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__init__.py

import string
import re
import fssp_rec
from Bio.Align import Generic
from Bio import Alphabet
fff_rec = fssp_rec.fff_rec
"""
A module to handle FSSP files. For now it parses only the header, summary and alignment
sections.

functions: read_fssp(file_handle): reads an fssp file into the records. Returns a
tuple of two instances.
mult_align: returns a Biopyton alignment object
"""
header_records = {
   'database' : re.compile('^DATABASE'),
   'pdbid': re.compile('^PDBID'),
   'header': re.compile('^HEADER'),
   'compnd': re.compile('^COMPND'),
   'author': re.compile('^AUTHOR'),
   'source': re.compile('^SOURCE'),
   'seqlength': re.compile('^SEQLENGTH'),
   'nalign': re.compile('^NALIGN')
}

summary_title = re.compile('## +SUMMARY')
summary_rec = re.compile(' *[0-9]+: +[1-9][0-9a-z]{3,3}')
alignments_title= re.compile('## +ALIGNMENTS')
alignments_rec = re.compile(' *[0-9]+ +-{0,1}[0-9]+')
equiv_title = re.compile('## +EQUIVALENCES')

class FSSPHeader:
   def __init__(self):
      self.database = None
      self.pdbid = ''
      self.header = ''
      self.compnd = ''
      self.source = ''
      self.author = []
      self.seqlength = 0
      self.nalign = 0
   def fill_header(self,inline):
      for i in header_records.keys():
         if header_records[i].match(inline):
            if i == 'database' or i == 'seqlength' or i == 'nalign':
               setattr(self,i,int(string.split(inline)[1]))
            elif i == 'compnd' or i == 'author':
               setattr(self,i,string.split(inline)[1:])
            elif i == 'source' or i == 'header':
               attr = inline[inline.find(' ')+1:].strip()
               setattr(self,i,attr)
            else:
               setattr(self,i,string.split(inline)[1])

class PosAlign:
   def __init__(self,inStr):
      inStr = string.strip(inStr)
      if len(inStr) <> 1 and len(inStr)<> 2:
         raise ValueError, 'PosAlign: length not 2 chars' + inStr
      if inStr == '..':
         self.aa = '-'
         self.gap = 1
      else:
         self.gap = 0
         self.aa = inStr[0]
         if self.aa == string.lower(self.aa):
            self.aa = 'C'
         if len(inStr) == 2:
            self.ss = string.upper(inStr[1])
         else:
            self.ss = '0'

   def __repr__(self):
      if self.gap:
         outstring = '..'
      else:
         outstring = self.aa+string.lower(self.ss)
      return outstring

   __str__  = __repr__




00085 class FSSPSumRec:
   """ Contains info from an FSSP summary record"""
   def __init__(self,in_str):
      self.raw = in_str
      in_rec = string.split(string.strip(in_str))
      # print in_rec
      self.nr = string.atoi(in_rec[0][:-1])
      self.pdb1 = in_rec[1][:4]
      if len(in_rec[1]) == 4:
         self.chain1='0'
      elif len(in_rec[1]) == 5:
         self.chain1=in_rec[1][4]
      else:
         raise ValueError, 'Bad PDB ID 1'
      self.pdb2 = in_rec[2][:4]
      if len(in_rec[2]) == 4:
         self.chain2='0'
      elif len(in_rec[2]) == 5:
         self.chain2=in_rec[2][4]
      else:
         raise ValueError, 'Bad PDB ID 2'
      self.zscore = string.atof(in_rec[3])
      self.rmsd = string.atof(in_rec[4])
      self.lali = string.atof(in_rec[5])
      self.lseq2 = string.atof(in_rec[6])
      self.pID = string.atof(in_rec[7])
      self.revers = string.atoi(in_rec[8])
      self.permut = string.atoi(in_rec[9])
      self.nfrag = string.atoi(in_rec[10])
      self.topo = in_rec[11]
      self.doc = ''
      for i in in_rec[12:]:
         self.doc = self.doc + i + ' '
      self.doc = string.rstrip(self.doc) + '\n'

   def __repr__(self):
      return self.raw
   __str__ = __repr__

class FSSPAlignRec:
   def __init__(self,in_fff_rec):
      # print in_fff_rec
      self.abs_res_num = string.atoi(in_fff_rec[fssp_rec.align.abs_res_num])
      self.pdb_res_num = string.strip(in_fff_rec[fssp_rec.align.pdb_res_num])
      self.chain_id  = in_fff_rec[fssp_rec.align.chain_id]
      if self.chain_id == ' ':
         self.chain_id = '0'
      self.res_name = in_fff_rec[fssp_rec.align.res_name]
      if self.res_name == string.lower(self.res_name):
         self.res_name = 'C'
      self.ss1 = in_fff_rec[fssp_rec.align.ss1]
      self.turn3 = in_fff_rec[fssp_rec.align.turn3]
      self.turn4 = in_fff_rec[fssp_rec.align.turn4]
      self.turn5 = in_fff_rec[fssp_rec.align.turn5]
      self.pos_align_dict = {}
      self.PosAlignList = []
   def add_align_list(self,align_list):
      for i in align_list:
         self.PosAlignList.append(PosAlign(i))
   def pos_align_list2dict(self):
      j = 1
      for i in self.PosAlignList:
         self.pos_align_dict[j] = i
         j = j + 1


class FSSPAlignDict(dict):
   def __init__(self):
      # The following two dictionaries are pointers to records in self
      # The first dictionary is a "pdb_residue_number: self_key"
      # The second dictionary is a "absolute_residue_number: self_key"
      self.pdb_res_dict = {}
      self.abs_res_dict = {}
      self.data = {}
   def build_resnum_list(self):
      for i in self.keys():
         self.abs_res_dict[self[i].abs_res_num] = i
         self.pdb_res_dict[self[i].pdb_res_num] = i
   # Given an absolute residue number & chain, returns the relevant fssp
   # record
   def abs(self,num):
      return self[self.abs_res_dict[num]]
   # Given an PDB residue number & chain, returns the relevant fssp
   # record
   def pdb(self,num):
      return self[self.pdb_res_dict[num]]
   # Returns a sequence string

   def sequence(self,num):
      s = ''
      sorted_pos_nums = self.abs_res_dict.keys()
      sorted_pos_nums.sort()
      for i in sorted_pos_nums:
         s += self.abs(i).pos_align_dict[num].aa
      return s

   def fasta_mult_align(self):
      mult_align_dict = {}
      for j in self.abs(1).pos_align_dict.keys():
         mult_align_dict[j] = ''
      for fssp_rec in self.values():
         for j in fssp_rec.pos_align_dict.keys():
            mult_align_dict[j] += fssp_rec.pos_align_dict[j].aa
      seq_order = mult_align_dict.keys()
      seq_order.sort()
      out_str = ''
      for i in seq_order:
         out_str += '> %d\n' % i
         k = 0
         for j in mult_align_dict[i]:
            k += 1
            if k % 72 == 0:
               out_str += '\n'
            out_str += j
         out_str += '\n'
      return out_str

class FSSPSumDict(dict):
   pass

#
# Process a fssp file into its constituents. Return a 2-tuple containing
# a list of FSSPSumRecs and a dictionary of alignment records.
#
def read_fssp(fssp_handle):
   header = FSSPHeader()
   sum_dict = FSSPSumDict()
   align_dict = FSSPAlignDict()
   # fssp_handle=open(fssp_handlename)
   curline = fssp_handle.readline()
   while not summary_title.match(curline):
      # Still in title
      header.fill_header(curline)
      curline = fssp_handle.readline()
      
   if not summary_title.match(curline):
      raise ValueError,'Bad FSSP file: no summary record found'
   curline = fssp_handle.readline()  #Read the title line, discard
   curline = fssp_handle.readline()  #Read the next line
   # Process the summary records into a list
   while summary_rec.match(curline):
      cur_sum_rec = FSSPSumRec(curline)
      sum_dict[cur_sum_rec.nr] = cur_sum_rec
      curline = fssp_handle.readline()

   # Outer loop: process everything up to the EQUIVALENCES title record
   while not equiv_title.match(curline):
      while (not alignments_title.match(curline) and
             not equiv_title.match(curline)):
         curline = fssp_handle.readline()
      if not alignments_title.match(curline):
         if equiv_title.match(curline):
            # print "Reached equiv_title"
            break
         else:
            raise ValueError,'Bad FSSP file: no alignments title record found'

      if equiv_title.match(curline):
         break
      # If we got to this point, this means that we have matched an
      # alignments title. Parse the alignment records in a loop.
      curline = fssp_handle.readline()  #Read the title line, discard
      curline = fssp_handle.readline()  #Read the next line
      while alignments_rec.match(curline):
         align_rec = FSSPAlignRec(fff_rec(curline))
         key = align_rec.chain_id+align_rec.res_name+str(align_rec.pdb_res_num)
         align_list = string.split(curline[fssp_rec.align.start_aa_list:])
         if not align_dict.has_key(key):
            align_dict[key] = align_rec
         align_dict[key].add_align_list(align_list)
         curline = fssp_handle.readline()
         if not curline:
            print 'EOFEOFEOF'
            raise EOFError
   for i in align_dict.values():
      i.pos_align_list2dict()
      del i.PosAlignList
   align_dict.build_resnum_list()
   return (header, sum_dict, align_dict)


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