Revision: 20509
http://sourceforge.net/p/jmol/code/20509
Author: hansonr
Date: 2015-05-20 03:14:54 +0000 (Wed, 20 May 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.13_2015.05.19"
bug fix: CML reader not recognizing "fragment/join/fragment" sequence
from http://www.xml-cml.org/schema/schema3/schema.xsd (Stuart Chalk)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlHandler.java
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
2015-05-19 00:52:27 UTC (rev 20508)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
2015-05-20 03:14:54 UTC (rev 20509)
@@ -26,13 +26,18 @@
import org.jmol.adapter.smarter.Bond;
import org.jmol.adapter.smarter.Atom;
+import java.util.Hashtable;
+import java.util.Map;
import java.util.NoSuchElementException;
import java.util.Properties;
import java.util.StringTokenizer;
+import javajs.util.Lst;
import javajs.util.PT;
+import org.jmol.java.BS;
import org.jmol.api.JmolAdapter;
+import org.jmol.util.BSUtil;
import org.jmol.util.Logger;
/**
@@ -112,6 +117,12 @@
private boolean haveMolecule = false;
private String localSpaceGroupName;
protected boolean processing = true;
+ protected int state = START;
+ private int atomIndex0;
+ private Lst<String[]> joinList;
+ private Map<Atom, String> mapRtoA;
+ private BS deleteAtoms;
+
/**
* state constants
*/
@@ -137,9 +148,6 @@
/**
* the current state
*/
- protected int state = START;
- private int atomIndex0;
-
/*
* added 2/2007 Bob Hanson:
*
@@ -176,6 +184,7 @@
}
protected void processStart2(String name) {
+ name = name.toLowerCase();
switch (state) {
case START:
if (name.equals("molecule")) {
@@ -198,7 +207,7 @@
} else if (name.equals("module")) {
moduleNestingLevel++;
//nModules++;
- } else if (name.equalsIgnoreCase("latticeVector")) {
+ } else if (name.equals("latticevector")) {
state = LATTICE_VECTOR;
setKeepChars(true);
}
@@ -222,7 +231,7 @@
localSpaceGroupName = localSpaceGroupName.substring(0, i)
+ localSpaceGroupName.substring((i--) + 1);
}
- } else if (name.equalsIgnoreCase("cellParameter")) {
+ } else if (name.equals("cellparameter")) {
if (atts.containsKey("parameterType")) {
cellParameterType = atts.get("parameterType");
setKeepChars(true);
@@ -251,15 +260,28 @@
break;
case CRYSTAL_SYMMETRY_TRANSFORM3:
case MOLECULE:
- if (name.equals("crystal")) {
+ if (name.equals("fragmentlist")) {
+ joinList = new Lst<String[]>();
+ mapRtoA = new Hashtable<Atom, String>();
+ if (deleteAtoms == null)
+ deleteAtoms = new BS();
+ } else if (name.equals("crystal")) {
state = CRYSTAL;
embeddedCrystal = true;
- }
- if (name.equals("molecule")) {
+ } else if (name.equals("molecule")) {
state = MOLECULE;
moleculeNesting++;
- }
- if (name.equalsIgnoreCase("bondArray")) {
+ } else if (name.equalsIgnoreCase("join")) {
+ int order = -1;
+ tokenCount = 0;
+ if (atts.containsKey("atomRefs2")) {
+ breakOutTokens(atts.get("atomRefs2"));
+ if (atts.containsKey("order"))
+ order = parseBondToken(atts.get("order"));
+ if (tokenCount == 2 && order > 0)
+ joinList.addLast(new String[] { tokens[0], tokens[1], "" + order
});
+ }
+ } else if (name.equals("bondarray")) {
state = MOLECULE_BOND_ARRAY;
bondCount = 0;
if (atts.containsKey("order")) {
@@ -277,8 +299,7 @@
for (int i = tokenCount; --i >= 0;)
bondArray[i].atomIndex2 = asc.getAtomIndex(tokens[i]);
}
- }
- if (name.equalsIgnoreCase("atomArray")) {
+ } else if (name.equals("atomarray")) {
state = MOLECULE_ATOM_ARRAY;
aaLen = 0;
boolean coords3D = false;
@@ -324,8 +345,7 @@
atom.z = 0;
addAtom(atom);
}
- }
- if (name.equals("formula")) {
+ } else if (name.equals("formula")) {
state = MOLECULE_FORMULA;
}
break;
@@ -436,6 +456,7 @@
}
public void processEnd2(String name) {
+ name = name.toLowerCase();
switch (state) {
case START:
if (name.equals("module")) {
@@ -454,7 +475,7 @@
} else {
state = START;
}
- } else if (name.equalsIgnoreCase("cellParameter") && keepChars) {
+ } else if (name.equals("cellparameter") && keepChars) {
String[] tokens = PT.getTokens(chars);
setKeepChars(false);
if (tokens.length != 3 || cellParameterType == null) {
@@ -510,6 +531,20 @@
applySymmetryAndSetTrajectory();
break;
case MOLECULE:
+ if (name.equals("fragmentlist")) {
+ for (int i = joinList.size(); --i >= 0;) {
+ String[] join = joinList.get(i);
+ Atom r1 = asc.getAtomFromName(fixSerialName(join[0]));
+ Atom r2 = asc.getAtomFromName(fixSerialName(join[1]));
+ if (r1 != null && r2 != null) {
+ deleteAtoms.set(r1.index);
+ deleteAtoms.set(r2.index);
+ addNewBond(mapRtoA.get(r1), mapRtoA.get(r2), parseIntStr(join[2]));
+ }
+ }
+ joinList = null;
+ mapRtoA = null;
+ }
if (name.equals("molecule")) {
if (--moleculeNesting == 0) {
// if <molecule> is within <molecule>, then
@@ -524,15 +559,15 @@
}
break;
case MOLECULE_BOND_ARRAY:
- if (name.equalsIgnoreCase("bondArray")) {
+ if (name.equals("bondarray")) {
state = MOLECULE;
for (int i = 0; i < bondCount; ++i)
- asc.addBond(bondArray[i]);
+ addBond(bondArray[i]);
parent.applySymmetryToBonds = true;
}
break;
case MOLECULE_ATOM_ARRAY:
- if (name.equalsIgnoreCase("atomArray")) {
+ if (name.equals("atomarray")) {
state = MOLECULE;
for (int i = 0; i < aaLen; ++i)
addAtom(atomArray[i]);
@@ -598,6 +633,35 @@
}
}
+ private void addBond(Bond bond) {
+ Atom a1 = asc.atoms[bond.atomIndex1];
+ Atom a2 = asc.atoms[bond.atomIndex2];
+ if (joinList != null && !checkBondToR(a1.atomName, a2.atomName))
+ asc.addBond(bond);
+ }
+
+ /**
+ * Checks to see if we have a bond to R and, if so, adds this R atom
+ * as a key to its attached atom
+ * @param a1name
+ * @param a2name
+ * @return true if handled so no need to add a bond
+ */
+ private boolean checkBondToR(String a1name, String a2name) {
+ Atom a1 = asc.getAtomFromName(a1name);
+ Atom a2 = asc.getAtomFromName(a2name);
+ if (a1 == null || a2 == null)
+ return true;
+ if ("R".equals(a1.elementSymbol)) {
+ mapRtoA.put(a1, a2.atomName);
+ return true;
+ } else if ("R".equals(a2.elementSymbol)) {
+ mapRtoA.put(a2, a1.atomName);
+ return true;
+ }
+ return false;
+ }
+
private void setAtomNames() {
// for CML reader "a3" --> "N3"
if (atomIdNames == null)
@@ -612,13 +676,19 @@
}
private void addNewBond(String a1, String a2, int order) {
+ if (a1 == null || a2 == null)
+ return;
parent.applySymmetryToBonds = true;
- if (isSerial)
- asc.addNewBondFromNames(a1.substring(1), a2.substring(1), order);
- else
+ a1 = fixSerialName(a1);
+ a2 = fixSerialName(a2);
+ if (joinList == null || !checkBondToR(a1, a2))
asc.addNewBondFromNames(a1, a2, order);
}
+ private String fixSerialName(String a) {
+ return (isSerial ? a.substring(1) : a);
+ }
+
private void getDictRefValue() {
scalarDictRef = atts.get("dictRef");
if (scalarDictRef != null) {
@@ -745,4 +815,15 @@
parent.applySymmetryAndSetTrajectory();
}
+ @Override
+ public void endDocument() {
+ // CML reader uses this
+ if (deleteAtoms != null) {
+ BS bs = (asc.bsAtoms == null ? asc.bsAtoms = BSUtil.newBitSet2(0,
asc.ac) : asc.bsAtoms);
+ bs.andNot(deleteAtoms);
+ }
+ }
+
+
+
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlHandler.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlHandler.java 2015-05-19
00:52:27 UTC (rev 20508)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlHandler.java 2015-05-20
03:14:54 UTC (rev 20509)
@@ -27,6 +27,8 @@
import java.io.BufferedReader;
+import org.jmol.java.BS;
+import org.jmol.util.BSUtil;
import org.jmol.util.Logger;
import org.xml.sax.Attributes;
import org.xml.sax.InputSource;
@@ -65,6 +67,7 @@
@Override
public void endDocument() {
+ xmlReader.endDocument();
}
/*
@@ -148,7 +151,6 @@
public void error(SAXParseException exception) {
Logger.error("SAX ERROR:" + exception.getMessage());
}
-
@Override
public void fatalError(SAXParseException exception) {
Logger.error("SAX FATAL:" + exception.getMessage());
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java 2015-05-19
00:52:27 UTC (rev 20508)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java 2015-05-20
03:14:54 UTC (rev 20509)
@@ -33,8 +33,10 @@
import java.util.Hashtable;
import java.util.Map;
+import org.jmol.java.BS;
import javajs.util.Rdr;
+import org.jmol.util.BSUtil;
import org.jmol.util.Logger;
/**
@@ -427,4 +429,8 @@
return parent.vwr.apiPlatform.getJsObjectInfo(jsObject, name, null);
}
+ public void endDocument() {
+ // CML reader uses this
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-05-19 00:52:27 UTC
(rev 20508)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-05-20 03:14:54 UTC
(rev 20509)
@@ -14,8 +14,13 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.13_2015.05.14"
+Jmol.___JmolVersion="14.3.13_2015.05.19"
+bug fix: CML reader not recognizing "fragment/join/fragment" sequence
+ from http://www.xml-cml.org/schema/schema3/schema.xsd (Stuart Chalk)
+
+JmolVersion="14.3.13_2015.05.14"
+
new feature: set contextDepthMax
-- sets the maximum depth of contexts, including {}, if{} for{} while{}
function{}
as well as the SCRIPT command and a number of expression-related
situations
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-05-19 00:52:27 UTC (rev
20508)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-05-20 03:14:54 UTC (rev
20509)
@@ -1435,7 +1435,7 @@
// delegated to FileManager
// ///////////////////////////////////////////////////////////////
- String getDefaultDirectory() {
+ public String getDefaultDirectory() {
return g.defaultDirectory;
}
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