1.1 --- a/geometrical_core/geometrical_core.py	Sun Oct 24 17:06:15 2010 +0400
     1.2 +++ b/geometrical_core/geometrical_core.py	Sun Oct 24 17:29:59 2010 +0400
     1.3 @@ -109,19 +109,20 @@
     1.4  
     1.5  try:
     1.6      args = p.parse_args()
     1.7 +    
     1.8 +    if not args.l and not args.f and not args.g and not args.p and not args.s:
     1.9 +        print 'Error: no output file provided'
    1.10 +        exit()
    1.11 +    if not (args.p and args.s) and not (not args.p and not args.s):
    1.12 +        print 'Error: provide both pdb and spt file or none of them'
    1.13 +        exit()
    1.14 +
    1.15 +    project = Project(args.i)
    1.16 +    project
    1.17 +    
    1.18  except Exception, t:
    1.19      print t
    1.20      exit()
    1.21 -    
    1.22 -if not args.l and not args.f and not args.g and not args.p and not args.s:
    1.23 -    print 'Error: no output file provided'
    1.24 -    exit()
    1.25  
    1.26 -if not (args.p and args.s) and not (not args.p and not args.s):
    1.27 -    print 'Error: provide both pdb and spt file or none of them'
    1.28 -    exit()
    1.29  
    1.30  
    1.31 -
    1.32 -
    1.33 -

     2.1 --- a/lib/allpy_pdb.py	Sun Oct 24 17:06:15 2010 +0400
     2.2 +++ b/lib/allpy_pdb.py	Sun Oct 24 17:29:59 2010 +0400
     2.3 @@ -1,62 +1,59 @@
     2.4  
     2.5  import re
     2.6  
     2.7 +"""
     2.8 +Functions to get pdb information from fasta id
     2.9 +and to generate fasta id from pdb information
    2.10 +
    2.11 +pdb information: code, chain, model
    2.12 +
    2.13 +TODO: same for local pdb files
    2.14 +"""
    2.15 +
    2.16  # for pdb-codes
    2.17 -re1 = re.compile(r"(^|[^a-z0-9])([0-9][0-9a-z]{3})([^a-z0-9]([0-9a-z ]?)([^a-z0-9]([0-9]{1,3}))?)?($|[^a-z0-9])")
    2.18 +re1 = re.compile(r"(^|[^a-z0-9])(?P<code>[0-9][0-9a-z]{3})([^a-z0-9](?P<chain>[0-9a-z ]?)(?P<model>[^a-z0-9]([0-9]{1,3}))?)?($|[^a-z0-9])")
    2.19  
    2.20 -# for files
    2.21 -re2 = re.compile(r"(^)([^^]+\.(ent|pdb))([^a-zA-Z0-9]([0-9A-Za-z ]?)([^a-zA-Z0-9]([0-9]{1,3}))?)?$")
    2.22 +#~ # for files
    2.23 +#~ re2 = re.compile(r"(^)([^^]+\.(ent|pdb))([^a-zA-Z0-9]([0-9A-Za-z ]?)([^a-zA-Z0-9]([0-9]{1,3}))?)?$")
    2.24  
    2.25 -class Pdb(object):
    2.26 -    """
    2.27 -    """
    2.28 -    @staticmethod
    2.29 -    def std_id(pdb_id, pdb_chain, pdb_model=None):
    2.30 -        if pdb_model:
    2.31 -            return "%s_%s_%s" % \
    2.32 -            (pdb_id.lower().strip(), pdb_chain.upper().strip(), pdb_model)
    2.33 -        else:
    2.34 -            return "%s_%s" % \
    2.35 -            (pdb_id.lower().strip(), pdb_chain.upper().strip())
    2.36 +def std_id(pdb_id, pdb_chain, pdb_model=None):
    2.37 +    if pdb_model:
    2.38 +        return "%s_%s_%s" % \
    2.39 +        (pdb_id.lower().strip(), pdb_chain.upper().strip(), pdb_model)
    2.40 +    else:
    2.41 +        return "%s_%s" % \
    2.42 +        (pdb_id.lower().strip(), pdb_chain.upper().strip())
    2.43      
    2.44 +def pdb_id_parse(ID):
    2.45 +    match = re1.search(ID, re.I)
    2.46 +    if not match:
    2.47 +        return None
    2.48 +    return match.groupdict()
    2.49      
    2.50 -    def std_id_parse(ID):
    2.51 -        """
    2.52 -        Parse standart ID to pdb_code, chain and model
    2.53 -        """
    2.54 -        if '.ent' in ID.lower() or '.pdb' in ID.lower():
    2.55 -            # it is file
    2.56 -            parseO = self.re2.search(ID) # files
    2.57 -        else:
    2.58 -            parseO = self.re1.search(ID.lower()) # pdb codes
    2.59 -        if not parseO:
    2.60 -            return None
    2.61 -        parse = parseO.groups()
    2.62 -        if len(parse) < 2:
    2.63 -            return None
    2.64 -        code = parse[1]
    2.65 -        chain = ''
    2.66 -        model = None
    2.67 -        if len(parse) >= 4:
    2.68 -            chain = parse[3]
    2.69 -            if chain:
    2.70 -                chain = chain.upper()
    2.71 -            if len(parse) >= 6:
    2.72 -                if parse[5]:
    2.73 -                    model = parse[5]
    2.74 -        return code, chain, model
    2.75      
    2.76 +#~ def std_id_parse(ID):
    2.77 +    #~ """
    2.78 +    #~ Parse standart ID to pdb_code, chain and model
    2.79 +    #~ """
    2.80 +    #~ if '.ent' in ID.lower() or '.pdb' in ID.lower():
    2.81 +        #~ # it is file
    2.82 +        #~ parseO = self.re2.search(ID) # files
    2.83 +    #~ else:
    2.84 +        #~ parseO = self.re1.search(ID.lower()) # pdb codes
    2.85 +    #~ if not parseO:
    2.86 +        #~ return None
    2.87 +    #~ parse = parseO.groups()
    2.88 +    #~ if len(parse) < 2:
    2.89 +        #~ return None
    2.90 +    #~ code = parse[1]
    2.91 +    #~ chain = ''
    2.92 +    #~ model = None
    2.93 +    #~ if len(parse) >= 4:
    2.94 +        #~ chain = parse[3]
    2.95 +        #~ if chain:
    2.96 +            #~ chain = chain.upper()
    2.97 +        #~ if len(parse) >= 6:
    2.98 +            #~ if parse[5]:
    2.99 +                #~ model = parse[5]
   2.100 +    #~ return code, chain, model
   2.101      
   2.102 -    
   2.103 -    
   2.104 -    
   2.105 -
   2.106 -#~ class Coordinates(object):
   2.107 -    """
   2.108 -    float x, y, z
   2.109 -    
   2.110 -    Coordinates(x, y, z) -> Coordinates
   2.111 -    Coordinates() -> new Coordinates
   2.112 -    """
   2.113 -
   2.114 -

     3.1 --- a/lib/project.py	Sun Oct 24 17:06:15 2010 +0400
     3.2 +++ b/lib/project.py	Sun Oct 24 17:29:59 2010 +0400
     3.3 @@ -212,3 +212,9 @@
     3.4                  else:
     3.5                      yield (column[indexes[original]], dict([(s, column[indexes[s]]) for s in sequences]))
     3.6          
     3.7 +    def add_pdb(self, conformity_file=None):
     3.8 +        pass
     3.9 +        
    3.10 +        
    3.11 +        
    3.12 +        

     4.1 --- a/lib/sequence.py	Sun Oct 24 17:06:15 2010 +0400
     4.2 +++ b/lib/sequence.py	Sun Oct 24 17:29:59 2010 +0400
     4.3 @@ -1,7 +1,7 @@
     4.4  #!/usr/bin/python
     4.5  from monomer import AminoAcidType
     4.6  from Bio.PDB import PDBParser, CaPPBuilder
     4.7 -from allpy_pdb import Pdb
     4.8 +from allpy_pdb import std_id
     4.9  import project
    4.10  import sys
    4.11  
    4.12 @@ -45,7 +45,7 @@
    4.13          Reads Pdb chain from file 
    4.14          and align each Monomer with PDB.Residue (TODO)
    4.15          """
    4.16 -        name = Pdb.std_id(pdb_id, pdb_chain, pdb_model)
    4.17 +        name = std_id(pdb_id, pdb_chain, pdb_model)
    4.18          chain = PDBParser().get_structure(name, pdb_file)[pdb_model][pdb_chain]
    4.19          self.pdb_chains.append(chain)
    4.20          pdb_sequence = Sequence.from_pdb_chain(chain)