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[Jmol-commits] SF.net SVN: jmol:[14983] trunk/Jmol/src/org/jmol
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From: <ha...@us...> - 2011-01-17 04:59:32
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Revision: 14983
http://jmol.svn.sourceforge.net/jmol/?rev=14983&view=rev
Author: hansonr
Date: 2011-01-17 04:59:25 +0000 (Mon, 17 Jan 2011)
Log Message:
-----------
version=12.1.31_dev # new feature: write xxxx.xyzrn -- input for MSMS
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-01-17 04:27:43 UTC (rev 14982)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-01-17 04:59:25 UTC (rev 14983)
@@ -13318,7 +13318,7 @@
&& tokAt(pt + 1, args) == Token.integer) {
quality = ScriptVariable.iValue(tokenAt(++pt, args));
} else if (Parser.isOneOf(val.toLowerCase(),
- "xyz;mol;sdf;v2000;v3000;pdb;cml")) {
+ "xyz;xyzrn;mol;sdf;v2000;v3000;pdb;cml")) {
type = val.toUpperCase();
if (pt + 1 == argCount)
pt++;
@@ -13416,12 +13416,12 @@
&& !Parser
.isOneOf(
type,
- "ZIP;ZIPALL;SPT;HIS;MO;ISO;ISOX;MESH;PMESH;VAR;FILE;FUNCS;CML;XYZ;MENU;MOL;PDB;PGRP;QUAT;RAMA;SDF;V2000;V3000;"))
+ "ZIP;ZIPALL;SPT;HIS;MO;ISO;ISOX;MESH;PMESH;VAR;FILE;FUNCS;CML;XYZ;XYZRN;MENU;MOL;PDB;PGRP;QUAT;RAMA;SDF;V2000;V3000;"))
error(
ERROR_writeWhat,
"COORDS|FILE|FUNCTIONS|HISTORY|IMAGE|ISOSURFACE|JMOL|MENU|MO|POINTGROUP|QUATERNION [w,x,y,z] [derivative]"
+ "|RAMACHANDRAN|SPT|STATE|VAR x|ZIP|ZIPALL CLIPBOARD",
- "CML|GIF|JPG|JPG64|JVXL|MESH|MOL|PDB|PMESH|PNG|PPM|SDF|V2000|V3000|SPT|XJVXL|XYZ|ZIP"
+ "CML|GIF|JPG|JPG64|JVXL|MESH|MOL|PDB|PMESH|PNG|PPM|SDF|V2000|V3000|SPT|XJVXL|XYZ|XYZRN|ZIP"
+ driverList.toUpperCase().replace(';', '|'));
if (isSyntaxCheck)
return "";
@@ -13487,7 +13487,7 @@
data == "V3000");
if (data.startsWith("ERROR:"))
bytes = data;
- } else if (data == "XYZ" || data == "MOL" || data == "SDF"
+ } else if (data == "XYZ" || data == "XYZRN" || data == "MOL" || data == "SDF"
|| data == "V2000" || data == "V3000" || data == "CML") {
data = viewer.getData("selected", data);
if (data.startsWith("ERROR:"))
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-01-17 04:27:43 UTC (rev 14982)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-01-17 04:59:25 UTC (rev 14983)
@@ -3,6 +3,7 @@
version=12.1.31_dev
+# new feature: write xxxx.xyzrn -- input for MSMS
# bug fix: fails: load 1mbo.cif; isosurface select(not solvent) ignore(none) sasurface;
# new feature: y == x[3] (double "=" in context of assignment)
# -- y is now an alias for x[3], not a copy
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-01-17 04:27:43 UTC (rev 14982)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-01-17 04:59:25 UTC (rev 14983)
@@ -7684,6 +7684,8 @@
// old crude
exp = "{selected and not hetero}.label(\"ATOM %5i %-4a%1A%3.3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e \").lines"
+ "+{selected and hetero}.label(\"HETATM%5i %-4a%1A%3.3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e \").lines";
+ else if (type.equalsIgnoreCase("XYZRN"))
+ exp = "{selected}.label(\"%8.3x %8.3y %8.3z %4.2[vdw] 1 [%n]%r.%a#%i\").lines";
else if (type.startsWith("USER:"))
exp = "{selected}.label(\"" + type.substring(5) + "\").lines";
else
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