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2014-03-28T02:16:24Z

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Hongbo zhu: add reference to Psico function select_pepseq

2013-01-03T15:19:07Z

add reference to Psico function select_pepseq

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{{Infobox script-repo
|type = script
|filename = findseq.py
|author = [[User:Inchoate|Jason Vertrees]]
|license = BSD
}}

= Overview & Motivation =
Anyone ever give you a protein and then say, find the sequence "FLVEW"? Well, this script will find any string or regular expression in a given object and return that selection for you. Here's an example,
<syntaxhighlight lang="python">
reinitialize
import findseq
# fetch two sugar-binding PDB
fetch 1tvn, async=0
# Now, find FATEW in 1tvn, similarly
findseq FATEW, 1tvn
# lower-case works, too
findseq fatew, 1tvn
# how about a regular expression?
findseq F.*W, 1tvn

# Find the regular expression:
# ..H[TA]LVWH
# in the few proteins loaded.
# I then showed them as sticks and colored them to highlight matched AAs
for x in cmd.get_names(): findseq.findseq("..H[TA]LVWH", x, "sele_"+x, firstOnly=1)
</syntaxhighlight>

[[Image:SeqFinder.png|center|thumb|400px|Red residues were those matching the regular expression '..H[TA]LVWH'.]]

= Usage =
I built this to be rather flexible. You call it as:
<source lang="python">findseq needle, haystack[, selName[, het[, firstOnly ]]]</source> where the options are:
:: '''needle''' the sequence of amino acids to find. Should be a string of one letter amino acid abbreviations. Can also be a string-style regular expression (eg. FW.*QQ).
:: '''haystack''' the PyMOL object or selection in which to search
:: '''selName''' the name of the returned selection. If you leave this blank, it'll be ''foundSeqXYZ'' where XYZ is some random integer (eg. foundSeq1435); if you supply ''sele'' then the usual PyMOL ''(sele)'' is used; and, finally, if it's anything else, then that will be used verbatim. Defaults to ''foundSeqXYZ'' so as not to overwrite any selections you might have in ''sele''.
:: '''het''' 0/1 -- if 0 then heteroatoms are not considered; if 1 then they are; defaults to 0
:: '''firstOnly''' 0/1 -- if 0 then all matches are selected and returned; if 1 then only the first is returned

= See Also =
select_pepseq@[[Psico]]

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Pymol-script-repo]]

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Hongbo zhu: add reference to Psico function select_pepseq