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#!/usr/bin/env python
# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from __future__ import print_function
import getopt
import sys
from Bio._py3k import urlretrieve as _urlretrieve
from Bio.SCOP import Raf, Cla
def usage():
print("""Extract a SCOP domain's ATOM and HETATOM records from the relevant PDB file.
For example:
scop_pdb.py astral-rapid-access-1.55.raf dir.cla.scop.txt_1.55 d3hbib_
A result file, d3hbib_.ent, will be generated in the working directory.
The required RAF file can be found at [http://astral.stanford.edu/raf.html],
and the SCOP CLA file at [http://scop.berkeley.edu/parse/index.html].
Note: Errors will occur if the PDB file has been altered since the creation
of the SCOP CLA and ASTRAL RAF files.
Usage: scop_pdb [-h] [-i file] [-o file] [-p pdb_url_prefix]
raf_url cla_url [sid] [sid] [sid] ...
-h -- Print this help message.
-i file -- Input file name. Each line should start with an sid (Scop domain
identifier). Blank lines, and lines starting with '#' are
ignored. If file is '-' then data is read from stdin. If not
given then sids are taken from the command line.
-o file -- Output file name. If '-' then data is written to stdout. If not
given then data is written to files named sid+'.ent'.
-p pdb_url-- A URL for PDB files. The token '%s' will be replaced with the
4 character PDB ID. If the pdb_url is not given then the latest
PDB file is retrieved directly from rcsb.org.
raf_url -- The URL or filename of an ASTRAL Rapid Access File sequence map.
See [http://astral.stanford.edu/raf.html]
cla_url -- The URL or filename of a SCOP parsable CLA file.
See [http://scop.berkeley.edu/parse/index.html]
sid -- A SCOP domain identifier. e.g. d3hbib_
""")
default_pdb_url = "http://www.rcsb.org/pdb/cgi/export.cgi/somefile.pdb?" \
"format=PDB&pdbId=%s&compression=None"
# default_pdb_url = "file://usr/local/db/pdb/data/010331/snapshot/all/pdb%s.ent"
def open_pdb(pdbid, pdb_url=None):
if pdb_url is None:
pdb_url = default_pdb_url
url = pdb_url % pdbid
fn, header = _urlretrieve(url)
return open(fn)
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], "hp:o:i:",
["help", "usage", "pdb=", "output=", "input="])
except getopt.GetoptError:
# show help information and exit:
usage()
sys.exit(2)
input = None
in_handle = None
output = None
pdb_url = None
cla_url = None
raf_url = None
for o, a in opts:
if o in ("-h", "--help", "--usage"):
usage()
sys.exit()
elif o in ("-o", "--output"):
output = a
elif o in ("-i", "--input"):
input = a
elif o in ("-p", "--pdb"):
pdb_url = a
if len(args) < 2:
sys.stderr.write("Not enough arguments. Try --help for more details.\n")
sys.exit(2)
raf_url = args[0]
cla_url = args[1]
(raf_filename, headers) = _urlretrieve(raf_url)
seqMapIndex = Raf.SeqMapIndex(raf_filename)
(cla_filename, headers) = _urlretrieve(cla_url)
claIndex = Cla.Index(cla_filename)
if input is None:
sids = args[2:]
elif input == '-':
sids = sys.stdin
else:
in_handle = open(input)
sids = in_handle
try:
for sid in sids:
if not sid or sid[0:1] == '#':
continue
id = sid[0:7]
pdbid = id[1:5]
s = pdbid[0:1]
if s == '0' or s == 's':
sys.stderr.write("No coordinates for domain %s\n" % id)
continue
if output is None:
filename = id + ".ent"
out_handle = open(filename, "w+")
elif output == '-':
out_handle = sys.stdout
else:
out_handle = open(output, "w+")
try:
try:
claRec = claIndex[id]
residues = claRec.residues
seqMap = seqMapIndex.getSeqMap(residues)
pdbid = residues.pdbid
f = open_pdb(pdbid, pdb_url)
try:
seqMap.getAtoms(f, out_handle)
finally:
f.close()
except (IOError, KeyError, RuntimeError) as e:
sys.stderr.write("I cannot do SCOP domain %s : %s\n" % (id, e))
finally:
out_handle.close()
finally:
if in_handle is not None:
in_handle.close()
if __name__ == "__main__":
main()
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