Revision: 20846
http://sourceforge.net/p/jmol/code/20846
Author: hansonr
Date: 2015-10-27 11:42:29 +0000 (Tue, 27 Oct 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.0_2015.10.24"
bug fix: polyhedra not read from state (14.5 only)
code: unnecessary FRAME commands removed from state
JmolVersion="14.5.0_2015.10.24"
bug fix: [{1,2,3},{4,5,6}].average fails
bug fix: [{1,2,3},{4,5,6}].pivot should return "NaN"
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/shape/Axes.java
trunk/Jmol/src/org/jmol/shape/FontLineShape.java
trunk/Jmol/src/org/jmol/shape/Uccage.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-10-22 18:25:23 UTC
(rev 20845)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-10-27 11:42:29 UTC
(rev 20846)
@@ -674,7 +674,7 @@
case T.pointgroup:
if (!chk) {
if (eval.tokAt(2) == T.polyhedra) {
- showString((String) getShapePropertyIndex(JC.SHAPE_POLYHEDRA,
"symmetry", 0));
+ showString((String) getShapePropertyIndex(JC.SHAPE_POLYHEDRA,
"symmetry", tokAt(3) == T.off ? 0 : 1));
} else {
showString(vwr.ms.calculatePointGroup(vwr.bsA()));
}
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-22 18:25:23 UTC
(rev 20845)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-27 11:42:29 UTC
(rev 20846)
@@ -726,9 +726,8 @@
*
*
*/
-
- boolean isBondCount = (tok == T.bondcount);
- if (args.length > 5 || isBondCount && args.length != 1)
+
+ if (args.length > 5)
return false;
float min = Integer.MIN_VALUE, max = Integer.MAX_VALUE;
float fmin = 0, fmax = Float.MAX_VALUE;
@@ -740,6 +739,9 @@
boolean isBonds = false;
switch (tok) {
case T.polyhedra:
+ // polyhedra()
+ // polyhedra(3)
+ // polyhedra(smilesString)
int nv = Integer.MIN_VALUE;
String smiles = null;
if (args.length > 0) {
@@ -756,8 +758,9 @@
vwr.shm.getShapePropertyData(JC.SHAPE_POLYHEDRA, "centers", data);
return mp.addXBs(data[2] == null ? new BS() : (BS) data[2]);
case T.bondcount:
+ // {atoms1}.bondCount({atoms2})
SV x1 = mp.getX();
- if (x1.tok != T.bitset)
+ if (x1.tok != T.bitset || args.length != 1 || args[0].tok != T.bitset)
return false;
atoms1 = SV.bsSelectVar(x1);
atoms2 = SV.bsSelectVar(args[0]);
@@ -773,6 +776,8 @@
}
return mp.addXList(list);
}
+
+ // connected(
for (int i = 0; i < args.length; i++) {
SV var = args[i];
switch (var.tok) {
@@ -2134,7 +2139,7 @@
* @param mp
* @param args
* @param tok
- * @return
+ * @return true
* @throws ScriptException
*/
private boolean evaluatePlane(ScriptMathProcessor mp, SV[] args, int tok)
@@ -3303,6 +3308,8 @@
Map<String, Integer> htPivot = null;
while (true) {
if (AU.isAF(floatOrSVArray)) {
+ if (tok == T.pivot)
+ return "NaN";
data = (float[]) floatOrSVArray;
ndata = data.length;
if (ndata == 0)
@@ -3315,6 +3322,8 @@
break;
} else {
SV sv0 = sv.get(0);
+ if (sv0.tok == T.point3f)
+ return getMinMaxPoint(sv, tok);
if (sv0.tok == T.string && ((String) sv0.value).startsWith("{")) {
Object pt = SV.ptValue(sv0);
if (pt instanceof P3)
@@ -3352,7 +3361,7 @@
boolean isInt = true;
boolean isPivot = (tok == T.pivot);
for (int i = ndata; --i >= 0;) {
- SV svi = sv.get(i);
+ SV svi = (sv == null ? SV.vF : sv.get(i));
float v = (isPivot ? 1 : data == null ? SV.fValue(svi) : data[i]);
if (Float.isNaN(v))
continue;
@@ -3433,52 +3442,44 @@
sv = (Lst<SV>) pointOrSVArray;
ndata = sv.size();
}
- if (sv != null || data != null) {
- P3 result = new P3();
- float[] fdata = new float[ndata];
- boolean ok = true;
- for (int xyz = 0; xyz < 3 && ok; xyz++) {
- for (int i = 0; i < ndata; i++) {
- P3 pt = (data == null ? SV.ptValue(sv.get(i)) : data[i]);
- if (pt == null) {
- ok = false;
- break;
- }
- switch (xyz) {
- case 0:
- fdata[i] = pt.x;
- break;
- case 1:
- fdata[i] = pt.y;
- break;
- case 2:
- fdata[i] = pt.z;
- break;
- }
- }
- if (!ok)
+ if (sv == null && data == null)
+ return "NaN";
+ P3 result = new P3();
+ float[] fdata = new float[ndata];
+ for (int xyz = 0; xyz < 3; xyz++) {
+ for (int i = 0; i < ndata; i++) {
+ P3 pt = (data == null ? SV.ptValue(sv.get(i)) : data[i]);
+ if (pt == null)
+ return "NaN";
+ switch (xyz) {
+ case 0:
+ fdata[i] = pt.x;
break;
- Object f = getMinMax(fdata, tok);
- if (f instanceof Number) {
- float value = ((Number) f).floatValue();
- switch (xyz) {
- case 0:
- result.x = value;
- break;
- case 1:
- result.y = value;
- break;
- case 2:
- result.z = value;
- break;
- }
- } else {
+ case 1:
+ fdata[i] = pt.y;
break;
+ case 2:
+ fdata[i] = pt.z;
+ break;
}
}
- return result;
+ Object f = getMinMax(fdata, tok);
+ if (!(f instanceof Number))
+ return "NaN";
+ float value = ((Number) f).floatValue();
+ switch (xyz) {
+ case 0:
+ result.x = value;
+ break;
+ case 1:
+ result.y = value;
+ break;
+ case 2:
+ result.z = value;
+ break;
+ }
}
- return "NaN";
+ return result;
}
private Object getMinMaxQuaternion(Lst<SV> svData, int tok) {
Modified: trunk/Jmol/src/org/jmol/shape/Axes.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Axes.java 2015-10-22 18:25:23 UTC (rev
20845)
+++ trunk/Jmol/src/org/jmol/shape/Axes.java 2015-10-27 11:42:29 UTC (rev
20846)
@@ -198,7 +198,7 @@
if (axisType != null) {
sb.append(" axes type " + PT.esc(axisType));
}
- return super.getShapeState() + sb;
+ return getShapeStateFL() + sb;
}
}
Modified: trunk/Jmol/src/org/jmol/shape/FontLineShape.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/FontLineShape.java 2015-10-22 18:25:23 UTC
(rev 20845)
+++ trunk/Jmol/src/org/jmol/shape/FontLineShape.java 2015-10-27 11:42:29 UTC
(rev 20846)
@@ -66,6 +66,10 @@
@Override
public String getShapeState() {
+ return getShapeStateFL();
+ }
+
+ protected String getShapeStateFL() {
String s = vwr.getFontState(myType, font3d);
return (tickInfos == null ? s : vwr.getFontLineShapeState(s, myType,
tickInfos));
}
Modified: trunk/Jmol/src/org/jmol/shape/Uccage.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Uccage.java 2015-10-22 18:25:23 UTC (rev
20845)
+++ trunk/Jmol/src/org/jmol/shape/Uccage.java 2015-10-27 11:42:29 UTC (rev
20846)
@@ -38,7 +38,7 @@
public String getShapeState() {
if (!ms.haveUnitCells)
return "";
- String st = super.getShapeState();
+ String st = getShapeStateFL();
String s = st;
int iAtom = vwr.am.cai;
if (iAtom >= 0)
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-10-22 18:25:23 UTC
(rev 20845)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-10-27 11:42:29 UTC
(rev 20846)
@@ -358,7 +358,7 @@
public Object getProperty(String propertyName, int index) {
if (propertyName == "symmetry") {
String s = "";
- for (int i = polyhedronCount; --i >= 0;)
+ for (int i = 0; i < polyhedronCount; i++)
s += polyhedrons[i].getSymmetry(vwr, true) + "\n";
return s;
}
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-10-22
18:25:23 UTC (rev 20845)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-10-27
11:42:29 UTC (rev 20846)
@@ -8,6 +8,7 @@
import javajs.util.M4;
import javajs.util.Measure;
import javajs.util.P3;
+import javajs.util.T3;
import javajs.util.V3;
import org.jmol.api.SmilesMatcherInterface;
@@ -45,7 +46,14 @@
private short[] normixes;
public String smiles, smarts, polySmiles;
+ /**
+ * includes vertices as atoms, with atomic numbers
+ */
private SymmetryInterface pointGroup;
+ /**
+ * includes vertices as generic points
+ */
+ private SymmetryInterface pointGroupFamily;
private Float volume;
boolean visible = true;
@@ -89,7 +97,7 @@
Polyhedron setInfo(Map<String, SV> info, Atom[] at) {
try {
collapsed = info.containsKey("collapsed");
- id = info.get("id").asString();
+ id = (info.containsKey("id") ? info.get("id").asString() : null);
if (id == null) {
centralAtom = at[info.get("atomIndex").intValue];
} else {
@@ -174,6 +182,9 @@
info.put("atomNumber", Integer.valueOf(centralAtom.getAtomNumber()));
info.put("atomName", centralAtom.getInfo());
info.put("element", centralAtom.getElementSymbol());
+ Object energy = vwr.ms.getInfo(centralAtom.mi, "Energy");
+ if (energy != null)
+ info.put("energy", energy);
}
info.put("triangleCount", Integer.valueOf(triangles.length));
info.put("volume", getVolume());
@@ -195,9 +206,8 @@
info.put("polySmiles", polySmiles);
if (pointGroup != null)
info.put("pointGroup", pointGroup.getPointGroupName());
- Object energy = vwr.ms.getInfo(centralAtom.mi, "Energy");
- if (energy != null)
- info.put("energy", energy);
+ if (pointGroupFamily != null)
+ info.put("pointGroupFamily", pointGroupFamily.getPointGroupName());
}
if (id != null) {
info.put("id", id);
@@ -239,25 +249,40 @@
}
String getSymmetry(Viewer vwr, boolean withPointGroup) {
- if (id != null)
- return "";
- info = null;
- SmilesMatcherInterface sm = vwr.getSmilesMatcher();
- try {
- String details = (distanceRef <= 0 ? null : "r=" + distanceRef);
- if (smarts == null) {
- smarts = sm.polyhedronToSmiles(centralAtom, faces, nVertices, null,
JC.SMILES_TOPOLOGY, null);
- smiles = sm.polyhedronToSmiles(centralAtom, faces, nVertices,
vertices, JC.SMILES_TYPE_SMILES, null);
- polySmiles = sm.polyhedronToSmiles(centralAtom, faces, nVertices,
vertices, JC.SMILES_TYPE_SMILES | JC.SMILES_POLYHEDRAL |
JC.SMILES_ATOM_COMMENT, details);
+ if (id == null) {
+ info = null;
+ SmilesMatcherInterface sm = vwr.getSmilesMatcher();
+ try {
+ String details = (distanceRef <= 0 ? null : "r=" + distanceRef);
+ if (smarts == null) {
+ smarts = sm.polyhedronToSmiles(centralAtom, faces, nVertices, null,
+ JC.SMILES_TOPOLOGY, null);
+ smiles = sm.polyhedronToSmiles(centralAtom, faces, nVertices,
+ vertices, JC.SMILES_TYPE_SMILES, null);
+ polySmiles = sm.polyhedronToSmiles(centralAtom, faces, nVertices,
+ vertices, JC.SMILES_TYPE_SMILES | JC.SMILES_POLYHEDRAL
+ | JC.SMILES_ATOM_COMMENT, details);
+ }
+ } catch (Exception e) {
}
- } catch (Exception e) {
}
- if (pointGroup == null && withPointGroup)
- pointGroup = vwr.ms.getSymTemp(true).setPointGroup(null, vertices, null,
+ if (pointGroup == null && withPointGroup) {
+ T3[] pts = new T3[nVertices];
+ // first time through includes all atoms as atoms
+ for (int i = pts.length; --i >= 0;)
+ pts[i] = vertices[i];
+ pointGroup = vwr.ms.getSymTemp(true).setPointGroup(null, pts, null,
false, vwr.getFloat(T.pointgroupdistancetolerance),
vwr.getFloat(T.pointgrouplineartolerance), true);
- return centralAtom + " " + pointGroup.getPointGroupName();
-
+ // second time through includes all atoms as points only
+ for (int i = pts.length; --i >= 0;)
+ pts[i] = P3.newP(vertices[i]);
+ pointGroupFamily = vwr.ms.getSymTemp(true).setPointGroup(null, pts, null,
+ false, vwr.getFloat(T.pointgroupdistancetolerance),
+ vwr.getFloat(T.pointgrouplineartolerance), true);
+ }
+ return (center == null ? centralAtom : center) + " " +
pointGroup.getPointGroupName() + " "
+ + "("+pointGroupFamily.getPointGroupName()+")";
}
/**
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-22 18:25:23 UTC
(rev 20845)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-27 11:42:29 UTC
(rev 20846)
@@ -64,8 +64,18 @@
TODO: working on ID for polyhedra without atom refs
-Jmol.___JmolVersion="14.5.0_2015.10.22"
+Jmol.___JmolVersion="14.5.0_2015.10.24"
+bug fix: polyhedra not read from state (14.5 only)
+code: unnecessary FRAME commands removed from state
+
+JmolVersion="14.5.0_2015.10.24"
+
+bug fix: [{1,2,3},{4,5,6}].average fails
+bug fix: [{1,2,3},{4,5,6}].pivot should return "NaN"
+
+JmolVersion="14.5.0_2015.10.22"
+
bug fix: CIF parser fails to read CIF files containing only a single
(non-loop) _struct_ref_seq_dif.align_id
bug fix: WRITE .... AS does not properly allow for unquoted file name
@@ -8179,7 +8189,7 @@
version=13.1.7
FEATURE CHANGE: getProperty isosurfaceInfo no longer returns vertex data
-
+
new feature: getProperty isosurfaceData returns vertex data
new feature: set cartoonFancy -- creates elliptical ribbon for cartoons
-- if ribbonAspectRatio is its default value of 16, it is reset to 4
while cartoonFancy = true.
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-10-22 18:25:23 UTC
(rev 20845)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-10-27 11:42:29 UTC
(rev 20846)
@@ -315,32 +315,34 @@
needOrientations = true;
break;
}
+ SB sb = new SB();
for (int i = 0; i < modelCount; i++) {
- String fcmd = " frame " + ms.getModelNumberDotted(i);
+ sb.setLength(0);
String s = (String) ms.getInfo(i, "modelID");
if (s != null
&& !s.equals(ms.getInfo(i, "modelID0")))
- commands.append(fcmd).append("; frame ID ").append(PT.esc(s))
+ sb.append(" frame ID ").append(PT.esc(s))
.append(";\n");
String t = ms.frameTitles[i];
if (t != null && t.length() > 0)
- commands.append(fcmd).append("; frame title ").append(PT.esc(t))
+ sb.append(" frame title ").append(PT.esc(t))
.append(";\n");
if (needOrientations && models[i].orientation != null
&& !ms.isTrajectorySubFrame(i))
- commands.append(fcmd).append("; ").append(
+ sb.append(" ").append(
models[i].orientation.getMoveToText(false)).append(";\n");
if (models[i].frameDelay != 0 && !ms.isTrajectorySubFrame(i))
- commands.append(fcmd).append("; frame delay ").appendF(
+ sb.append(" frame delay ").appendF(
models[i].frameDelay / 1000f).append(";\n");
if (models[i].simpleCage != null) {
- commands.append(fcmd).append("; unitcell ").append(
+ sb.append(" unitcell ").append(
Escape.eAP(models[i].simpleCage.getUnitCellVectors())).append(
";\n");
- getShapeState(commands, isAll, JC.SHAPE_UCCAGE);
+ getShapeState(sb, isAll, JC.SHAPE_UCCAGE);
}
+ if (sb.length() > 0)
+ commands.append(" frame " + ms.getModelNumberDotted(i) +
";\n").appendSB(sb);
}
-
boolean loadUC = false;
if (ms.unitCells != null) {
boolean haveModulation = false;
@@ -348,10 +350,13 @@
SymmetryInterface symmetry = ms.getUnitCell(i);
if (symmetry == null)
continue;
- commands.append(" frame ").append(ms.getModelNumberDotted(i));
- if (symmetry.getState(commands))
+ sb.setLength(0);
+ if (symmetry.getState(sb)) {
loadUC = true;
- commands.append(";\n");
+ commands.append(" frame ")
+ .append(ms.getModelNumberDotted(i))
+ .appendSB(sb).append(";\n");
+ }
haveModulation |= (vwr.ms.getLastVibrationVector(i, T.modulation) >=
0);
}
if (loadUC)
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