Revision: 20848
http://sourceforge.net/p/jmol/code/20848
Author: hansonr
Date: 2015-10-28 03:40:52 +0000 (Wed, 28 Oct 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.4.0_2015.10.28"
bug fix: XODYDATA file reader does not read bond info or formal charge //
changes in 14.4.0_2015.10.28
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/adapter/readers/xml/XmlOdysseyReader.java
branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
Modified:
branches/v14_4/Jmol/src/org/jmol/adapter/readers/xml/XmlOdysseyReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/readers/xml/XmlOdysseyReader.java
2015-10-27 11:50:31 UTC (rev 20847)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/xml/XmlOdysseyReader.java
2015-10-28 03:40:52 UTC (rev 20848)
@@ -43,8 +43,11 @@
private String[] myAttributes = { "id", "label", //general
"xyz", "element", "hybrid", //atoms
"a", "b", "order", //bond
+ "charge", // group
+ "entity", // member
"box" // boundary
};
+ private int formalCharge = Integer.MIN_VALUE;
public XmlOdysseyReader() {
}
@@ -63,11 +66,11 @@
}
if ("atom".equals(localName)) {
- atom = new Atom();
- if (atts.containsKey("label"))
- atom.atomName = atts.get("label");
- else
- atom.atomName = atts.get("id");
+ String id = atts.get("id");
+ (atom = new Atom()).atomName = atts
+ .get(atts.containsKey("label") ? "label" : "id");
+ if (id != null && stateScriptVersionInt >= 140400)
+ asc.atomSymbolicMap.put(id, atom);
if (atts.containsKey("xyz")) {
String xyz = atts.get("xyz");
String[] tokens = PT.getTokens(xyz);
@@ -77,7 +80,6 @@
if (atts.containsKey("element")) {
atom.elementSymbol = atts.get("element");
}
-
return;
}
if ("bond".equals(localName)) {
@@ -89,7 +91,19 @@
asc.addNewBondFromNames(atom1, atom2, order);
return;
}
-
+ if ("group".equals(localName)) {
+ String charge = atts.get("charge");
+ if (charge != null && charge.indexOf(".") < 0) {
+ formalCharge = PT.parseInt(charge);
+ }
+ return;
+ }
+ if ("member".equals(localName) && formalCharge != Integer.MIN_VALUE) {
+ Atom atom = asc.getAtomFromName(atts.get("entity"));
+ if (atom != null)
+ atom.formalCharge = formalCharge;
+ return;
+ }
if ("boundary".equals(localName)) {
String[] boxDim = PT.getTokens(atts.get("box"));
float x = parseFloatStr(boxDim[0]);
@@ -115,7 +129,6 @@
parent.applySymmetryAndSetTrajectory();
return;
}
-
if ("odyssey_simulation".equals(localName)) {
if (modelName != null && phase != null)
modelName += " - " + phase;
@@ -155,13 +168,13 @@
atom = null;
return;
}
- if ("title".equals(localName)) {
+ if ("group".equals(localName)) {
+ formalCharge = Integer.MIN_VALUE;
+ } else if ("title".equals(localName)) {
modelName = chars;
- }
- if ("formula".equals(localName)) {
+ } else if ("formula".equals(localName)) {
formula = chars;
- }
- if ("phase".equals(localName)) {
+ } else if ("phase".equals(localName)) {
phase = chars;
}
keepChars = false;
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-27
11:50:31 UTC (rev 20847)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-28
03:40:52 UTC (rev 20848)
@@ -3233,6 +3233,8 @@
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)
@@ -3245,6 +3247,8 @@
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)
@@ -3282,7 +3286,7 @@
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;
@@ -3363,52 +3367,44 @@
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: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-27
11:50:31 UTC (rev 20847)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-28
03:40:52 UTC (rev 20848)
@@ -7,8 +7,17 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.0_2015.10.22b"
+Jmol.___JmolVersion="14.4.0_2015.10.28"
+bug fix: XODYDATA file reader does not read bond info or formal charge //
changes in 14.4.0_2015.10.28
+
+JmolVersion="14.4.0_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="14.4.0_2015.10.22b"
+
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
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