Get fastastr: Difference between revisions
Jump to navigation
Jump to search
(Created page with "== cmd.get_fastastr == Do you have a pdb file which come from a modelling program?<br> Are you unsure about which amino sequence is in the "long" pdb file? What you really want...") |
(rewrite of page) |
||
| Line 1: | Line 1: | ||
[[get_fastastr]] is an API-only function which returns the one-letter amino acid sequence in FASTA format. | |||
== PyMOL API == | |||
<syntaxhighlight lang="python"> | |||
cmd.get_fastastr(string selection='all', int state=-1, int quiet=1) | |||
</syntaxhighlight> | |||
== Example == | |||
<syntaxhighlight lang="python"> | |||
fetch 1ubq, async=0 | |||
print cmd.get_fastastr('all') | |||
</syntaxhighlight> | |||
>1ubq | |||
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV | |||
LRLRGG | |||
== Known Issues == | |||
* Due to a bug this function currently only works for selections from a single object (see [https://sourceforge.net/tracker/?func=detail&aid=3466472&group_id=4546&atid=104546 #3466472]) | |||
* The sequences of different chains are just concatenated and returned as a single sequence | |||
== See Also == | |||
* [[Aa codes]] | |||
Revision as of 10:30, 8 February 2012
get_fastastr is an API-only function which returns the one-letter amino acid sequence in FASTA format.
PyMOL API
cmd.get_fastastr(string selection='all', int state=-1, int quiet=1)
Example
fetch 1ubq, async=0
print cmd.get_fastastr('all')
>1ubq MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV LRLRGG
Known Issues
- Due to a bug this function currently only works for selections from a single object (see #3466472)
- The sequences of different chains are just concatenated and returned as a single sequence