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Bio::Tools::Run::PiseApplication::CSR.3pm

NAME

Bio::Tools::Run::PiseApplication::CSR

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::CSR

       Bioperl class for:
 
         CSR     Maximal Common 3D Substructure Searching (M.Petitjean)
 
         References:
 
                 M.Petitjean, Interactive Maximal Common 3D Substructure Searching with the Combined SDM/RMS Algorithm. Comput.Chem.1998,22[6],pp.463-465. 
 
 
       Parameters:
 
 
                 CSR (String)
 
 
                 param (Results)
 
 
                 endparams (String)
 
 
                 pdbfile (InFile)
                         File containing both molecules
                         pipe: pdbfile
 
                 file_format (Excl)
                         Input file format
 
                 imol1 (Integer)
                         Position of the 1st molecule in the file (IMOL1)
 
                 imol2 (Integer)
                         Position of the 2d molecule in the file (IMOL2)
 
                 itermx (Integer)
                         How many iterations (ITERMX)
 
                 cutoff (Excl)
                         Cutoff distance (CUT-OFF DIST)
 
                 substructure (OutFile)
 
 
                 pdb_outfile (Results)
 
                         pipe: pdbfile
 
 

new

  Title   : new()
  Usage   : my $CSR = Bio::Tools::Run::PiseApplication::CSR->new($remote, $email, @params);
  Function: Creates a Bio::Tools::Run::PiseApplication::CSR object.
            This method should not be used directly, but rather by 
            a Bio::Factory::Pise instance:
            my $factory = Bio::Factory::Pise->new(-email => 'me@myhome');
            my $CSR = $factory->program('CSR');
  Example :
  Returns : An instance of Bio::Tools::Run::PiseApplication::CSR.