Difference between revisions of "Get fastastr"
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(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...") |
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| − | + | [[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 11:30, 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