Bell: 6 revisions

2014-03-28T03:09:16Z

6 revisions

Rlc: Fixed error in example for passing command line options to a script.

2014-01-15T16:42:45Z

Fixed error in example for passing command line options to a script.

Cank: Scripting FAQa moved to Scripting FAQs

2009-03-11T18:31:21Z

Scripting FAQa moved to Scripting FAQs

Cank: Scripting moved to Scripting FAQa

2009-03-11T18:31:13Z

Scripting moved to Scripting FAQa

New page

==Script within a Structure==
Q: Is there a way to embed a script within a PDB structure?

A: Yes, there are two ways
* Use the [[Read_Pdbstr]] command like,
delete all
cmd.read_pdbstr("""HETATM 1985 O00 MOH 132 18.797 6.477 -12.112 0.00 0.00 O\
HETATM 1988 H03 MOH 132 18.437 7.229 -11.665 0.00 0.00 H\
HETATM 1989 C04 MOH 132 17.737 5.662 -12.563 0.00 0.00 C\
HETATM 1990 H05 MOH 132 18.129 4.785 -13.080 0.00 0.00 H\
HETATM 1991 H06 MOH 132 17.096 6.211 -13.253 0.00 0.00 H\
HETATM 1992 H07 MOH 132 17.130 5.322 -11.722 0.00 0.00 H""","mymolecule")
show sticks

Don't forget the backslashes there -- it's one long command.
[http://chips.csb.ki.se/pymol/msg02104.html Example]

* Or, as Warren noted, you can do with with a "p1m" file, which is like a "pml" file, but data can be included as well. Also note that p1m files are intended for web publishing, so embedded Python is disallowed. In p1m files, there is an "embed" command that enables this for PDB, MOL, MOL2, SDF, and XPLOR data. It works like this:
embed tag, format
****REPLACE THIS LINE WITH YOUR DATA FILE****
embed end

load_embedded tag
where tag is some identifier of your choice.

==Scripting and Command Line Options==
PyMol will allow you to use command line options in a script. That means, the following
<source lang="python">
pymol -qrc script.py arg1 arg2
</source>
will work if you add a double-hyphen before the first argument in order
to signal Pymol to stop interpreting arguments:

<source lang="python">
pymol -qrc script.py -- arg1 arg2
</source>

Then your script can get these arguments as follows:

<source lang="python">
from sys import argv
my_argv =3D argv[argv.index("--"):]
print my_argv[1], my_argv[2]
</source>

[[Category:Scripting]]

← Older revision	Revision as of 03:09, 28 March 2014
(No difference)

@@ Line 40: / Line 40: @@
 <source lang="python">
 from sys import argv
-my_argv =3D argv[argv.index("--"):]
+my_argv = argv[1:]
-print my_argv[1], my_argv[2]
+print my_argv[0], my_argv[1]
 </source>
 [[Category:Scripting]]

← Older revision	Revision as of 18:31, 11 March 2009
(No difference)

Scripting FAQs - Revision history

Bell: 6 revisions

Rlc: Fixed error in example for passing command line options to a script.

Cank: Scripting FAQa moved to Scripting FAQs

Cank: Scripting moved to Scripting FAQa