolumeOrArea(meshData,
thisMesh.jvxlData.thisSet, isArea, false);
- if (thisMesh.nSets <= 0)
- thisMesh.nSets = -meshData.nSets;
+ Object ret = MeshData.calculateVolumeOrArea(meshData,
mesh.jvxlData.thisSet, isArea, false);
+ if (mesh.nSets <= 0)
+ mesh.nSets = -meshData.nSets;
if (isArea)
- thisMesh.calculatedArea = ret;
+ mesh.calculatedArea = ret;
else
- thisMesh.calculatedVolume = ret;
+ mesh.calculatedVolume = ret;
return ret;
}
Modified: trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2015-10-17
23:45:49 UTC (rev 20836)
+++ trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2015-10-19
06:22:30 UTC (rev 20837)
@@ -1003,4 +1003,15 @@
recalcAltVertices = true;
}
+ float[] getDataRange() {
+ return (jvxlData.jvxlPlane != null
+ && colorEncoder == null ? null : new float[] {
+ jvxlData.mappedDataMin,
+ jvxlData.mappedDataMax,
+ (jvxlData.isColorReversed ? jvxlData.valueMappedToBlue
+ : jvxlData.valueMappedToRed),
+ (jvxlData.isColorReversed ? jvxlData.valueMappedToRed
+ : jvxlData.valueMappedToBlue) });
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java 2015-10-17
23:45:49 UTC (rev 20836)
+++ trunk/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java 2015-10-19
06:22:30 UTC (rev 20837)
@@ -315,11 +315,11 @@
@SuppressWarnings("unchecked")
@Override
- public Object getProperty(String propertyName, int param) {
+ public Object getProperty(String propertyName, int index) {
if (propertyName.startsWith("list")) {
String s = "";
if (propertyName.equals("list")) {
- s = (String) getPropI("list");
+ s = (String) getPropI("list", index);
if (s.length() > 1)
s += "cutoff = " + jvxlData.cutoff + "\n";
s = "\n" + s;
@@ -335,7 +335,7 @@
Lst<Map<String, Object>> mos = (Lst<Map<String, Object>>)
(sg.params.moData
.get("mos"));
int nOrb = (mos == null ? 0 : mos.size());
- int thisMO = param;
+ int thisMO = index;
int currentMO = moNumber;
boolean isShowCurrent = (thisMO == Integer.MIN_VALUE);
if (thisMO == Integer.MAX_VALUE) {
@@ -374,7 +374,7 @@
true, 0, null, null));
return str.toString();
}
- return getPropI(propertyName);
+ return getPropI(propertyName, index);
}
@SuppressWarnings("unchecked")
Modified: trunk/Jmol/src/org/jmol/shapesurface/Pmesh.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/Pmesh.java 2015-10-17 23:45:49 UTC
(rev 20836)
+++ trunk/Jmol/src/org/jmol/shapesurface/Pmesh.java 2015-10-19 06:22:30 UTC
(rev 20837)
@@ -24,10 +24,106 @@
package org.jmol.shapesurface;
+import java.util.Hashtable;
+import java.util.Map;
+
+import org.jmol.shape.Mesh;
+
+import javajs.util.Measure;
+import javajs.util.P3;
+import javajs.util.T3;
+import javajs.util.V3;
+
public class Pmesh extends Isosurface {
@Override
public void initShape() {
super.initShape();
myType = "pmesh";
}
+
+ @Override
+ public Object getProperty(String property, int index) {
+ if (property == "face") {
+ Mesh m = currentMesh;
+ if (index >= 0
+ && (index >= meshCount || (m = meshes[index]) == null))
+ return null;
+ return m == null ? null : getFace(m);
+ }
+ return getPropI(property, index);
+ }
+
+ /**
+ * return a cycle of points generating this face
+ * used after slabbing
+ *
+ * @param m
+ * @return set of points constituting this face
+ */
+ private P3[] getFace(Mesh m) {
+ if (m.haveQuads)
+ return null;
+ T3[] vs = m.vs;
+ Map<String, int[]> htEdges = new Hashtable<String, int[]>();
+ int v1 = 0;
+ int n = 0;
+ for (int i = m.pc; --i >= 0;) {
+ if (m.bsSlabDisplay != null && !m.bsSlabDisplay.get(i))
+ continue;
+ int[] face = m.pis[i];
+ int mask = face[3];
+ for (int j = 0; j < 3; j++)
+ if ((mask & (1 << j)) != 0) {
+ v1 = face[j];
+ int v2 = face[(j + 1) % 3];
+ String key = v2 + "_" + v1;
+ if (htEdges.containsKey(key)) {
+ htEdges.remove(key);
+ n--;
+ } else {
+ n++;
+ htEdges.put(v1 + "_" + v2, new int[] { v1, v2 });
+ htEdges.put("" + v1, new int[] { v1, v2 });
+ }
+ }
+ }
+ if (n == 0)
+ return null;
+ int[][] a = new int[n][2];
+ for (String e : htEdges.keySet()) {
+ a[0] = htEdges.get(e);
+ break;
+ }
+ V3 vectorBA = new V3();
+ V3 vectorBC = new V3();
+ int v0 = a[0][0];
+ int v01 = v0;
+ v1 = a[0][1];
+ int pt = 0;
+ while (v1 != v0) {
+ int[] edge = htEdges.get("" + v1);
+ if (edge == null)
+ break;
+ float angle = Measure.computeAngle(vs[v01], vs[v1], vs[edge[1]],
+ vectorBA, vectorBC, true);
+ v1 = edge[1];
+ if (angle < 179) {
+ a[++pt] = edge;
+ v01 = edge[0];
+ } else {
+ a[pt][1] = v1;
+ }
+ }
+ if (Measure.computeAngle(vs[v01], vs[v1], vs[a[0][1]],
+ vectorBA, vectorBC, true) >= 179) {
+ a[0][0] = a[pt--][0];
+ }
+ n = ++pt;
+ P3[] pts = new P3[n];
+ for (int i = 0; i < n; i++)
+ pts[i] = P3.newP(vs[a[i][0]]);
+ return pts;
+ }
+
+
}
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-10-17 23:45:49 UTC
(rev 20836)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-10-19 06:22:30 UTC
(rev 20837)
@@ -318,12 +318,12 @@
@Override
public int[] getCellRange() {
- return symmetryInfo.cellRange;
+ return symmetryInfo == null ? null : symmetryInfo.cellRange;
}
@Override
public String getSymmetryInfoStr() {
- return symmetryInfo.infoStr;
+ return (symmetryInfo == null ? "" : symmetryInfo.infoStr);
}
@Override
Modified: trunk/Jmol/src/org/jmol/util/MeshCapper.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/MeshCapper.java 2015-10-17 23:45:49 UTC
(rev 20836)
+++ trunk/Jmol/src/org/jmol/util/MeshCapper.java 2015-10-19 06:22:30 UTC
(rev 20837)
@@ -85,6 +85,8 @@
private Lst<int[]> lstTriangles;
+ private int nPoints;
+
/////////////// initialization //////////////////
/**
@@ -107,21 +109,22 @@
* generic entry for a polygon
*
* @param points
- * @return int[][i j k 7]
+ * @return int[][i j k mask]
*/
public int[][] triangulatePolygon(P3[] points) {
clear();
-
- int n = points.length;
+ // this is winding backward
+ nPoints = points.length;
CapVertex v0 = null;
- for (int i = 0; i < n; i++) {
+ for (int i = 0; i < nPoints; i++) {
CapVertex v = new CapVertex(points[i], i);
vertices.addLast(v);
- if (v0 != null)
- v.link(v0);
+ if (v0 != null) {
+ v0.link(v);
+ }
v0 = v;
}
- vertices.get(0).link(v0);
+ v0.link(vertices.get(0));
lstTriangles = new Lst<int[]>();
createCap(null);
int[][] a = AU.newInt2(lstTriangles.size());
@@ -188,12 +191,24 @@
* @param ipt3
*/
private void outputTriangle(int ipt1, int ipt2, int ipt3) {
- if (slicer == null)
- lstTriangles.addLast(new int[] { ipt1, ipt2, ipt3, 7 });
- else
+ if (slicer == null) {
+ int mask = 0;
+ if (isEdge(ipt1, ipt2))
+ mask |= 1;
+ if (isEdge(ipt2, ipt3))
+ mask |= 2;
+ if (isEdge(ipt3, ipt1))
+ mask |= 4;
+ lstTriangles.addLast(new int[] { ipt1, ipt2, ipt3, mask });
+ } else {
slicer.addTriangle(ipt1, ipt2, ipt3);
+ }
}
+ private boolean isEdge(int i, int j) {
+ return (j == (i + 1) % nPoints);
+ }
+
private CapVertex[] test(CapVertex[] vs) {
// dumping = testing = true;
// int n = 0;
@@ -242,7 +257,7 @@
V3 vab = V3.newVsub(vertices.get(0), vertices.get(1));
V3 vac;
if (norm == null) {
- vac = V3.newVsub(vertices.get(vertices.size() - 1), vertices.get(0));
+ vac = V3.newVsub(vertices.get(0), vertices.get(vertices.size() - 1));
} else {
vac = V3.newV(norm);
vac.cross(vac, vab);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-17 23:45:49 UTC
(rev 20836)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-19 06:22:30 UTC
(rev 20837)
@@ -62,8 +62,16 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.0_2015.10.17"
+TODO: working on ID for polyhedra without atom refs
+Jmol.___JmolVersion="14.4.0_2015.10.18"
+
+bug fix: Polyhedra can have missing triangle for hexagonal faces
+bug fix: calculate symmetry can break Jmol if unit cell has been changed
+bug fix: DRAW POLYGON front/back nature of winding was reversed.
+
+JmolVersion="14.5.0_2015.10.17"
+
bug fix: if (...) \n { .... not working
bug fix: CIF reader will read empty second model for IUCr files with terminal
data_global block
bug fix: polyhedra bonds unitcell can cause error in HTML5
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-10-17 23:45:49 UTC
(rev 20836)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-10-19 06:22:30 UTC
(rev 20837)
@@ -779,9 +779,9 @@
params.indexOf("g64") < 0 && params.indexOf("base64") < 0
&& (returnType == null || returnType.equalsIgnoreCase("java")));
case PROP_ISOSURFACE_INFO:
- return vwr.getShapeProperty(JC.SHAPE_ISOSURFACE, "getInfo");
+ return vwr.getShapeProperty(JC.SHAPE_ISOSURFACE, "info");
case PROP_ISOSURFACE_DATA:
- return vwr.getShapeProperty(JC.SHAPE_ISOSURFACE, "getData");
+ return vwr.getShapeProperty(JC.SHAPE_ISOSURFACE, "data");
case PROP_NMR_INFO:
return vwr.getNMRCalculation().getInfo(myParam.toString());
case PROP_VAR_INFO:
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