Scripting FAQs: Difference between revisions
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(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("...) |
m (Fixed error in example for passing command line options to a script.) |
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Don't forget the backslashes there -- it's one long command. | 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: | * 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: | ||
| Line 40: | Line 40: | ||
<source lang="python"> | <source lang="python"> | ||
from sys import argv | from sys import argv | ||
my_argv = | my_argv = argv[1:] | ||
print my_argv[ | print my_argv[0], my_argv[1] | ||
</source> | </source> | ||
[[Category:Scripting]] | |||
Latest revision as of 11:42, 15 January 2014
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. 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
pymol -qrc script.py arg1 arg2
will work if you add a double-hyphen before the first argument in order to signal Pymol to stop interpreting arguments:
pymol -qrc script.py -- arg1 arg2
Then your script can get these arguments as follows:
from sys import argv
my_argv = argv[1:]
print my_argv[0], my_argv[1]