Pyadmin: 4 revisions

2014-03-28T01:21:03Z

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= Overview =
[[CollapseSel]] is a small utility function to compress strings for selections. So, if you have a selection with residues 1+2+3+4+20+21+22+100-120 this will return, 1-4+20-22+100-120.

'''CollapseIDs''' is a small utility function to compress strings for an array of IDs. This does NOT have the logic for detecting duplicates, [[CollapseSel]] does.

=Example=
<source lang="python">
run /dir/to/collapseSel.py
fetch 1cll
select EE, resn GLU
print collapseSel("EE")
#
# and PyMOL should output:
#
# 6-7+11+14+31+45+47+54+67+82-84+87+104+114+119-120+123+127+139-140
#
</source>

=The Code=
<source lang="python">
import pymol
from pymol import stored

def collapseIDs(ids):
"""
Helper function to make a smart list of IDs: eg turns 1+2+3+4+5 into 1-5.
"""
rVal = []
if len(ids)==0:
return ""

scanning=False
anchor = 0
start = 0
# 1-5 7-10 12 21-23
for cur in range(0,len(ids)-1):
if ids[cur]+1 == ids[cur+1]:
if scanning:
scanning=True
continue
else:
scanning=True
start = cur
else:
if scanning:
scanning=False
rVal.append(str(ids[start]) + "-" + str(ids[cur]))
start = cur
else:
scanning=False
rVal.append(str(ids[cur]))
if scanning:
rVal.append( str(ids[start]) + "-" + str(ids[cur+1]))
else:
rVal.append(str(ids[-1]))
return rVal

def collapseSel(sel=None,lType="resi"):
"""
collapseSel -- given a valid PyMOL selection and list type, return a collapsed
list of numbers corresponding to the lType. For example, to compactly
print the residue identifiers for all the waters, try:
select theWaters, resn HOH
print collapseSel( "theWaters" )

This will convert: 1+2+3+4+10+11+12 into 1-4+10-12

PARAMS
sel
The selection to collapse
lType
The identifier type: 'resi', 'ID', 'id', or any numerical property.

RETURNS
a string of collapsed IDs.
"""
if sel==None:
return ""

stored.s = set()
cmd.iterate( sel, "stored.s.add(int(float(%s)))" % lType)
l = list(stored.s)
l.sort()
return "+".join(collapseIDs(list(l)))

cmd.extend("collapseSel", collapseSel)
</source>

[[Category:ObjSel_Scripts]]
[[Category:Script_Library]]

CollapseSel - Revision history

Pyadmin: 4 revisions