Revision: 20252
http://sourceforge.net/p/jmol/code/20252
Author: hansonr
Date: 2015-01-28 17:04:11 +0000 (Wed, 28 Jan 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.01.28"
new feature: MUTATE command
-- replaces one amino acid group with another
-- can read from RCSB or from user-specified file
-- examples:
mutate 33 lys // uses last occurrence of resno=33
mutate @@3 arg // replaces group of atom 3 in current model
mutate @r @g // replaces resno in variable r with group in
variable g
mutate {r} his // same as above; r must be an atom selection
mutate 22 "myfile.cif" // user-defined replacement
bug fix: write "t.pdb" now correctly sequences groups and atoms, even after
mutation
new feature: resno is user settable
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-01-28 16:16:02 UTC
(rev 20251)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-01-28 17:04:11 UTC
(rev 20252)
@@ -1736,6 +1736,7 @@
@Override
public boolean mutate(int iatom, String fileName) {
+ String[] info = vwr.fm.getFileInfo();
boolean b = vwr.getBoolean(T.appendnew);
Group g = vwr.ms.at[iatom].group;
//try {
@@ -1812,6 +1813,7 @@
// System.out.println("" + e);
// }
vwr.setBooleanProperty("appendNew", b);
+ vwr.fm.setFileInfo(info);
return true;
}
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2015-01-28 16:16:02 UTC
(rev 20251)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2015-01-28 17:04:11 UTC
(rev 20252)
@@ -102,7 +102,19 @@
private String nameAsGiven = JC.ZAP_TITLE, fullPathName, lastFullPathName,
lastNameAsGiven = JC.ZAP_TITLE, fileName;
+ /**
+ * Set fullPathName, fileName, and nameAsGiven
+ *
+ * @param fileInfo if null, replace fullPathName and nameAsGiven with last
version of such
+ *
+ *
+ */
public void setFileInfo(String[] fileInfo) {
+ if (fileInfo == null) {
+ fullPathName = lastFullPathName;
+ nameAsGiven = lastNameAsGiven;
+ return;
+ }
// used by ScriptEvaluator dataFrame and load methods to temporarily save
the state here
fullPathName = fileInfo[0];
fileName = fileInfo[Math.min(1, fileInfo.length - 1)];
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-28 16:16:02 UTC
(rev 20251)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-28 17:04:11 UTC
(rev 20252)
@@ -26,6 +26,8 @@
mutate @r @g // replaces resno in variable r with group in
variable g
mutate {r} his // same as above; r must be an atom selection
mutate 22 "myfile.cif" // user-defined replacement
+
+bug fix: write "t.pdb" now correctly sequences groups and atoms, even after
mutation
new feature: resno is user settable
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