Revision: 20840
http://sourceforge.net/p/jmol/code/20840
Author: hansonr
Date: 2015-10-20 22:41:32 +0000 (Tue, 20 Oct 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.0_2015.10.20"
new feature: polyhedra with arbitrary center and vertices, without atom center
-- for example:
polyhedra ID "myid" {0 0 0} TO [{1 0 0}, {0 1 0}, {0 0 1}, {-1 -1 -1}]
bug fix: set platformSpeed 1 for pmesh fails
bug fix: polyhedron EDGES fails
bug fix: @{ {"hash":{0.1 0.1 0.1},...} } fails (attempts to turn "," into "OR")
-- solution is to not allow "," for OR within associative arrays
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/render/MeshRenderer.java
trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/render/MeshRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/MeshRenderer.java 2015-10-20 22:40:08 UTC
(rev 20839)
+++ trunk/Jmol/src/org/jmol/render/MeshRenderer.java 2015-10-20 22:41:32 UTC
(rev 20840)
@@ -290,7 +290,7 @@
protected void renderPoints() {
if (!mesh.isTriangleSet || mesh.pc < 0) {
for (int i = vertexCount; --i >= 0;)
- if (!frontOnly || normixes == null ||
transformedVectors[normixes[i]].z >= 0)
+ if (!frontOnly || normixes == null || isVisibleNormix(normixes[i]))
drawPoint(i, false);
return;
}
@@ -304,7 +304,7 @@
if (!isPolygonDisplayable(i))
continue;
int[] p = polygonIndexes[i];
- if (frontOnly && transformedVectors[normixes[i]].z < 0)
+ if (frontOnly && !isVisibleNormix(normixes[i]))
continue;
for (int j = p.length - 1; --j >= 0;) {
int pt = p[j];
@@ -370,7 +370,7 @@
int check;
if (mesh.isTriangleSet) {
short normix = normixes[i];
- if (!vwr.gdata.isDirectedTowardsCamera(normix))
+ if (frontOnly && !isVisibleNormix(normix))
continue;
if (fill) {
if (isPrecision)
@@ -458,6 +458,10 @@
exportSurface(colix);
}
+ private boolean isVisibleNormix(short normix) {
+ return (normix < 0 || transformedVectors[normix].z > 0);
+ }
+
private void drawTriangleBits(P3 screenA, short colixA, P3 screenB, short
colixB,
P3 screenC, short colixC, int check, int diam)
{
if (!antialias && diam == 1) {
Modified: trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
2015-10-20 22:40:08 UTC (rev 20839)
+++ trunk/Jmol/src/org/jmol/renderspecial/PolyhedraRenderer.java
2015-10-20 22:41:32 UTC (rev 20840)
@@ -67,11 +67,16 @@
if (p.visibilityFlags == 0)
return false;
short[] colixes = ((Polyhedra) shape).colixes;
- int iAtom = (p.id == null ? p.centralAtom.i : -1);
- short colix = (p.id != null ? p.colix : colixes == null || iAtom >=
colixes.length ? C.INHERIT_ALL
+ int iAtom = -1;
+ short colix;
+ if (p.id == null) {
+ iAtom = p.centralAtom.i;
+ colix = (colixes == null || iAtom >= colixes.length ? C.INHERIT_ALL
: colixes[iAtom]);
- if (p.centralAtom != null)
colix = C.getColixInherited(colix, p.centralAtom.colixAtom);
+ } else {
+ colix = p.colix;
+ }
boolean needTranslucent = false;
if (C.renderPass2(colix)) {
needTranslucent = true;
@@ -115,14 +120,13 @@
if (!needTranslucent || g3d.setC(colix))
for (int i = planes.length; --i >= 0;) {
int[] pl = planes[i];
- //if (i != m)continue;
try {
g3d.fillTriangleTwoSided(normixes[i], sc[pl[0]], sc[pl[1]],
sc[pl[2]]);
} catch (Exception e) {
- System.out.println("heorhe");
+ System.out.println("PolyhedraRendererError");
}
- if (pl[3] >= 0)
- g3d.fillTriangleTwoSided(normixes[i], sc[pl[2]], sc[pl[3]],
sc[pl[0]]);
+// if (pl[3] >= 0)
+ // g3d.fillTriangleTwoSided(normixes[i], sc[pl[2]], sc[pl[3]],
sc[pl[0]]);
}
// edges are not drawn translucently ever
if (bsSelected != null && bsSelected.get(iAtom))
@@ -132,18 +136,19 @@
if (g3d.setC(C.getColixTranslucent3(colix, false, 0)))
for (int i = planes.length; --i >= 0;) {
int[] pl = planes[i];
- if (pl[3] < 0) {
- drawFace(normixes[i], sc[pl[0]], sc[pl[1]], sc[pl[2]], -pl[3]);
- } else {
- drawFace(normixes[i], sc[pl[0]], sc[pl[1]], sc[pl[2]], 3);
- drawFace(normixes[i], sc[pl[0]], sc[pl[2]], sc[pl[3]], 6);
- }
+ // if (pl[3] < 0) {
+ drawEdges(normixes[i], sc[pl[0]], sc[pl[1]], sc[pl[2]], -pl[3]);
+// break;
+// } else {
+// drawFace(normixes[i], sc[pl[0]], sc[pl[1]], sc[pl[2]], 3);
+// drawFace(normixes[i], sc[pl[0]], sc[pl[2]], sc[pl[3]], 6);
+// }
}
return needTranslucent;
}
- private void drawFace(short normix, P3 a, P3 b, P3 c, int edgeMask) {
+ private void drawEdges(short normix, P3 a, P3 b, P3 c, int edgeMask) {
if (isAll || frontOnly && vwr.gdata.isDirectedTowardsCamera(normix)) {
int d = (g3d.isAntialiased() ? 6 : 3);
if ((edgeMask & 1) == 1)
Modified: trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java 2015-10-20
22:40:08 UTC (rev 20839)
+++ trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java 2015-10-20
22:41:32 UTC (rev 20840)
@@ -422,7 +422,7 @@
boolean haveString;
- private boolean clauseOr(boolean allowComma) {
+ private boolean clauseOr(boolean allowCommaAsOr) {
haveString = false;
if (!clauseAnd())
return false;
@@ -433,14 +433,14 @@
//OrNot: First OR, but if that makes no change, then NOT (special toggle)
int tok;
while ((tok = tokPeek())== T.opOr || tok == T.opXor
- || tok==T.opToggle|| allowComma && tok == T.comma) {
+ || tok==T.opToggle|| allowCommaAsOr && tok == T.comma) {
if (tok == T.comma && !haveString)
addSubstituteTokenIf(T.comma, T.tokenOr);
else
addNextToken();
if (!clauseAnd())
return false;
- if (allowComma && (lastToken.tok == T.rightbrace || lastToken.tok ==
T.bitset))
+ if (allowCommaAsOr && (lastToken.tok == T.rightbrace || lastToken.tok ==
T.bitset))
haveString = true;
}
return true;
@@ -596,7 +596,7 @@
if (isExpressionNext()) {
addTokenToPostfixToken(T.o(T.expressionBegin,
"implicitExpressionBegin"));
- if (!clauseOr(true))
+ if (!clauseOr(false)) // changed to FALSE 10/20 because
@({"center":{0.0 0.0 0.0}, "xxx"...}} failed
return false;
if (lastToken != T.tokenCoordinateEnd) {
addTokenToPostfixToken(T.tokenExpressionEnd);
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-10-20 22:40:08 UTC
(rev 20839)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-10-20 22:41:32 UTC
(rev 20840)
@@ -3187,13 +3187,14 @@
* polyhedra [at most one selection set] [type-and/or-edge or
on/off/delete]
*/
boolean haveBonds = (slen == 1);
+ boolean haveCenter = false;
boolean needsGenerating = haveBonds;
boolean onOffDelete = false;
boolean typeSeen = false;
boolean edgeParameterSeen = false;
// int lighting = T.nada; // never implemented; fullyLit does nothing
int nAtomSets = 0;
- e.sm.loadShape(JC.SHAPE_POLYHEDRA);
+ eval.sm.loadShape(JC.SHAPE_POLYHEDRA);
setShapeProperty(JC.SHAPE_POLYHEDRA, "init", Boolean.TRUE);
float translucentLevel = Float.MAX_VALUE;
int[] colorArgb = new int[] { Integer.MIN_VALUE };
@@ -3208,6 +3209,8 @@
needsGenerating = true;
break;
case T.unitcell:
+ if (id != null)
+ invArg();
propertyName = "unitCell";
propertyValue = Boolean.TRUE;
needsGenerating = true;
@@ -3226,13 +3229,17 @@
onOffDelete = true;
break;
case T.integer:
+ if (id != null)
+ invArg();
propertyName = "nVertices";
propertyValue = Integer.valueOf(intParameter(i));
needsGenerating = true;
- if (tokAt(i + 1) == T.comma)
+ if (tokAt(i + 1) == T.comma)
i++;
break;
case T.bonds:
+ if (id != null)
+ invArg();
if (nAtomSets > 0)
invPO();
needsGenerating = true;
@@ -3243,6 +3250,8 @@
i++;
//$FALL-THROUGH$
case T.decimal:
+ if (id != null)
+ invArg();
if (nAtomSets > 0)
invPO();
propertyName = "radius";
@@ -3267,17 +3276,14 @@
}
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.model:
+ if (id == null)
+ invArg();
+ propertyName = "model";
+ propertyValue = Integer.valueOf(intParameter(++i));
+ break;
case T.to:
- if (nAtomSets > 1)
+ if (nAtomSets > 1 || id != null && !haveCenter)
invPO();
if ((tokAt(++i) == T.bitset || tokAt(i) == T.expressionBegin)
&& !needsGenerating) {
@@ -3301,6 +3307,8 @@
invPO();
switch (++nAtomSets) {
case 1:
+ if (id != null)
+ invArg();
propertyName = "centers";
break;
case 2:
@@ -3340,7 +3348,7 @@
if (edgeParameterSeen)
error(ScriptError.ERROR_incompatibleArguments);
edgeParameterSeen = true;
- propertyName = T.nameOf(eval.iToken);
+ propertyName = T.nameOf(eval.theTok);
break;
case T.triangles:
case T.notriangles:
@@ -3350,6 +3358,28 @@
// never implemented or
// lighting = eval.theTok;
continue;
+ case T.id:
+ case T.times:
+ case T.identifier:
+ if (!eval.isColorParam(i)) {
+ if (i != 1)
+ invPO();
+ setShapeProperty(
+ JC.SHAPE_POLYHEDRA,
+ "thisID",
+ id = (eval.theTok == T.id ? stringParameter(++i) : eval
+ .optParameterAsString(i)));
+ setShapeProperty(JC.SHAPE_POLYHEDRA, "model",
+ Integer.valueOf(vwr.am.cmi));
+ if (!eval.isCenterParameter(i + 1))
+ continue;
+ propertyName = "center";
+ propertyValue = centerParameter(++i);
+ i = eval.iToken;
+ haveCenter = true;
+ break;
+ }
+ //$FALL-THROUGH$
default:
if (eval.isColorParam(i)) {
colorArgb[0] = eval.getArgbParam(i);
@@ -3358,7 +3388,8 @@
}
invArg();
}
- setShapeProperty(JC.SHAPE_POLYHEDRA, propertyName, propertyValue);
+ if (propertyName != null)
+ setShapeProperty(JC.SHAPE_POLYHEDRA, propertyName, propertyValue);
if (onOffDelete)
return false;
}
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-10-20 22:40:08 UTC
(rev 20839)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-10-20 22:41:32 UTC
(rev 20840)
@@ -105,11 +105,13 @@
private float planarParam;
private Map<String, SV> info;
private float distanceRef;
+ private int modelIndex;
@SuppressWarnings("unchecked")
@Override
public void setProperty(String propertyName, Object value, BS bs) {
-
+ if (thisID != null)
+ bs = new BS();
if ("init" == propertyName) {
faceCenterOffset = DEFAULT_FACECENTEROFFSET;
//distanceFactor =
@@ -117,6 +119,7 @@
radius = 0.0f;
nVertices = 0;
nPoints = 0;
+ modelIndex = -1;
bsVertices = null;
thisID = null;
center = null;
@@ -141,13 +144,20 @@
return;
}
+ // thisID, center, and model all involve polyhedron ID ...
+
+ if ("thisID" == propertyName) {
+ thisID = (String) value;
+ return;
+ }
+
if ("center" == propertyName) {
center = (P3) value;
return;
}
- if ("id" == propertyName) {
- thisID = (String) value;
+ if ("model" == propertyName) {
+ modelIndex = ((Integer) value).intValue();
return;
}
@@ -224,7 +234,8 @@
if ("info" == propertyName) {
info = (Map<String, SV>) value;
- centers = BSUtil.newAndSetBit(info.get("atomIndex").intValue);
+ centers = (info.containsKey("center") ? null : BSUtil.newAndSetBit(info
+ .get("atomIndex").intValue));
iHaveCenterBitSet = true;
return;
}
@@ -264,23 +275,20 @@
// 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;) {
- Polyhedron p = polyhedrons[i];
- if (thisID != null) {
- if (thisID == p.id) {
- p.colixEdge = colixEdge;
- isActive = true;
- p.colix = C.getColixO(value);
- return;
- }
+ boolean isPhase = ("colorPhase" == propertyName);
+ Object cvalue = (isPhase ? ((Object[]) value)[1] : value);
+ short colixEdge = (isPhase ? C.getColix(((Integer) ((Object[]) value)[0])
+ .intValue()) : C.INHERIT_ALL);
+ short colix = C.getColixO(isPhase ? cvalue : value);
+ Polyhedron p;
+ BS bs1 = findPolyBS(bs);
+ for (int i = bs1.nextSetBit(0); i >= 0; i = bs1.nextSetBit(i + 1)) {
+ p = polyhedrons[i];
+ if (p.id == null) {
+ p.colixEdge = colixEdge;
} else {
- if (bs.get(p.centralAtom.i))
- p.colixEdge = colixEdge;
+ p.colixEdge = colixEdge;
+ p.colix = colix;
}
}
if (thisID != null)
@@ -293,6 +301,20 @@
if (propertyName.indexOf("translucency") == 0) {
// from polyhedra command, we may not be using the prior select
// but from Color we need to identify the centers.
+ boolean isTranslucent = (value.equals("translucent"));
+ if (thisID != null) {
+ BS bs1 = findPolyBS(bs);
+ Polyhedron p;
+ for (int i = bs1.nextSetBit(0); i >= 0; i = bs1.nextSetBit(i + 1)) {
+ p = polyhedrons[i];
+ p.colix = C.getColixTranslucent3(p.colix, isTranslucent,
+ translucentLevel);
+ if (p.colixEdge != 0)
+ p.colixEdge = C.getColixTranslucent3(p.colixEdge, isTranslucent,
+ translucentLevel);
+ }
+ return;
+ }
bs = ("translucentThis".equals(value) && iHaveCenterBitSet ? centers
: andBitSet(bs));
if (value.equals("translucentThis"))
@@ -318,8 +340,9 @@
if (propertyName == "deleteModelAtoms") {
int modelIndex = ((int[]) ((Object[]) value)[2])[0];
for (int i = polyhedronCount; --i >= 0;) {
- polyhedrons[i].info = null;
- int mi = polyhedrons[i].centralAtom.mi;
+ Polyhedron p = polyhedrons[i];
+ p.info = null;
+ int mi = (p.id == null ? p.centralAtom.mi : p.modelIndex);
if (mi == modelIndex) {
polyhedronCount--;
polyhedrons = (Polyhedron[]) AU.deleteElements(polyhedrons, i, 1);
@@ -344,29 +367,27 @@
@Override
public boolean getPropertyData(String property, Object[] data) {
- int iatom;
+ int iatom = (data[0] instanceof Integer ? ((Integer) data[0]).intValue()
+ : -1);
+ String id = (data[0] instanceof String ? (String) data[0] : null);
+ Polyhedron p;
+ if (property == "checkID") {
+ return checkID(id);
+ }
if (property == "points") {
- iatom = ((Integer) data[0]).intValue();
- for (int i = polyhedronCount; --i >= 0;) {
- if (polyhedrons[i].centralAtom.i == iatom) {
- if (polyhedrons[i].collapsed)
- break;
- data[1] = polyhedrons[i].vertices;
- return true;
- }
- }
- return false;
+ p = findPoly(id, iatom, false);
+ if (p == null)
+ return false;
+ data[1] = p.vertices;
+ return true;
}
if (property == "move") {
M4 mat = (M4) data[1];
if (mat == null)
return false;
- BS bs = (BS) data[0];
- for (int i = polyhedronCount; --i >= 0;) {
- Polyhedron p = polyhedrons[i];
- if (bs.get(p.centralAtom.i))
- p.move(mat);
- }
+ BS bs = findPolyBS((BS) data[0]);
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ polyhedrons[i].move(mat);
return true;
}
if (property == "centers") {
@@ -382,17 +403,20 @@
if (smiles != null && nv == 0)
nv = Integer.MIN_VALUE;
for (int i = polyhedronCount; --i >= 0;) {
- if (nv > 0 && polyhedrons[i].nVertices != nv || nv > Integer.MIN_VALUE
- && nv < 0 && polyhedrons[i].triangles.length != -nv)
+ p = polyhedrons[i];
+ if (p.id != null)
+ continue; // for now
+ if (nv > 0 && p.nVertices != nv || nv > Integer.MIN_VALUE && nv < 0
+ && p.triangles.length != -nv)
continue;
if (smiles == null) {
- bs.set(polyhedrons[i].centralAtom.i);
+ bs.set(p.centralAtom.i);
} else if (sm != null) {
- polyhedrons[i].getSymmetry(vwr, false);
- String smiles0 = polyhedrons[i].polySmiles;
+ p.getSymmetry(vwr, false);
+ String smiles0 = p.polySmiles;
try {
if (sm.areEqual(smiles, smiles0) > 0)
- bs.set(polyhedrons[i].centralAtom.i);
+ bs.set(p.centralAtom.i);
} catch (Exception e) {
e.printStackTrace();
}
@@ -404,23 +428,53 @@
if (property == "allInfo") {
Lst<Map<String, Object>> info = new Lst<Map<String, Object>>();
for (int i = polyhedronCount; --i >= 0;)
- info.addLast(polyhedrons[i].getInfo(vwr, true));
+ info.addLast(polyhedrons[i].getInfo(vwr, true));
data[1] = info;
- return false;
+ return true;
}
if (property == "info") {
- iatom = ((Integer) data[0]).intValue();
- for (int i = polyhedronCount; --i >= 0;) {
- if (polyhedrons[i].centralAtom.i == iatom) {
- data[1] = polyhedrons[i].getInfo(vwr, true);
- return true;
- }
- }
- return false;
+ p = findPoly(id, iatom, true);
+ if (p == null)
+ return false;
+ data[1] = p.getInfo(vwr, true);
+ return true;
}
return getPropShape(property, data);
}
+ private boolean checkID(String thisID) {
+ this.thisID = thisID;
+ return (findPolyBS(null).cardinality() > 0);
+ }
+
+ private Polyhedron findPoly(String id, int iatom, boolean allowCollapsed) {
+ for (int i = polyhedronCount; --i >= 0;) {
+ Polyhedron p = polyhedrons[i];
+ if (p.id == null ? p.centralAtom.i == iatom : p.id.equalsIgnoreCase(id))
+ return (allowCollapsed || !polyhedrons[i].collapsed ? polyhedrons[i] :
null);
+ }
+ return null;
+ }
+
+ private BS bsPolys = new BS();
+
+ private BS findPolyBS(BS bsCenters) {
+ BS bs = bsPolys;
+ bs.clearAll();
+ Polyhedron p;
+ for (int i = polyhedronCount; --i >= 0;) {
+ p = polyhedrons[i];
+ if (p.id == null ? bsCenters != null && bsCenters.get(p.centralAtom.i) :
isMatch(p.id))
+ bs.set(i);
+ }
+ return bs;
+ }
+
+ private boolean isMatch(String id) {
+ // could implement wildcards
+ return thisID != null && PT.isMatch(id.toLowerCase(),
thisID.toLowerCase(), true, true);
+ }
+
@Override
public Lst<Map<String, Object>> getShapeDetail() {
Lst<Map<String, Object>> lst = new Lst<Map<String, Object>>();
@@ -429,22 +483,13 @@
return lst;
}
-// private void setLighting(boolean isFullyLit, BS bs) {
-// for (int i = polyhedronCount; --i >= 0;)
-// if (bs.get(polyhedrons[i].centralAtom.i)) {
-// short[] normixes = polyhedrons[i].getNormixes();
-// polyhedrons[i].isFullyLit = isFullyLit;
-// for (int j = normixes.length; --j >= 0;) {
-// if (normixes[j] < 0 != isFullyLit)
-// normixes[j] = (short) ~normixes[j];
-// }
-// }
-// }
-
private BS andBitSet(BS bs) {
BS bsCenters = new BS();
- for (int i = polyhedronCount; --i >= 0;)
- bsCenters.set(polyhedrons[i].centralAtom.i);
+ for (int i = polyhedronCount; --i >= 0;) {
+ Polyhedron p = polyhedrons[i];
+ if (p.id == null)
+ bsCenters.set(p.centralAtom.i);
+ }
bsCenters.and(bs);
return bsCenters;
}
@@ -452,13 +497,15 @@
private void deletePolyhedra() {
int newCount = 0;
byte pid = PAL.pidOf(null);
+ BS bs = findPolyBS(centers);
for (int i = 0; i < polyhedronCount; ++i) {
Polyhedron p = polyhedrons[i];
- int iAtom = p.centralAtom.i;
- if (centers.get(iAtom))
- setColixAndPalette(C.INHERIT_ALL, pid, iAtom);
- else
- polyhedrons[newCount++] = p;
+ if (bs.get(i)) {
+ if (p.id == null)
+ setColixAndPalette(C.INHERIT_ALL, pid, p.centralAtom.i);
+ continue;
+ }
+ polyhedrons[newCount++] = p;
}
for (int i = newCount; i < polyhedronCount; ++i)
polyhedrons[i] = null;
@@ -466,58 +513,63 @@
}
private void setVisible(boolean visible) {
- for (int i = polyhedronCount; --i >= 0;) {
- Polyhedron p = polyhedrons[i];
- if (p != null && centers.get(p.centralAtom.i))
- p.visible = visible;
- }
+ BS bs = findPolyBS(centers);
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ polyhedrons[i].visible = visible;
}
private void buildPolyhedra() {
Polyhedron p = null;
- if (center != null) {
- p = validatePolyhedron(center, nPoints);
+ if (thisID != null) {
+ if (PT.isWild(thisID))
+ return;
+ if (center != null)
+ p = validatePolyhedron(center, nPoints);
+ } else if (info != null && info.containsKey("id")) {
+ thisID = info.get("id").asString();
+ p = new Polyhedron().setInfo(info, vwr.ms.at);
+ }
+ if (p != null) {
+ addPolyhedron(p);
+ return;
+ }
+ 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);
- } 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 (iter != null)
- iter.release();
+ if (haveBitSetVertices)
+ break;
}
+ if (iter != null)
+ iter.release();
}
private void addPolyhedron(Polyhedron p) {
@@ -731,7 +783,7 @@
Logger.info("Polyhedron " + PT.toJSON("face[" +i + "]", triangles[i]));
}
//System.out.println(PT.toJSON(null, htEdgeMap));
- return new Polyhedron().set(thisID, atomOrPt, points, nPoints, vertexCount,
+ return new Polyhedron().set(thisID, modelIndex, atomOrPt, points, nPoints,
vertexCount,
triangles, triangleCount, getFaces(triangles, triangleCount,
htNormMap), normals, bsCenterPlanes, collapsed, distanceRef);
}
@@ -813,8 +865,6 @@
}
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) {
@@ -875,7 +925,6 @@
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);
@@ -995,9 +1044,7 @@
*/
for (int i = polyhedronCount; --i >= 0;) {
Polyhedron p = polyhedrons[i];
- if (p.id != null) {
- p.visibilityFlags = (p.visible ? vf : 0);
- } else {
+ if (p.id == null) {
if (ms.at[p.centralAtom.i].isDeleted())
p.isValid = false;
p.visibilityFlags = (p.visible && bsModels.get(p.centralAtom.mi)
@@ -1005,6 +1052,8 @@
&& !ms.at[p.centralAtom.i].isDeleted() ? vf : 0);
if (p.visibilityFlags != 0)
setShapeVisibility(atoms[p.centralAtom.i], true);
+ } else {
+ p.visibilityFlags = (p.visible && (p.modelIndex < 0 ||
bsModels.get(p.modelIndex)) ? vf : 0);
}
}
}
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-10-20
22:40:08 UTC (rev 20839)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-10-20
22:41:32 UTC (rev 20840)
@@ -28,6 +28,11 @@
public class Polyhedron {
+ Map<String, Object> info;
+
+ public String id;
+ P3 center;
+
public Atom centralAtom;
public P3[] vertices;
public int[][] triangles;
@@ -48,18 +53,21 @@
public boolean isValid = true;
public short colixEdge = C.INHERIT_ALL;
public int visibilityFlags = 0;
- P3 center;
- public String id;
+ public short colix = C.GOLD;
+ public int modelIndex = Integer.MIN_VALUE;
+
+
Polyhedron() {
}
- Polyhedron set(String id, P3 atomOrPt, P3[] points, int nPoints, int
vertexCount,
+ Polyhedron set(String id, int modelIndex, 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;
centralAtom = (id == null ? (Atom) atomOrPt : null);
center = (centralAtom == null ? (P3) atomOrPt : null);
+ this.modelIndex = (centralAtom == null ? modelIndex : centralAtom.mi);
this.id = id;
this.nVertices = vertexCount;
this.vertices = new P3[nPoints + 1];
@@ -81,10 +89,14 @@
Polyhedron setInfo(Map<String, SV> info, Atom[] at) {
try {
collapsed = info.containsKey("collapsed");
- center = (info.containsKey("center") ? P3.newP(SV.ptValue(info
- .get("center"))) : null);
- if (center == null) {
+ id = info.get("id").asString();
+ if (id == null) {
centralAtom = at[info.get("atomIndex").intValue];
+ } else {
+ center = P3.newP(SV.ptValue(info.get("center")));
+ modelIndex = info.get("modelIndex").intValue;
+ colix = C.getColixS(info.get("color").asString());
+ colixEdge = C.getColixS(info.get("colorEdge").asString());
}
Lst<SV> lst = info.get("vertices").getList();
SV vc = info.get("vertexCount");
@@ -149,23 +161,20 @@
return ai;
}
- Map<String, Object> info;
- public short colix;
-
Map<String, Object> getInfo(Viewer vwr, boolean isAll) {
if (isAll && this.info != null && !Logger.debugging)
return this.info;
Map<String, Object> info = new Hashtable<String, Object>();
+ int mi = (id == null ? centralAtom.mi : modelIndex);
if (isAll) {
this.info = info;
- info.put("modelIndex", Integer.valueOf(centralAtom.mi));
- info.put("modelNumber", Integer.valueOf(centralAtom.getModelNumber()));
- info.put("center", P3.newP(centralAtom));
- if (center == null) {
+ if (id == null) {
+ info.put("center", P3.newP(centralAtom));
+ info.put("modelNumber", Integer.valueOf(centralAtom.getModelNumber()));
info.put("atomNumber", Integer.valueOf(centralAtom.getAtomNumber()));
info.put("atomName", centralAtom.getInfo());
+ info.put("element", centralAtom.getElementSymbol());
}
- info.put("element", centralAtom.getElementSymbol());
info.put("triangleCount", Integer.valueOf(triangles.length));
info.put("volume", getVolume());
String[] names = new String[nVertices];
@@ -190,6 +199,12 @@
if (energy != null)
info.put("energy", energy);
}
+ if (id != null) {
+ info.put("id", id);
+ info.put("modelIndex", Integer.valueOf(mi));
+ info.put("color", C.getHexCode(colix));
+ info.put("colorEdge", C.getHexCode(colixEdge == 0 ? colix : colixEdge));
+ }
if (faces != null)
info.put("faces", faces);
if (!isAll || Logger.debugging) {
@@ -281,7 +296,7 @@
String getState(Viewer vwr) {
String ident = (id == null ? "({"+centralAtom.i+"})" : "ID " +
Escape.e(id));
- return " polyhedron @{" + Escape.e(getInfo(vwr, false)) + "} "
+ return " polyhedron" + " @{" + Escape.e(getInfo(vwr, false)) + "} "
+ (isFullyLit ? " fullyLit" : "") + ";"
+ (visible ? "" : "polyhedra " + ident + " off;") + "\n";
}
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-10-20 22:40:08 UTC (rev
20839)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-10-20 22:41:32 UTC (rev
20840)
@@ -689,11 +689,10 @@
public final static int SHAPE_MAX_SIZE_ZERO_ON_RESTRICT = 21; //////////
- public final static int SHAPE_POLYHEDRA = 21; // for restrict, uses
setProperty(), not setSize()
+ public final static int SHAPE_MIN_HAS_ID = 21; //////////
- public final static int SHAPE_MIN_HAS_ID = 22; //////////
- public final static int SHAPE_MIN_MESH_COLLECTION = 22; //////////
-
+ public final static int SHAPE_POLYHEDRA = 21; // for restrict, uses
setProperty(), not setSize()
+
public final static int SHAPE_DRAW = 22;
public final static int SHAPE_MAX_SPECIAL = 23; //////////
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-20 22:40:08 UTC
(rev 20839)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-20 22:41:32 UTC
(rev 20840)
@@ -64,8 +64,19 @@
TODO: working on ID for polyhedra without atom refs
-Jmol.___JmolVersion="14.5.0_2015.10.18"
+Jmol.___JmolVersion="14.5.0_2015.10.20"
+new feature: polyhedra with arbitrary center and vertices, without atom center
+ -- for example:
+ polyhedra ID "myid" {0 0 0} TO [{1 0 0}, {0 1 0}, {0 0 1}, {-1 -1 -1}]
+
+bug fix: set platformSpeed 1 for pmesh fails
+bug fix: polyhedron EDGES fails
+bug fix: @{ {"hash":{0.1 0.1 0.1},...} } fails (attempts to turn "," into "OR")
+ -- solution is to not allow "," for OR within associative arrays
+
+JmolVersion="14.5.0_2015.10.18"
+
new feature: x = within(0.01, [array of points])
-- cleans points of duplicates with a tolerance of 0.001 Angstroms
-- allows multiple pmesh faces to be turned into polyhedra using:
@@ -85,7 +96,6 @@
new feature: resolution 0.001 with PMESH and ISOSURFACE planes
-- allows for minimum number of triangles.
-
bug fix: Polyhedra can have missing triangle for hexagonal faces
@@ -94,7 +104,7 @@
JmolVersion="14.5.0_2015.10.17"
-bug fix: if (...) \n { .... not working
+bug fix: if (...) \n { .... not working (where brace is on next line)
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
bug fix: nucleic backbone should include O atoms on P and C
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