File formats/Scripting - Revision history

AngelHerraez: /* Script inline within a molecular coordinates file */

2015-01-07T20:11:50Z

‎Script inline within a molecular coordinates file

AngelHerraez: Reverted edits by Bevmorguson (talk) to last revision by AngelHerraez

2012-10-24T19:53:38Z

Reverted edits by Bevmorguson (talk) to last revision by AngelHerraez

: /* Script input */

2012-10-24T08:40:24Z

‎Script input

AngelHerraez: Script inline in Z-matrix file

2011-11-20T17:34:06Z

Script inline in Z-matrix file

AngelHerraez: Script inline within MOL2 files (new feature in 11.9.22)

2010-01-24T20:40:17Z

Script inline within MOL2 files (new feature in 11.9.22)

AngelHerraez: /* Script inline within a molecular coordinates file */

2009-11-29T13:36:23Z

‎Script inline within a molecular coordinates file

AngelHerraez: fill content brought from File formats page

2009-04-25T17:18:52Z

fill content brought from File formats page

AngelHerraez: for splitting the contents of File formats page

2009-04-23T19:08:00Z

for splitting the contents of File formats page

New page

for splitting the contents of [[File formats]] page
--to be done

@@ Line 58: / Line 58: @@
 * In an '''XYZ''' file, use <code>jmolscript:</code> in the '''second line''', followed by the script commands in the same line.
 * In a '''CIF''' file or a '''Z-matrix''' file, use <code>#jmolscript:</code> followed by the script commands in the same line. It may be in any line as long as it does not interfere with the data structure, so it is better to put it either at the beginning or the end of the file.
+* Other file formats where embedded scripts are supported (using <code>jmolscript:</code> in any line) are: Gromacs, Cube, JME, Wien2k.
 In all cases, the script will be applied after the whole molecule has loaded and after whatever script commands may have been set using <code>set defaultLoadScript</code>.

@@ Line 3: / Line 3: @@
 == Script input ==
-Jmol reads script files, using not the <code>load</code> command, but the <code>script</code> command. These are plain-text files containing commands in the Jmol scripting language (in part common with Rasmol and Chime), that will modify the way the molecular model is shown. The file can have any extension (though {{file|.spt}} is the acknowledged standard). [http://dissertations.biz/ professional dissertation]
+Jmol reads script files, using not the <code>load</code> command, but the <code>script</code> command. These are plain-text files containing commands in the Jmol scripting language (in part common with Rasmol and Chime), that will modify the way the molecular model is shown. The file can have any extension (though {{file|.spt}} is the acknowledged standard).
 For details on the scripting language, visit the [{{ScriptingDoc}} Interactive Scripting Documentation].
@@ Line 9: / Line 9: @@
 In the Jmol application, you can also read a script file using the top menu, <code>File > Open</code>.
 In both the application and the signed applet, the pop-up menu <code>Load > Script</code>.
 == Script output ==

@@ Line 3: / Line 3: @@
 == Script input ==
-Jmol reads script files, using not the <code>load</code> command, but the <code>script</code> command. These are plain-text files containing commands in the Jmol scripting language (in part common with Rasmol and Chime), that will modify the way the molecular model is shown. The file can have any extension (though {{file|.spt}} is the acknowledged standard).
+Jmol reads script files, using not the <code>load</code> command, but the <code>script</code> command. These are plain-text files containing commands in the Jmol scripting language (in part common with Rasmol and Chime), that will modify the way the molecular model is shown. The file can have any extension (though {{file|.spt}} is the acknowledged standard). [http://dissertations.biz/ professional dissertation]
 For details on the scripting language, visit the [{{ScriptingDoc}} Interactive Scripting Documentation].
@@ Line 9: / Line 9: @@
 In the Jmol application, you can also read a script file using the top menu, <code>File > Open</code>.
 In both the application and the signed applet, the pop-up menu <code>Load > Script</code>.
 == Script output ==

@@ Line 57: / Line 57: @@
 :: Note that, for a multimodel file, although you may include scripts within each of the <code>@<TRIPOS>MOLECULE</code> sections, they will not be applied specifically to that model, but globally to the whole file. So, if the scripts are meant to be model-specific, you should make sure to reference the model in the script.
 * In an '''XYZ''' file, use <code>jmolscript:</code> in the '''second line''', followed by the script commands in the same line.
-* In a '''CIF''' file, use <code>#jmolscript:</code> followed by the script commands in the same line. It may be in any line as long as it does not interfere with the data structure, so it is better to put it either at the beginning or the end of the file.
+* In a '''CIF''' file or a '''Z-matrix''' file, use <code>#jmolscript:</code> followed by the script commands in the same line. It may be in any line as long as it does not interfere with the data structure, so it is better to put it either at the beginning or the end of the file.
 In all cases, the script will be applied after the whole molecule has loaded and after whatever script commands may have been set using <code>set defaultLoadScript</code>.

@@ Line 49: / Line 49: @@
 === Script inline within a molecular coordinates file ===
 Scripts can be included, in a single line, after a <code>jmolscript:</code> tag (case-sensitive; the final colon is needed). This must be taken as a comment by the molecular file parser, so its location depends on the file format:
-* In a PDB file, use <code>REMARK jmolscript:</code> in any line, followed by the script commands in the same line.
+* In a '''PDB''' file, use <code>REMARK jmolscript:</code> in any line, followed by the script commands in the same line.
-:(Several <code>REMARK jmolscript:</code> lines are also supported)
+:(Several <code>REMARK jmolscript:</code> lines are also supported.)
-* In a MOL file (both v2000 and v3000), use <code>jmolscript:</code> in the '''third line''', followed by the script commands in the same line.
+* In a '''MOL''' file (both v2000 and v3000), use <code>jmolscript:</code> in the '''third line''', followed by the script commands in the same line.
-* In an XYZ file, use <code>jmolscript:</code> in the '''second line''', followed by the script commands in the same line.
+* In a '''MOL2''' file, use <code>jmolscript:</code> followed by the script commands in the same line. There are two possible locations for this:
-* In a CIF file, use <code>#jmolscript:</code> followed by the script commands in the same line. It may be in any line as long as it does not interfere with the data structure, so it is better to put it either at the beginning or the end of the file.
+** In the header section (i.e. before the first <code>@<TRIPOS>MOLECULE</code> line), as a general comment, so the line must start with <code>#</code>. (Several <code>jmolscript:</code> lines are also supported.)
 In all cases, the script will be applied after the whole molecule has loaded and after whatever script commands may have been set using <code>set defaultLoadScript</code>.

← Older revision		Revision as of 17:18, 25 April 2009
Line 1:		Line 1:
−	for ~~splitting~~ the ~~contents~~ of [[~~File formats~~]] ~~page~~	+	{{File_Formats}}
−	--to be ~~done~~	+	= File Formats for Scripting Jmol =
		+
		+	== Script input ==
		+	Jmol reads script files, using not the <code>load</code> command, but the <code>script</code> command. These are plain-text files containing commands in the Jmol scripting language (in part common with Rasmol and Chime), that will modify the way the molecular model is shown. The file can have any extension (though {{file\|.spt}} is the acknowledged standard).
		+
		+	For details on the scripting language, visit the [{{ScriptingDoc}} Interactive Scripting Documentation].
		+
		+	In the Jmol application, you can also read a script file using the top menu, <code>File > Open</code>.
		+	In both the application and the signed applet, the pop-up menu <code>Load > Script</code>.
		+
		+
		+	== Script output ==
		+	The Jmol application and the signed applet can write a script file that will restore the current appearance and state of the model.
		+	The unsigned applet cannot save files, but can output the data to the console, from where they can be copied and then pasted and saved to a file by the user.
		+
		+	Using the application's top menu bar:
		+	<code>File > Export > Write State</code>
		+	write a filename and click on <code>Save</code>.
		+	Or you can use the button in the toolbar.
		+	:''In older versions of Jmol:''
		+	:<code>File > Export > Export Image or Script</code>
		+	:and in the <code>Image Type</code> drop-down list, choose <code>SPT</code>, write a filename and click on <code>Save</code>.
		+
		+	Using the pop-up menu:
		+	<code>Save > Script with state</code>
		+
		+	or <code>Show > Current state</code>
		+
		+
		+	== Inline formats ==
		+	Molecular data are usually contained in an external file and loaded into Jmol using the <code>load</code> command, but they can also be contained within the webpage (or fed into it using JavaScript or PHP, e.g. from a database).
		+
		+	In turn, script commands can also be contained in the molecular file.
		+
		+	To allow for this "inline" formats, several methods are implemented:
		+
		+	''Please, note that these are advanced procedures. For normal needs, they can be avoided in favour of using normal scripting practices.''
		+
		+
		+	=== Molecular coordinates inline within a webpage ===
		+	Can be done using direct instructions for the applet or, more easily, using functions in the Jmol.js library: <code>[http://jmol.org/jslibrary/#jmolAppletInline jmolAppletInline], [http://jmol.org/jslibrary/#jmolLoadInline jmolLoadInline], [http://jmol.org/jslibrary/#jmolLoadInlineScript jmolLoadInlineScript]</code>.
		+
		+
		+	=== Molecular coordinates inline within a script or script file ===
		+	Can be done using the <code>[{{ScriptingDoc}}#data data "model"]</code> command.
		+
		+
		+	=== Script inline within a molecular coordinates file ===
		+	Scripts can be included, in a single line, after a <code>jmolscript:</code> tag (case-sensitive; the final colon is needed). This must be taken as a comment by the molecular file parser, so its location depends on the file format:
		+	* In a PDB file, use <code>REMARK jmolscript:</code> in any line, followed by the script commands in the same line.
		+	* In a MOL file (both v2000 and v3000), use <code>jmolscript:</code> in the '''third line''', followed by the script commands in the same line.
		+	* In an XYZ file, use <code>jmolscript:</code> in the '''second line''', followed by the script commands in the same line.
		+	* In a CIF file, use <code>#jmolscript:</code> followed by the script commands in the same line. It may be in any line as long as it does not interfere with the data structure, so it is better to put it either at the beginning or the end of the file.
		+
		+	In all cases, the script will be applied after the whole molecule has loaded and after whatever script commands may have been set using <code>set defaultLoadScript</code>.