Revision: 20849
http://sourceforge.net/p/jmol/code/20849
Author: hansonr
Date: 2015-10-28 03:41:32 +0000 (Wed, 28 Oct 2015)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlOdysseyReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlOdysseyReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlOdysseyReader.java
2015-10-28 03:40:52 UTC (rev 20848)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlOdysseyReader.java
2015-10-28 03:41:32 UTC (rev 20849)
@@ -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: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-28 03:40:52 UTC
(rev 20848)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-28 03:41:32 UTC
(rev 20849)
@@ -64,8 +64,16 @@
TODO: working on ID for polyhedra without atom refs
-Jmol.___JmolVersion="14.5.0_2015.10.27"
+Jmol.___JmolVersion="14.5.0_2015.10.28"
+bug fix: XODYDATA file reader does not read bond info or formal charge //
changes in 14.4.0_2015.10.28
+
+FEATURE CHANGE: default RCSB/PDB load format (=xxxx) changed to
http://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/%c2%c3/pdb%file.ent.gz
+
+new feature: (JSmol) adding access-allow-origin status for cdn.rcsb.org and
ftp.wwpdb.org.
+
+JmolVersion="14.5.0_2015.10.27"
+
code: unnecessary FRAME commands removed from state
bug fix: polyhedra not read from state (14.5 only)
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