1.1 --- a/allpy/structure.py	Tue Mar 01 00:17:13 2011 +0300
     1.2 +++ b/allpy/structure.py	Fri Mar 04 15:16:28 2011 +0300
     1.3 @@ -9,7 +9,6 @@
     1.4  import re
     1.5  import os
     1.6  import os.path
     1.7 -from tempfile import NamedTemporaryFile
     1.8  import urllib2
     1.9  from copy import copy
    1.10  
    1.11 @@ -39,10 +38,15 @@
    1.12      d['model'] = int(d['model'])
    1.13      return d
    1.14  
    1.15 -
    1.16  def get_structure(file, name):
    1.17      return PDBParser().get_structure(name, file)
    1.18  
    1.19 +def download_pdb(code, pdb_url=config.pdb_url):
    1.20 +    """ Download pdb_file from web and return unnamed tempfile """
    1.21 +    url = pdb_url % code
    1.22 +    print "Download %s" % url
    1.23 +    return urllib2.urlopen(url)
    1.24 +
    1.25  class SequenceMixin(base.Sequence):
    1.26      """Mixin for adding PDB data to a Sequence.
    1.27  
    1.28 @@ -106,7 +110,7 @@
    1.29                  sequence.append(monomer)
    1.30          return sequence
    1.31  
    1.32 -    def auto_pdb(self, conformity=None, dir='/tmp', mask='%s.pdb'):
    1.33 +    def auto_pdb(self, conformity=None, pdb_getter=download_pdb):
    1.34          """ Adds pdb information to each monomer
    1.35  
    1.36          Returns if information has been successfully added
    1.37 @@ -120,20 +124,8 @@
    1.38          code = match['code']
    1.39          chain = match['chain']
    1.40          model = match['model']
    1.41 -        user_path = os.path.join(dir, mask % code)
    1.42 -        path = user_path
    1.43 -        if not os.path.exists(path) or not os.path.getsize(path):
    1.44 -            path = config.pdb_path % code
    1.45 -        if not os.path.exists(path) or not os.path.getsize(path):
    1.46 -            url = config.pdb_url % code
    1.47 -            print "Download %s" % url
    1.48 -            path = user_path
    1.49 -            data = urllib2.urlopen(url).read()
    1.50 -            pdb_file = open(path, 'w')
    1.51 -            pdb_file.write(data)
    1.52 -            pdb_file.close()
    1.53 -            print "Save %s" % path
    1.54 -        self.set_pdb_chain(open(path), code, chain, model)
    1.55 +        pdb_file = pdb_getter(code)
    1.56 +        self.set_pdb_chain(pdb_file, code, chain, model)
    1.57          return True
    1.58  
    1.59      def save_pdb(self, out_filename, new_chain=None, new_model=None):