1.1 --- a/geometrical_core/geometrical_core.py	Sun Oct 24 23:17:24 2010 +0400
     1.2 +++ b/geometrical_core/geometrical_core.py	Mon Oct 25 00:03:35 2010 +0400
     1.3 @@ -8,7 +8,7 @@
     1.4  Project = project.Project
     1.5  import argparse
     1.6  import os
     1.7 -from tempfile import mkstemp
     1.8 +from tempfile import NamedTemporaryFile
     1.9  
    1.10  r = argparse.FileType('r')
    1.11  w = argparse.FileType('w')
    1.12 @@ -99,6 +99,8 @@
    1.13  p.add_argument('-a',help='Cores count',metavar='NEW_ATOMS',type=pos,default=c.ac_count)
    1.14  p.add_argument('-x',help='Superposition core identifier',type=i_nng,default=0)
    1.15  
    1.16 +tmp_file = None
    1.17 +
    1.18  try:
    1.19      args = p.parse_args()
    1.20      
    1.21 @@ -113,12 +115,11 @@
    1.22          project = Project(args.i)
    1.23      except:
    1.24          args.i.close()
    1.25 -        tmp_file, tmp_filename = mkstemp()
    1.26 -        os.close(tmp_file) # this is file descriptor, not normal file object.
    1.27 -        
    1.28 +        tmp_file = NamedTemporaryFile(delete=False)
    1.29 +        tmp_file.close()
    1.30          os.system('seqret %(msf)s %(fasta)s' % \
    1.31 -        {'fasta': tmp_filename, 'msf': args.i.name})
    1.32 -        args.i = open(tmp_filename)
    1.33 +        {'msf': args.i.name, 'fasta': tmp_file.name})
    1.34 +        args.i = open(tmp_file.name)
    1.35          project = Project(args.i)
    1.36      
    1.37      project.pdb_auto_add(args.c)
    1.38 @@ -175,5 +176,6 @@
    1.39      print t
    1.40      exit()
    1.41  
    1.42 +if tmp_file:
    1.43 +    os.unlink(tmp_file)
    1.44  
    1.45 -

     2.1 --- a/lib/block.py	Sun Oct 24 23:17:24 2010 +0400
     2.2 +++ b/lib/block.py	Mon Oct 25 00:03:35 2010 +0400
     2.3 @@ -8,6 +8,8 @@
     2.4  import config
     2.5  from graph import Graph
     2.6  from Bio.PDB import Superimposer
     2.7 +from tempfile import NamedTemporaryFile
     2.8 +import os
     2.9  
    2.10  class Block(object):
    2.11      """ Block of alignment
    2.12 @@ -147,8 +149,8 @@
    2.13      
    2.14      def superimpose(self):
    2.15          """ Superimpose all pdb_chains in this block """
    2.16 -        sequences_chains = []
    2.17 -        if len(self.sequences) >= 1:
    2.18 +        sequences_chains = list(self.sequences_chains())
    2.19 +        if len(sequences_chains) >= 1:
    2.20              sup = Superimposer()
    2.21              fixed_sequence, fixed_chain = sequences_chains.pop()
    2.22              fixed_atoms = self.ca_atoms(fixed_sequence, fixed_chain)
    2.23 @@ -159,10 +161,20 @@
    2.24                  sup.apply(moving_atoms)
    2.25      
    2.26      def pdb_save(self, out_file):
    2.27 -        """ Superimpose all pdb_chains in this block """
    2.28 -        tmp_file, tmp_filename = mkstemp()
    2.29 -        os.close(tmp_file) # this is file descriptor, not normal file object.
    2.30 -        sequence.pdb_save(tmp_filename, chain)
    2.31 +        """ Save all sequences 
    2.32 +        
    2.33 +        Returns {(sequence, chain): CHAIN}
    2.34 +        CHAIN is chain letter in new file
    2.35 +        """
    2.36 +        tmp_file = NamedTemporaryFile(delete=False)
    2.37 +        tmp_file.close()
    2.38 +        
    2.39 +        for sequence, chain in self.sequences_chains():
    2.40 +            sequence.pdb_save(tmp_file.name, chain)
    2.41 +            # TODO: read from tmp_file.name
    2.42 +            # change CHAIN
    2.43 +            # add to out_file
    2.44 +        
    2.45 +        os.unlink(NamedTemporaryFile)
    2.46      
    2.47      
    2.48 -    

     3.1 --- a/lib/project.py	Sun Oct 24 23:17:24 2010 +0400
     3.2 +++ b/lib/project.py	Mon Oct 25 00:03:35 2010 +0400
     3.3 @@ -12,7 +12,8 @@
     3.4  from monomer import AminoAcidType
     3.5  import allpy_data
     3.6  import os
     3.7 -from tempfile import mkstemp
     3.8 +from tempfile import NamedTemporaryFile
     3.9 +import os
    3.10  import block
    3.11  
    3.12  Block = block.Block
    3.13 @@ -178,13 +179,11 @@
    3.14          
    3.15          uses old Monomers and Sequences objects
    3.16          """
    3.17 -        tmp_file, tmp_filename = mkstemp()
    3.18 -        os.close(tmp_file) # this is file descriptor, not normal file object.
    3.19 -        tmp_file = open(tmp_filename, 'w')
    3.20 +        tmp_file = NamedTemporaryFile(delete=False)
    3.21          self.save_fasta(tmp_file)
    3.22          tmp_file.close()
    3.23 -        os.system("muscle -in %(tmp)s -out %(tmp)s" % {'tmp': tmp_filename})
    3.24 -        sequences, alignment = Project.from_fasta(open(tmp_filename))
    3.25 +        os.system("muscle -in %(tmp)s -out %(tmp)s" % {'tmp': tmp_file.name})
    3.26 +        sequences, alignment = Project.from_fasta(open(tmp_file.name))
    3.27          for sequence in self.sequences:
    3.28              try:
    3.29                  new_sequence = [i for i in sequences if sequence==i][0]
    3.30 @@ -201,7 +200,9 @@
    3.31                      if monomer != old_monomer:
    3.32                          raise Exception("Align: alignment errors")
    3.33                      self.alignment[sequence].append(old_monomer)
    3.34 -    
    3.35 +        os.unlink(tmp_file.name)
    3.36 +        
    3.37 +        
    3.38      def column(self, sequence=None, sequences=None, original=None):
    3.39          """ returns list of columns of alignment
    3.40