Difference between revisions of "Get fastastr"

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[[get_fastastr]] is an API-only function which returns the one-letter amino acid sequence in FASTA format.
 
[[get_fastastr]] is an API-only function which returns the one-letter amino acid sequence in FASTA format.
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''Changed in PyMOL 2.2: Sequences per chain''
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''Changed in PyMOL 2.2: Nucleic acid support''
  
 
== PyMOL API ==
 
== PyMOL API ==
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  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV
 
  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV
 
  LRLRGG
 
  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 ==
 
== See Also ==
  
 
* [[Aa codes]]
 
* [[Aa codes]]

Latest revision as of 13:49, 30 July 2020

get_fastastr is an API-only function which returns the one-letter amino acid sequence in FASTA format.

Changed in PyMOL 2.2: Sequences per chain

Changed in PyMOL 2.2: Nucleic acid support

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

See Also