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#!/usr/bin/env python

docstring='''

strip_sidechain.py fullatom.pdb > backbone.pdb

strip side chain from full atom PDB "fullatom.pdb"

options:

-convertAA={GLY,ALA} convert any residue to one specific amino acid type

default is do not convert

-amide={true,false} whether preserve amide bond atomsbackbone atoms

'''

import sys

def strip_sidechain(fullatom,convertAA=False,amide=True):

'''strip side chain from full atom PDB file "fullatom"

convertAA - convert all amino acid to one specific type

amide - whether preserve amide bond atoms'''

atom_name_set=["CA","C ","N ","O "] if amide else ["CA"]

fp=open(fullatom,'rU')

fullatom_lines=fp.readlines()

fp.close()

backbone_txt=''

for line in fullatom_lines:

if line.startswith("ATOM") and line[13:15] in atom_name_set:

backbone_txt+=line if not convertAA else \

line[:17]+convertAA+line[20:]

return backbone_txt

if __name__=="__main__":

convertAA=False

amide=True

argv=[]

for arg in sys.argv[1:]:

if arg.startswith("-convertAA="):

convertAA=arg[len("-convertAA="):]

elif arg.startswith("-amide="):

amide=(arg[len("-amide="):].lower()=="true")

elif arg.startswith('-'):

sys.stderr.write("ERROR! Unknown argument %s\n"%arg)

exit()

else:

argv.append(arg)

if len(argv)<1:

sys.stderr.write(docstring)

exit()

for arg in argv:

sys.stdout.write(strip_sidechain(arg,convertAA,amide))