Revision: 20772
http://sourceforge.net/p/jmol/code/20772
Author: hansonr
Date: 2015-09-14 11:56:50 +0000 (Mon, 14 Sep 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.09.14"
bug fix: Crystallographic Open Database CIF files have unusual atom_site_label
("MgT")
and no atom_site_type_symbol, leading to missing element assignments
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/quantum/GamessUKReader.java
trunk/Jmol/src/org/jmol/adapter/readers/quantum/MopacGraphfReader.java
trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-09-14
04:27:09 UTC (rev 20771)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-09-14
11:56:50 UTC (rev 20772)
@@ -316,9 +316,8 @@
private void readSingleAtom() {
Atom atom = new Atom();
atom.set(0, 0, 0);
- String s = atom.atomName = parser.fullTrim(data);
- atom.elementSymbol = s.length() == 1 ? s : s.substring(0, 1)
- + s.substring(1, 2).toLowerCase();
+ atom.atomName = parser.fullTrim(data);
+ atom.getElementSymbol();
asc.addAtom(atom);
}
@@ -1246,13 +1245,8 @@
+ " has invalid/unknown coordinates");
continue;
}
- if (atom.elementSymbol == null && atom.atomName != null) {
- String sym = atom.atomName;
- int pt = 0;
- while (pt < sym.length() && PT.isLetter(sym.charAt(pt)))
- pt++;
- atom.elementSymbol = (pt == 0 || pt > 2 ? "Xx" : sym.substring(0, pt));
- }
+ if (atom.elementSymbol == null && atom.atomName != null)
+ atom.getElementSymbol();
if (!filterCIFAtom(atom, assemblyId))
continue;
setAtomCoord(atom);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/GamessUKReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/GamessUKReader.java
2015-09-14 04:27:09 UTC (rev 20771)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/GamessUKReader.java
2015-09-14 11:56:50 UTC (rev 20772)
@@ -110,7 +110,7 @@
String[] tokens = getTokens();
int atomicNumber = (int) parseFloatStr(tokens[2]);
Atom atom = setAtomCoordScaled(null, tokens, 3, ANGSTROMS_PER_BOHR);
- atom.elementSymbol =
AtomSetCollectionReader.getElementSymbol(atomicNumber);
+ atom.elementSymbol = getElementSymbol(atomicNumber);
atomNames.addLast(atom.atomName = tokens[1]);
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/MopacGraphfReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/MopacGraphfReader.java
2015-09-14 04:27:09 UTC (rev 20771)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/MopacGraphfReader.java
2015-09-14 11:56:50 UTC (rev 20772)
@@ -75,7 +75,7 @@
parseFloatRange(line, 29, 41));
if (line.length() > 41)
atom.partialCharge = parseFloatStr(line.substring(41));
- atom.elementSymbol =
AtomSetCollectionReader.getElementSymbol(atomicNumbers[i]);
+ atom.elementSymbol = getElementSymbol(atomicNumbers[i]);
//System.out.println(atom.elementSymbol + " " + atom.x + " " + atom.y +
" " + atom.z);
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanReader.java
2015-09-14 04:27:09 UTC (rev 20771)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanReader.java
2015-09-14 11:56:50 UTC (rev 20772)
@@ -76,11 +76,9 @@
private void readAtoms() throws Exception {
discardLinesUntilBlank();
while (rd() != null && (/* atomNum = */parseIntRange(line, 0, 3)) > 0) {
- String elementSymbol = parseTokenRange(line, 4, 6);
- String atomName = parseTokenRange(line, 7, 13);
Atom atom = asc.addNewAtom();
- atom.elementSymbol = elementSymbol;
- atom.atomName = atomName;
+ atom.elementSymbol = parseTokenRange(line, 4, 6);
+ atom.atomName = parseTokenRange(line, 7, 13);
setAtomCoordXYZ(atom, parseFloatRange(line, 17, 30),
parseFloatRange(line, 31, 44), parseFloatRange(
line, 45, 58));
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2015-09-14 04:27:09 UTC
(rev 20771)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2015-09-14 11:56:50 UTC
(rev 20772)
@@ -104,30 +104,29 @@
}
public String getElementSymbol() {
- if (elementSymbol == null)
- if (atomName != null) {
- int len = atomName.length();
- int ichFirst = 0;
- char chFirst = 0;
- while (ichFirst < len &&
- !isValidSymChar1(chFirst = atomName.charAt(ichFirst)))
- ++ichFirst;
- switch(len - ichFirst) {
- case 0:
+ if (elementSymbol == null && atomName != null) {
+ int len = atomName.length();
+ int ichFirst = 0;
+ char chFirst = 0;
+ while (ichFirst < len
+ && !isValidSymChar1(chFirst = atomName.charAt(ichFirst)))
+ ++ichFirst;
+ switch (len - ichFirst) {
+ case 0:
+ break;
+ default:
+ char chSecond = atomName.charAt(ichFirst + 1);
+ if (isValidSymNoCase(chFirst, chSecond)) {
+ elementSymbol = "" + chFirst + chSecond;
break;
- default:
- char chSecond = atomName.charAt(ichFirst + 1);
- if (isValidSymNoCase(chFirst, chSecond)) {
- elementSymbol = "" + chFirst + chSecond;
- break;
- }
- //$FALL-THROUGH$
- case 1:
- if (isValidSym1(chFirst))
- elementSymbol = "" + chFirst;
- break;
}
+ //$FALL-THROUGH$
+ case 1:
+ if (isValidSym1(chFirst))
+ elementSymbol = "" + chFirst;
+ break;
}
+ }
return elementSymbol;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-14 04:27:09 UTC
(rev 20771)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-14 11:56:50 UTC
(rev 20772)
@@ -58,8 +58,13 @@
TODO: image off stops JSmol
-Jmol.___JmolVersion="14.3.16_2015.09.09"
+Jmol.___JmolVersion="14.3.16_2015.09.14"
+bug fix: Crystallographic Open Database CIF files have unusual atom_site_label
("MgT")
+ and no atom_site_type_symbol, leading to missing element assignments
+
+JmolVersion="14.3.16_2015.09.09"
+
new feature: SMILES/SMARTS atom designations [C(xxxx)]
-- allows pointing to the same atom without connection numbers
-- (xxxx) may be anything, including just ()
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