Revision: 18514
http://sourceforge.net/p/jmol/code/18514
Author: hansonr
Date: 2013-07-31 01:52:42 +0000 (Wed, 31 Jul 2013)
Log Message:
-----------
___JmolVersion="13.2.4_dev_2013.07.30"
bug fix: minimization can fail after MMFF switches to UFF.
bug fix: CIF reader fix for no element given "phenyl1" in ZjzxlegN.cif
Modified Paths:
--------------
branches/v13_2/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
branches/v13_2/Jmol/src/org/jmol/minimize/Minimizer.java
branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java
Modified: branches/v13_2/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-07-31 01:46:28 UTC (rev 18513)
+++ branches/v13_2/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-07-31 01:52:42 UTC (rev 18514)
@@ -530,7 +530,8 @@
return;
}
if (str.startsWith("_symmetry_equiv_pos")
- || str.startsWith("_space_group_symop")) {
+ || str.startsWith("_space_group_symop")
+ || str.startsWith("_symmetry_ssg_equiv")) {
if (ignoreFileSymmetryOperators) {
Logger.warn("ignoring file-based symmetry operators");
skipLoop();
@@ -1022,6 +1023,13 @@
if (isAnisoData || !filterCIFAtom(atom, iAtom, assemblyId))
continue;
setAtomCoord(atom);
+ if (atom.elementSymbol == null && atom.atomName != null) {
+ String sym = atom.atomName;
+ int pt = 0;
+ while (pt < sym.length() && Character.isLetter(sym.charAt(pt)))
+ pt++;
+ atom.elementSymbol = (pt == 0 || pt > 2 ? "Xx" : sym.substring(0,
pt));
+ }
atomSetCollection.addAtomWithMappedName(atom);
if (assemblyId != '\0') {
if (assemblyIdAtoms == null)
@@ -1773,11 +1781,13 @@
final private static byte SYMOP_XYZ = 0;
final private static byte SYM_EQUIV_XYZ = 1;
- final private static byte SYM_SSG_OP = 2;
+ final private static byte SYM_SSG_XYZ = 2;
+ final private static byte SYM_SSG_OP = 3;
final private static String[] symmetryOperationsFields = {
"_space_group_symop_operation_xyz",
"_symmetry_equiv_pos_as_xyz",
+ "_symmetry_ssg_equiv_pos_as_xyz",
"_space_group_symop_ssg_operation_algebraic"
};
@@ -1800,6 +1810,11 @@
while (tokenizer.getData()) {
for (int i = 0; i < tokenizer.fieldCount; ++i) {
switch (fieldProperty(i)) {
+ case SYM_SSG_XYZ:
+ // check for non-standard record x~1~,x~2~,x~3~,x~4~ kIsfCqpM.cif
+ if (field.indexOf('~') >= 0)
+ field = TextFormat.simpleReplace(field, "~", "");
+ //$FALL-THROUGH$
case SYMOP_XYZ:
case SYM_EQUIV_XYZ:
case SYM_SSG_OP:
Modified: branches/v13_2/Jmol/src/org/jmol/minimize/Minimizer.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/minimize/Minimizer.java 2013-07-31
01:46:28 UTC (rev 18513)
+++ branches/v13_2/Jmol/src/org/jmol/minimize/Minimizer.java 2013-07-31
01:52:42 UTC (rev 18514)
@@ -215,6 +215,7 @@
if (minimizationOn)
return false;
+ ForceField pFF0 = pFF;
getForceField(ff);
if (pFF == null) {
Logger.error(GT._("Could not get class for force field {0}", ff));
@@ -234,6 +235,8 @@
boolean sameAtoms = BSUtil.areEqual(bsSelected, this.bsSelected);
this.bsSelected = bsSelected;
+ if (pFF0 != null && pFF != pFF0)
+ sameAtoms = false;
if (!sameAtoms)
pFF.clear();
if ((!sameAtoms || !BSUtil.areEqual(bsFixed, this.bsFixed))
Modified: branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-31
01:46:28 UTC (rev 18513)
+++ branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-31
01:52:42 UTC (rev 18514)
@@ -9,7 +9,11 @@
# Don't use ___ in your text, as that is the key for stripping out
# the information saved in the JAR version of this file.
-___JmolVersion="13.2.3"
+___JmolVersion="13.2.4_dev_2013.07.30"
+
+bug fix: minimization can fail after MMFF switches to UFF.
+bug fix: CIF reader fix for no element given "phenyl1" in ZjzxlegN.cif
+
JmolVersion="13.2.3_dev_2013.07.27"
bug fix: Gaussian cube format changed and not recognized (extra "1" in third
line).
Modified: branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java 2013-07-31 01:46:28 UTC
(rev 18513)
+++ branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java 2013-07-31 01:52:42 UTC
(rev 18514)
@@ -5920,7 +5920,7 @@
return;
case T.forcefield:
// 12.3.25
- global.forceField = value;
+ global.forceField = value = ("UFF".equalsIgnoreCase(value)? "UFF" :
"MMFF");
minimizer = null;
break;
case T.nmrurlformat:
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