1.1 --- a/geometrical_core/geometrical_core.py	Sun Oct 24 17:29:59 2010 +0400
     1.2 +++ b/geometrical_core/geometrical_core.py	Sun Oct 24 18:12:21 2010 +0400
     1.3 @@ -118,7 +118,7 @@
     1.4          exit()
     1.5  
     1.6      project = Project(args.i)
     1.7 -    project
     1.8 +    project.pdb_auto_add(args.c)
     1.9      
    1.10  except Exception, t:
    1.11      print t

     2.1 --- a/lib/allpy_pdb.py	Sun Oct 24 17:29:59 2010 +0400
     2.2 +++ b/lib/allpy_pdb.py	Sun Oct 24 18:12:21 2010 +0400
     2.3 @@ -11,7 +11,7 @@
     2.4  """
     2.5  
     2.6  # for pdb-codes
     2.7 -re1 = re.compile(r"(^|[^a-z0-9])(?P<code>[0-9][0-9a-z]{3})([^a-z0-9](?P<chain>[0-9a-z ]?)(?P<model>[^a-z0-9]([0-9]{1,3}))?)?($|[^a-z0-9])")
     2.8 +re1 = re.compile(r"(^|[^a-z0-9])(?P<code>[0-9][0-9a-z]{3})([^a-z0-9](?P<chain>[0-9a-z ]?)(?P<model>[^a-z0-9]([0-9]{1,3}))?)?($|[^a-z0-9])", re.I)
     2.9  
    2.10  #~ # for files
    2.11  #~ re2 = re.compile(r"(^)([^^]+\.(ent|pdb))([^a-zA-Z0-9]([0-9A-Za-z ]?)([^a-zA-Z0-9]([0-9]{1,3}))?)?$")
    2.12 @@ -25,11 +25,15 @@
    2.13          (pdb_id.lower().strip(), pdb_chain.upper().strip())
    2.14      
    2.15  def pdb_id_parse(ID):
    2.16 -    match = re1.search(ID, re.I)
    2.17 +    match = re1.search(ID)
    2.18      if not match:
    2.19          return None
    2.20 -    return match.groupdict()
    2.21 -    
    2.22 +    d = match.groupdict()
    2.23 +    if 'chain' not in d or not d['chain']:
    2.24 +        d['chain'] = ' '
    2.25 +    if 'model' not in d or not d['model']:
    2.26 +        d['model'] = 0
    2.27 +    return d
    2.28      
    2.29  #~ def std_id_parse(ID):
    2.30      #~ """

     3.1 --- a/lib/config.py	Sun Oct 24 17:29:59 2010 +0400
     3.2 +++ b/lib/config.py	Sun Oct 24 18:12:21 2010 +0400
     3.3 @@ -4,7 +4,8 @@
     3.4  maxabsent = 0.15 # deprecated?
     3.5  
     3.6  # pdb download url (XXXX is pdb code place)
     3.7 -pdb_url = 'http://www.pdb.org/pdb/files/XXXX.pdb'
     3.8 +pdb_url = 'http://www.pdb.org/pdb/files/%s.pdb'
     3.9 +pdb_dir = '/tmp/%s.pdb'
    3.10  timeout = 10 # time in sec. for BRON-KERBOSH algorithm
    3.11  
    3.12  

     4.1 --- a/lib/project.py	Sun Oct 24 17:29:59 2010 +0400
     4.2 +++ b/lib/project.py	Sun Oct 24 18:12:21 2010 +0400
     4.3 @@ -167,7 +167,7 @@
     4.4          uses old Monomers and Sequences objects
     4.5          """
     4.6          tmp_file, tmp_filename = mkstemp()
     4.7 -        os.close(tmp_file) # this is file descriptor, not normal file object. security issue )
     4.8 +        os.close(tmp_file) # this is file descriptor, not normal file object.
     4.9          tmp_file = open(tmp_filename, 'w')
    4.10          self.save_fasta(tmp_file)
    4.11          tmp_file.close()
    4.12 @@ -177,7 +177,8 @@
    4.13              try:
    4.14                  new_sequence = [i for i in sequences if sequence==i][0]
    4.15              except:
    4.16 -                raise Exception("Align: Cann't find sequence %s in muscle output" % sequence.name)
    4.17 +                raise Exception("Align: Cann't find sequence %s in muscle output" % \
    4.18 +                sequence.name)
    4.19              old_monomers = iter(sequence.monomers)
    4.20              self.alignment[sequence] = []
    4.21              for monomer in alignment[new_sequence]:
    4.22 @@ -194,7 +195,7 @@
    4.23          returns list of columns of alignment
    4.24          sequence or sequences:
    4.25              if sequence is given, then column is (original_monomer, monomer)
    4.26 -            if sequences is given, then column is dict (original_monomer, {sequence: monomer}) 
    4.27 +            if sequences is given, then column is (original_monomer, {sequence: monomer}) 
    4.28              if both of them are given, it is an error
    4.29          original (Sequence type):
    4.30              if given, this filters only columns represented by original sequence
    4.31 @@ -210,11 +211,17 @@
    4.32                  if sequence:
    4.33                      yield (column[indexes[original]], column[indexes[sequence]])
    4.34                  else:
    4.35 -                    yield (column[indexes[original]], dict([(s, column[indexes[s]]) for s in sequences]))
    4.36 +                    yield (column[indexes[original]], 
    4.37 +                    dict([(s, column[indexes[s]]) for s in sequences]))
    4.38          
    4.39 -    def add_pdb(self, conformity_file=None):
    4.40 -        pass
    4.41 +    def pdb_auto_add(self, conformity_file=None):
    4.42 +        """
    4.43 +        Adds pdb information to each sequence
    4.44          
    4.45 +        TODO: conformity_file
    4.46 +        """
    4.47 +        conformity = {}
    4.48          
    4.49 +        for sequence in self.sequences:
    4.50 +            sequence.pdb_auto_add(conformity.get(sequence.name, None))
    4.51          
    4.52 -        

     5.1 --- a/lib/sequence.py	Sun Oct 24 17:29:59 2010 +0400
     5.2 +++ b/lib/sequence.py	Sun Oct 24 18:12:21 2010 +0400
     5.3 @@ -1,10 +1,12 @@
     5.4  #!/usr/bin/python
     5.5  from monomer import AminoAcidType
     5.6  from Bio.PDB import PDBParser, CaPPBuilder
     5.7 -from allpy_pdb import std_id
     5.8 +from allpy_pdb import std_id, pdb_id_parse
     5.9  import project
    5.10  import sys
    5.11 -
    5.12 +import config
    5.13 +import os.path
    5.14 +import urllib2
    5.15  
    5.16  cappbuilder = CaPPBuilder()
    5.17  
    5.18 @@ -76,11 +78,36 @@
    5.19              monomer.pdb_residue_add(chain, residue)
    5.20              sequence.monomers.append(monomer)
    5.21          return sequence
    5.22 +    
    5.23 +    def pdb_auto_add(self, conformity_info=None):
    5.24 +        """
    5.25 +        Adds pdb information to each monomer
    5.26 +        Returns if information has been successfully added
    5.27          
    5.28 +        TODO: conformity_file
    5.29 +        """
    5.30 +        if not conformity_info:
    5.31 +            match = pdb_id_parse(self.name)
    5.32 +            if match:
    5.33 +                code = match['code']
    5.34 +                pdb_filename = config.pdb_dir % code
    5.35 +                if not os.path.exists(pdb_filename):
    5.36 +                    url = config.pdb_url % code
    5.37 +                    print "Download %s" % url
    5.38 +                    pdb_file = open(pdb_filename, 'w')
    5.39 +                    pdb_file.write(urllib2.urlopen(url).read())
    5.40 +                    pdb_file.close()
    5.41 +                    print "Save %s" % pdb_filename
    5.42 +                pdb_file = open(pdb_filename)
    5.43 +                try:
    5.44 +                    self.pdb_chain_add(pdb_file, code, match['chain'], match['model'])
    5.45 +                    return True
    5.46 +                except:
    5.47 +                    return False
    5.48 +            else:
    5.49 +                return False
    5.50          
    5.51          
    5.52          
    5.53          
    5.54          
    5.55 -        
    5.56 -