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parse_pdb_header.py
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parse_pdb_header.py
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#! /usr/bin/python
#
# parse_pdb_header.py
# parses header of PDB files into a python dictionary.
# emerged from the Columba database project www.columba-db.de.
#
# 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
__doc__="Parse the header of a PDB file."
import sys
import os,string,re
import urllib
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("\AJRNL",l):
journal+=string.lower(l[19:72])
journal=re.sub("\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("\AREMARK 1",l):
if re.search("\AREMARK 1 REFERENCE",l):
if actref!="":
actref=re.sub("\s\s+"," ",actref)
if actref!=" ":
references.append(actref)
actref=""
else:
actref+=string.lower(l[19:72])
if actref!="":
actref=re.sub("\s\s+"," ",actref)
if actref!=" ":
references.append(actref)
return references
# bring dates to format: 1909-01-08
def _format_date(pdb_date):
"""Converts dates from DD-Mon-YY to YYYY-MM-DD format."""
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."""
import re
return re.sub("\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."""
import re
return re.sub("\s\s\s\s+.*\Z","",line)
def _nice_case(line):
"""Makes A Lowercase String With Capitals."""
import string
l=string.lower(line)
s=""
i=0
nextCap=1
while i<len(l):
c=l[i]
if c>='a' and c<='z' and nextCap:
c=string.upper(c)
nextCap=0
elif c==' ' or c=='.' or c==',' or c==';' or c==':' or c=='\t' or\
c=='-' or c=='_':
nextCap=1
s+=c
i+=1
return s
def parse_pdb_header(file):
"""
Returns 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=[]
f=open(filename,'r')
while f:
l=f.readline()
if not re.search("\AATOM",l):
header.append(l)
else:
break
f.close()
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"
src_molid="1"
last_comp_key="misc"
last_src_key="misc"
for hh in header:
h=re.sub("[\s\n\r]*\Z","",hh) # chop linebreaks off
key=re.sub("\s.+\s*","",h)
tail=re.sub("\A\w+\s+\d*\s*","",h)
# print key+":"+tail
# From here, all the keys from the header are being parsed
if key=="TITLE":
name=string.lower(_chop_end_codes(tail))
if dict.has_key('name'):
dict['name'] += " "+name
else:
dict['name']=name
elif key=="HEADER":
rr=re.search("\d\d-\w\w\w-\d\d",tail)
if rr!=None:
dict['deposition_date']=_format_date(_nice_case(rr.group()))
head=string.lower(_chop_end_misc(tail))
dict['head']=head
elif key=="COMPND":
tt=string.lower(re.sub("\;\s*\Z","",_chop_end_codes(tail)))
# look for E.C. numbers in COMPND lines
rec = re.search('\d+\.\d+\.\d+\.\d+',tt)
if rec:
dict['compound'][comp_molid]['ec_number']=rec.group()
tt=re.sub("\((e\.c\.)*\d+\.\d+\.\d+\.\d+\)","",tt)
tok=tt.split(":")
if len(tok)>=2:
ckey=tok[0]
cval=re.sub("\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=string.lower(re.sub("\;\s*\Z","",_chop_end_codes(tail)))
tok=tt.split(":")
# print tok
if len(tok)>=2:
ckey=tok[0]
cval=re.sub("\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=string.lower(_chop_end_codes(tail))
if dict.has_key('keywords'):
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('\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']=string.lower(expd)
elif key=="CAVEAT":
# make Annotation entries out of these!!!
pass
elif key=="REVDAT":
rr=re.search("\d\d-\w\w\w-\d\d",tail)
if rr!=None:
dict['release_date']=_format_date(_nice_case(rr.group()))
elif key=="JRNL":
# print key,tail
if dict.has_key('journal'):
dict['journal']+=tail
else:
dict['journal']=tail
elif key=="AUTHOR":
auth = _nice_case(_chop_end_codes(tail))
if dict.has_key('author'):
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("\s+ANGSTROMS.*","",r)
try:
dict['resolution']=float(r)
except:
print 'nonstandard resolution',r
else:
# print key
pass
if dict['structure_method']=='unknown':
if dict['resolution']>0.0: dict['structure_method']='x-ray diffraction'
return dict
if __name__=='__main__':
"""
Reads a PDB file passed as argument, parses its header, extracts
some data and returns it as a dictionary.
"""
filename = sys.argv[1]
file = open(filename,'r')
dict = parse_pdb_header(file)
# print the dictionary
for d in dict.keys():
print "-"*40
print d
print dict[d]