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#!/usr/bin/env python
# Copyright 2004 Kristian Rother
#
# 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.
#
"""Parse header of PDB files into a python dictionary.
Emerged from the Columba database project www.columba-db.de.
Original author: Kristian Rother.
"""
# license: same as Biopython, read LICENSE.TXT from current Biopython release.
#
# last modified: 9.2.2004
#
# Added some small changes: the whole PDB file is not read in anymore, but just
# until the first ATOM record (faster). I also split parse_pdb_header into
# parse_pdb_header and parse_pdb_header_list, because parse_pdb_header_list
# can be more easily reused in PDBParser.
#
# Thomas, 19/03/04
#
# Renamed some clearly private functions to _something (ie. parse_pdb_header_list
# is now _parse_pdb_header_list)
# Thomas 9/05/04
from __future__ import print_function
import re
from Bio import File
def _get_journal(inl):
# JRNL AUTH L.CHEN,M.DOI,F.S.MATHEWS,A.Y.CHISTOSERDOV, 2BBK 7
journal = ""
for l in inl:
if re.search(r"\AJRNL", l):
journal += l[19:72].lower()
journal = re.sub(r"\s\s+", " ", journal)
return journal
def _get_references(inl):
# REMARK 1 REFERENCE 1 1CSE 11
# REMARK 1 AUTH W.BODE,E.PAPAMOKOS,D.MUSIL 1CSE 12
references = []
actref = ""
for l in inl:
if re.search(r"\AREMARK 1", l):
if re.search(r"\AREMARK 1 REFERENCE", l):
if actref != "":
actref = re.sub(r"\s\s+", " ", actref)
if actref != " ":
references.append(actref)
actref = ""
else:
actref += l[19:72].lower()
if actref != "":
actref = re.sub(r"\s\s+", " ", actref)
if actref != " ":
references.append(actref)
return references
# bring dates to format: 1909-01-08
def _format_date(pdb_date):
"""Convert dates from DD-Mon-YY to YYYY-MM-DD format (PRIVATE)."""
date = ""
year = int(pdb_date[7:])
if year < 50:
century = 2000
else:
century = 1900
date = str(century + year) + "-"
all_months = ['xxx', 'Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul',
'Aug', 'Sep', 'Oct', 'Nov', 'Dec']
month = str(all_months.index(pdb_date[3:6]))
if len(month) == 1:
month = '0' + month
date = date + month + '-' + pdb_date[:2]
return date
def _chop_end_codes(line):
"""Chops lines ending with ' 1CSA 14' and the like (PRIVATE)."""
return re.sub(r"\s\s\s\s+[\w]{4}.\s+\d*\Z", "", line)
def _chop_end_misc(line):
"""Chops lines ending with ' 14-JUL-97 1CSA' and the like (PRIVATE)."""
return re.sub(r"\s\s\s\s+.*\Z", "", line)
def _nice_case(line):
"""Make A Lowercase String With Capitals (PRIVATE)."""
line_lower = line.lower()
s = ""
i = 0
nextCap = 1
while i < len(line_lower):
c = line_lower[i]
if c >= 'a' and c <= 'z' and nextCap:
c = c.upper()
nextCap = 0
elif c in ' .,;:\t-_':
nextCap = 1
s += c
i += 1
return s
def parse_pdb_header(infile):
"""Return the header lines of a pdb file as a dictionary.
Dictionary keys are: head, deposition_date, release_date, structure_method,
resolution, structure_reference, journal_reference, author and
compound.
"""
header = []
with File.as_handle(infile, 'r') as f:
for l in f:
record_type = l[0:6]
if record_type in ("ATOM ", "HETATM", "MODEL "):
break
else:
header.append(l)
return _parse_pdb_header_list(header)
def _parse_pdb_header_list(header):
# database fields
dict = {
'name': "",
'head': '',
'deposition_date': "1909-01-08",
'release_date': "1909-01-08",
'structure_method': "unknown",
'resolution': 0.0,
'structure_reference': "unknown",
'journal_reference': "unknown",
'author': "",
'compound': {'1': {'misc': ''}}, 'source': {'1': {'misc': ''}}}
dict['structure_reference'] = _get_references(header)
dict['journal_reference'] = _get_journal(header)
comp_molid = "1"
last_comp_key = "misc"
last_src_key = "misc"
for hh in header:
h = re.sub(r"[\s\n\r]*\Z", "", hh) # chop linebreaks off
# key=re.sub("\s.+\s*","",h)
key = h[:6].strip()
# tail=re.sub("\A\w+\s+\d*\s*","",h)
tail = h[10:].strip()
# print("%s:%s" % (key, tail)
# From here, all the keys from the header are being parsed
if key == "TITLE":
name = _chop_end_codes(tail).lower()
if 'name' in dict:
dict['name'] += " " + name
else:
dict['name'] = name
elif key == "HEADER":
rr = re.search(r"\d\d-\w\w\w-\d\d", tail)
if rr is not None:
dict['deposition_date'] = _format_date(_nice_case(rr.group()))
head = _chop_end_misc(tail).lower()
dict['head'] = head
elif key == "COMPND":
tt = re.sub(r"\;\s*\Z", "", _chop_end_codes(tail)).lower()
# look for E.C. numbers in COMPND lines
rec = re.search(r'\d+\.\d+\.\d+\.\d+', tt)
if rec:
dict['compound'][comp_molid]['ec_number'] = rec.group()
tt = re.sub(r"\((e\.c\.)*\d+\.\d+\.\d+\.\d+\)", "", tt)
tok = tt.split(":")
if len(tok) >= 2:
ckey = tok[0]
cval = re.sub(r"\A\s*", "", tok[1])
if ckey == 'mol_id':
dict['compound'][cval] = {'misc': ''}
comp_molid = cval
last_comp_key = "misc"
else:
dict['compound'][comp_molid][ckey] = cval
last_comp_key = ckey
else:
dict['compound'][comp_molid][last_comp_key] += tok[0] + " "
elif key == "SOURCE":
tt = re.sub(r"\;\s*\Z", "", _chop_end_codes(tail)).lower()
tok = tt.split(":")
# print(tok)
if len(tok) >= 2:
ckey = tok[0]
cval = re.sub(r"\A\s*", "", tok[1])
if ckey == 'mol_id':
dict['source'][cval] = {'misc': ''}
comp_molid = cval
last_src_key = "misc"
else:
dict['source'][comp_molid][ckey] = cval
last_src_key = ckey
else:
dict['source'][comp_molid][last_src_key] += tok[0] + " "
elif key == "KEYWDS":
kwd = _chop_end_codes(tail).lower()
if 'keywords' in dict:
dict['keywords'] += " " + kwd
else:
dict['keywords'] = kwd
elif key == "EXPDTA":
expd = _chop_end_codes(tail)
# chop junk at end of lines for some structures
expd = re.sub(r'\s\s\s\s\s\s\s.*\Z', '', expd)
# if re.search('\Anmr',expd,re.IGNORECASE): expd='nmr'
# if re.search('x-ray diffraction',expd,re.IGNORECASE): expd='x-ray diffraction'
dict['structure_method'] = expd.lower()
elif key == "CAVEAT":
# make Annotation entries out of these!!!
pass
elif key == "REVDAT":
rr = re.search(r"\d\d-\w\w\w-\d\d", tail)
if rr is not None:
dict['release_date'] = _format_date(_nice_case(rr.group()))
elif key == "JRNL":
# print("%s:%s" % (key, tail))
if 'journal' in dict:
dict['journal'] += tail
else:
dict['journal'] = tail
elif key == "AUTHOR":
auth = _nice_case(_chop_end_codes(tail))
if 'author' in dict:
dict['author'] += auth
else:
dict['author'] = auth
elif key == "REMARK":
if re.search("REMARK 2 RESOLUTION.", hh):
r = _chop_end_codes(re.sub("REMARK 2 RESOLUTION.", '', hh))
r = re.sub(r"\s+ANGSTROM.*", "", r)
try:
dict['resolution'] = float(r)
except ValueError:
# print('nonstandard resolution %r' % r)
dict['resolution'] = None
else:
# print(key)
pass
if dict['structure_method'] == 'unknown':
if dict['resolution'] > 0.0:
dict['structure_method'] = 'x-ray diffraction'
return dict
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