Revision: 18482
http://sourceforge.net/p/jmol/code/18482
Author: hansonr
Date: 2013-07-20 23:27:53 +0000 (Sat, 20 Jul 2013)
Log Message:
-----------
___JmolVersion="13.3.1_dev_2013.07.20"
TODO: documentation (see below, including % units on measure distance)
TODO: isosurface SLAB TRANSLUCENT 0.x color
-- inherits color of isosurface when color parameter is absent
-- TODO - properly save in JVXL file
TODO: PyMOL uniqueAtomSettings for transparency
-- will require by-vertex translucent option
bug fix: MMCIF_PDBX structures not being read
bug fix: allow PyMOL PSE files reading as part of a set of files, not just by
itself
bug fix: quaternion plots not synched with originating structure
bug fix: 1skt.cif loses secondary structure (MMCIF_PDBX reader needed)
new feature: calculate formalCharge
bug fix: set showTiming not functional
bug fix: set pdbAddHydrogens does not set formal charge on O(1-) or "O" of H2O
(2-)
bug fix: PNGJ files not properly caching, and PSE files with DOCACHE option
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Structure.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-07-20 22:55:12 UTC (rev 18481)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-07-20 23:27:53 UTC (rev 18482)
@@ -1556,7 +1556,8 @@
structure.structureType = structure.substructureType =
EnumStructure.NONE;
break;
case BEG_ASYM_ID:
- structure.startChainID = firstChar;
+ structure.startChainStr = field;
+ structure.startChainID = viewer.getChainID(field);
break;
case BEG_SEQ_ID:
structure.startSequenceNumber = parseIntStr(field);
@@ -1565,7 +1566,8 @@
structure.startInsertionCode = firstChar;
break;
case END_ASYM_ID:
- structure.endChainID = firstChar;
+ structure.endChainStr = field;
+ structure.endChainID = viewer.getChainID(field);
break;
case END_SEQ_ID:
structure.endSequenceNumber = parseIntStr(field);
@@ -1624,7 +1626,7 @@
for (int i = 0; i < tokenizer.fieldCount; ++i) {
switch (fieldProperty(i)) {
case BEG_ASYM_ID:
- structure.startChainID = firstChar;
+ structure.startChainID = viewer.getChainID(field);;
break;
case BEG_SEQ_ID:
structure.startSequenceNumber = parseIntStr(field);
@@ -1633,7 +1635,7 @@
structure.startInsertionCode = firstChar;
break;
case END_ASYM_ID:
- structure.endChainID = firstChar;
+ structure.endChainID = viewer.getChainID(field);
break;
case END_SEQ_ID:
structure.endSequenceNumber = parseIntStr(field);
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Structure.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Structure.java 2013-07-20
22:55:12 UTC (rev 18481)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Structure.java 2013-07-20
23:27:53 UTC (rev 18482)
@@ -34,8 +34,11 @@
public int strandCount;
public int startChainID;
+ public String startChainStr;
public char startInsertionCode = '\0';
public int endChainID;
+ public String endChainStr;
+
public char endInsertionCode = '\0';
public int startSequenceNumber;
public int endSequenceNumber;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-20 22:55:12 UTC
(rev 18481)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-20 23:27:53 UTC
(rev 18482)
@@ -13,6 +13,18 @@
___JmolVersion="13.3.1_dev_2013.07.20"
+TODO: documentation (see below, including % units on measure distance)
+
+TODO: isosurface SLAB TRANSLUCENT 0.x color
+ -- inherits color of isosurface when color parameter is absent
+ -- TODO - properly save in JVXL file
+TODO: PyMOL uniqueAtomSettings for transparency
+ -- will require by-vertex translucent option
+
+bug fix: MMCIF_PDBX structures not being read
+
+bug fix: allow PyMOL PSE files reading as part of a set of files, not just by
itself
+
bug fix: quaternion plots not synched with originating structure
bug fix: 1skt.cif loses secondary structure (MMCIF_PDBX reader needed)
@@ -26,16 +38,6 @@
JmolVersion="13.1.19_dev_2013.07.18"
-TODO: documentation (see below, including % units on measure distance)
-
-TODO: isosurface SLAB TRANSLUCENT 0.x color
- -- inherits color of isosurface when color parameter is absent
- -- TODO - properly save in JVXL file
-TODO: PyMOL uniqueAtomSettings for transparency
- -- will require by-vertex translucent option
-TODO: allow PyMOL PSE files reading as part of a set of files, not just by
itself
- (AtomSetCollection appendAtomSetCollection)
-
new feature: set exportScale x.x
-- adjusts export scale
-- only implemented for VRML and X3D exporters
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