Revision: 20961
http://sourceforge.net/p/jmol/code/20961
Author: hansonr
Date: 2016-02-15 03:09:28 +0000 (Mon, 15 Feb 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.2_2016.02.14"
FEATURE CHANGE: JSmol default for Info._disableInitialConsole changed to true
-- no longer necessary with JSmol_spinner.gif
new feature: j2s/img/JSmol_spinner.gif implemented (Angel Herraez)
-- as default for Info._appletLoadingImage
-- use Info._appletLoadingImage = "none" to disable
new feature: j2s/img/cursor_wait.gif animation implemented
bug fix: STRUCTURE statement (utilized in RESTORE STRUCTURE) broken
-- broken in Jmol 14.4.0_2015.10.30
bug fix: EBI assembly CIF files that are multi-model files will be by chain,
not by model.
-- result was that each chain became a new model
-- for example: see
http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz
bug fix: XmlMolProReader does not recognize FILTER "NOMO"
bug fix: JSmol has never shown cursors
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/modelsetbio/BioModel.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelsetbio/BioModel.java 2016-02-15
01:27:16 UTC (rev 20960)
+++ branches/v14_4/Jmol/src/org/jmol/modelsetbio/BioModel.java 2016-02-15
03:09:28 UTC (rev 20961)
@@ -123,17 +123,17 @@
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
if (at[i].group.isAdded(i))
continue;
- monomerIndexCurrent = at[i].group.setProteinStructureType(type,
- iLast == i - 1 ? -1 : monomerIndexCurrent);
+ monomerIndexCurrent = at[i].group.setProteinStructureType(type,
+ iLast == i - 1 ? monomerIndexCurrent : -1);
int modelIndex = at[i].mi;
ms.proteinStructureTainted = am[modelIndex].structureTainted = true;
iLast = i = at[i].group.lastAtomIndex;
}
int[] lastStrucNo = new int[ms.mc];
- for (int i = 0; i < ms.ac;) {
+ for (int i = 0; i < ms.ac; i++) {
int modelIndex = at[i].mi;
if (!bsModels.get(modelIndex)) {
- i = am[modelIndex].firstAtomIndex + am[modelIndex].act;
+ i = am[modelIndex].firstAtomIndex + am[modelIndex].act - 1;
continue;
}
Group g = at[i].group;
@@ -143,12 +143,11 @@
lastStrucNo[modelIndex] = iLast;
i = g.lastAtomIndex;
}
- i++;
}
- for (int i = 0; i < ms.ac;) {
+ for (int i = 0; i < ms.ac; i++) {
int modelIndex = at[i].mi;
if (!bsModels.get(modelIndex)) {
- i = am[modelIndex].firstAtomIndex + am[modelIndex].act;
+ i = am[modelIndex].firstAtomIndex + am[modelIndex].act - 1;
continue;
}
Group g = at[i].group;
@@ -157,7 +156,6 @@
if (g.getStrucNo() > 1000)
g.setStrucNo(++lastStrucNo[modelIndex]);
}
- i++;
}
}
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-15
01:27:16 UTC (rev 20960)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-15
03:09:28 UTC (rev 20961)
@@ -18,6 +18,9 @@
new feature: j2s/img/cursor_wait.gif animation implemented
+bug fix: STRUCTURE statement (utilized in RESTORE STRUCTURE) broken
+ -- broken in Jmol 14.4.0_2015.10.30
+
bug fix: EBI assembly CIF files that are multi-model files will be by chain,
not by model.
-- result was that each chain became a new model
-- for example: see
http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2016-02-15 01:27:16 UTC
(rev 20960)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2016-02-15 03:09:28 UTC
(rev 20961)
@@ -123,17 +123,17 @@
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
if (at[i].group.isAdded(i))
continue;
- monomerIndexCurrent = at[i].group.setProteinStructureType(type,
- iLast == i - 1 ? -1 : monomerIndexCurrent);
+ monomerIndexCurrent = at[i].group.setProteinStructureType(type,
+ iLast == i - 1 ? monomerIndexCurrent : -1);
int modelIndex = at[i].mi;
ms.proteinStructureTainted = am[modelIndex].structureTainted = true;
iLast = i = at[i].group.lastAtomIndex;
}
int[] lastStrucNo = new int[ms.mc];
- for (int i = 0; i < ms.ac;) {
+ for (int i = 0; i < ms.ac; i++) {
int modelIndex = at[i].mi;
if (!bsModels.get(modelIndex)) {
- i = am[modelIndex].firstAtomIndex + am[modelIndex].act;
+ i = am[modelIndex].firstAtomIndex + am[modelIndex].act - 1;
continue;
}
Group g = at[i].group;
@@ -143,12 +143,11 @@
lastStrucNo[modelIndex] = iLast;
i = g.lastAtomIndex;
}
- i++;
}
- for (int i = 0; i < ms.ac;) {
+ for (int i = 0; i < ms.ac; i++) {
int modelIndex = at[i].mi;
if (!bsModels.get(modelIndex)) {
- i = am[modelIndex].firstAtomIndex + am[modelIndex].act;
+ i = am[modelIndex].firstAtomIndex + am[modelIndex].act - 1;
continue;
}
Group g = at[i].group;
@@ -157,7 +156,6 @@
if (g.getStrucNo() > 1000)
g.setStrucNo(++lastStrucNo[modelIndex]);
}
- i++;
}
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-15 01:27:16 UTC
(rev 20960)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-15 03:09:28 UTC
(rev 20961)
@@ -75,11 +75,15 @@
new feature: j2s/img/cursor_wait.gif animation implemented
+bug fix: STRUCTURE statement (utilized in RESTORE STRUCTURE) broken
+ -- broken in Jmol 14.4.0_2015.10.30
+
bug fix: EBI assembly CIF files that are multi-model files will be by chain,
not by model.
-- result was that each chain became a new model
-- for example: see
http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz
bug fix: XmlMolProReader does not recognize FILTER "NOMO"
+
bug fix: JSmol has never shown cursors
JmolVersion="14.5.2_2016.02.09"
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