NAME

Bio::Prospect::Thread - Representation of a Prospect thread.

$Id: Thread.pm,v 1.28 2003/11/18 19:45:45 rkh Exp $

SYNOPSIS

 my $in  = new IO::File  $ARGV[0]   or die( "can't open $ARGV[0] for reading" );
 my $out = new IO::File ">$ARGV[1]" or die( "can't open $ARGV[1] for writing" );
 my $xml = '';
 while(<$in>) { $xml .= $_; }
 close($in);
  
 my $t = new Bio::Prospect::Thread( $xml );
  
 print "tseq:  " . $t->tseq() . "\n";
 print "qseq:  " . $t->qseq() . "\n";
 print "raw:   " . $t->raw_score() . "\n";
 print "svm:   " . $t->svm_score() . "\n";
 print "align: " . $t->alignment() . "\n";
 $t->write_xml( $out );
 
 exit(0);

DESCRIPTION

Bio::Prospect::Thread -- Representation of a full Prospect thread this is really just a set of methods associated with the hash structure returned by XML::Simple.

METHODS

new()

 Name:      new()
 Purpose:   return Thread object
 Arguments: Prospect XML string 
 Returns:   Bio::Prospect::Thread

qname()

 Name:      qname()
 Purpose:   return the name of the query sequence
 Arguments: none
 Returns:   string

qseq()

 Name:      qseq()
 Purpose:   return the query sequence
 Arguments: none
 Returns:   string

qseq_align()

 Name:      qseq_align()
 Purpose:   return the aligned query sequence
 Arguments: none
 Returns:   string

qss()

 Name:      qss()
 Purpose:   return the secondary structure of the aligned query sequence
 Arguments: none
 Returns:   string

qlen()

 Name:      qlen()
 Purpose:   return the length of the query sequence
 Arguments: none
 Returns:   integer

qstart()

 Name:      qstart()
 Purpose:   return the start of the alignment on the query sequence
 Arguments: none
 Returns:   integer

qend()

 Name:      qend()
 Purpose:   return the end of the alignment on the query sequence
 Arguments: none
 Returns:   integer

target_start()

 Name:      target_start()
 Purpose:   return the start position of the query sequence
 Arguments: none
 Returns:   integer

target_end()

 Name:      target_end()
 Purpose:   return the end position of the query sequence
 Arguments: none
 Returns:   integer

tname()

 Name:      tname()
 Purpose:   return the name of the template sequence
 Arguments: none
 Returns:   string

pdbcode()

 Name:      pdbcode()
 Purpose:   return the PDB id
 Arguments: none
 Returns:   string

tseq()

 Name:      tseq()
 Purpose:   return the template sequence
 Arguments: none
 Returns:   string

tseq_align()

 Name:      tseq_align()
 Purpose:   return the aligned template sequence
 Arguments: none
 Returns:   string

tss()

 Name:      tss()
 Purpose:   return the secondary structure of the aligned template sequence
 Arguments: none
 Returns:   string

tlen()

 Name:      tlen()
 Purpose:   return the length of the template sequence
 Arguments: none
 Returns:   integer

tstart()

 Name:      tstart()
 Purpose:   return the start of the alignment on the template sequence.
            CURRENTLY, tstart and template_start are the same. Because the
            template residue numbering is not necessarily sequential (due
            to missing residues in the structure), I would need
            to parse the template xml files to correctly handle the 
            tstart value.  
 Arguments: none
 Returns:   integer

tend()

 Name:      tend()
 Purpose:   return the end of the alignment on the template sequence.
            CURRENTLY, tend and template_start are the same. Because the
            template residue numbering is not necessarily sequential (due
            to missing residues in the structure), I would need
            to parse the template xml files to correctly handle the 
            tend value.  
 Arguments: none
 Returns:   integer

template_start()

 Name:      template_start()
 Purpose:   return the start position of the template sequence
 Arguments: none
 Returns:   integer

target_end()

 Name:      target_end()
 Purpose:   return the end position of the template sequence
 Arguments: none
 Returns:   integer

isGlobal()

 Name:      isGlobal()
 Purpose:   return whether the alignment is global (1) or local (0)
 Arguments: none
 Returns:   integer

raw_align()

 Name:      align()
 Purpose:   return the raw alignment from the prospect output
 Arguments: none
 Returns:   string

align_len()

 Name:      align_len()
 Purpose:   return the alignment length
 Arguments: none
 Returns:   float

identities()

 Name:      identities()
 Purpose:   return the number of identities
 Arguments: none
 Returns:   float

svm_score()

 Name:      svm_score()
 Purpose:   get/set the svm score
 Arguments: none
 Returns:   float

raw_score()

 Name:      raw_score()
 Purpose:   return the raw score
 Arguments: none
 Returns:   float

gap_score()

 Name:      gap_score()
 Purpose:   return the gap score
 Arguments: none
 Returns:   float

mutation_score()

 Name:      mutation_score()
 Purpose:   return the mutation score
 Arguments: none
 Returns:   float

ssfit_score()

 Name:      ssfit_score()
 Purpose:   return the ssfit score
 Arguments: none
 Returns:   float

pair_score()

 Name:      pair_score()
 Purpose:   return the pairwise score
 Arguments: none
 Returns:   float

singleton_score()

 Name:      singleton_score()
 Purpose:   return the singletonwise score
 Arguments: none
 Returns:   float

rgyr()

 Name:      rgyr()
 Purpose:   return the radius of gyration
 Arguments: none
 Returns:   float

alignment()

 Name:      alignment()
 Purpose:   return the threading alignment as a set of line-wrapped rows.
 Arguments: query tag (optional), template tag (optional), width (optional)
 Returns:   string

write_xml()

 Name:      write_xml()
 Purpose:   output the xml to a file
 Arguments: IO::File object
 Returns:   none

output_rasmol_script()

 Name:      output_rasmol_script
 Purpose:   return a rasmol script for displaying a threaded structure
 Arguments: Bio::Structure::IO::Entry object
 Returns:   rasmol script

thread_structure()

 Name:      thread_structure
 Purpose:   modify a Bio::Structure::IO::Entry object to reflect a prospect
            threading alignment
 Arguments: Bio::Prospect::Thread object, Bio::Structure::IO::Entry object
 Returns:   nada

get_mismatches()

 Name:      get_mismatches
 Purpose:   return array of mismatches
 Argument:  nada
 Returns:   array of residue ids

get_similarities()

 Name:      get_similarities
 Purpose:   return array of similarities
 Argument:  nada
 Returns:   array of residue ids

get_deletions()

 Name:      get_deletions
 Purpose:   return array of deletions
 Argument:  nada
 Returns:   array of residue ids

get_inserts()

 Name:      get_inserts
 Purpose:   return array of inserts
 Argument:  nada
 Returns:   array of residue ids

get_inserts()

 Name:      get_inserted_residues
 Purpose:   return identities of inserted residues
 Argument:  position of insert
 Returns:   array of residue ids

get_identities()

 Name:      get_identities
 Purpose:   return array of identities
 Argument:  nada
 Returns:   array of residue ids

pdb_model()

 Name:      pdb_model()
 Purpose:   return a rudimentary 3D backbone model in PDB format
 Arguments: none
 Returns:   text

_add_similarity()

 Name:      _add_similarity
 Purpose:   add residue id to list of similarities
 Arguments: residue id
 Returns:   nada

_add_mismatch()

 Name:      _add_mismatch
 Purpose:   add residue id to list of mismatches
 Arguments: residue id
 Returns:   nada

_add_deletion()

 Name:      _add_deletion
 Purpose:   add residue id to list of deletions
 Arguments: residue id
 Returns:   nada

_add_insert($$;@)

 Name:      _add_insert
 Purpose:   add residue id to list of inserts
 Arguments: template residue id at which insert occurs
      optional: inserted query residues
 Returns:   nada

_add_identity()

 Name:      _add_identity
 Purpose:   add residue id to list of identities
 Arguments: residue id
 Returns:   nada

_a_to_aaa_code()

 Name:      _a_to_aaa_code
 Purpose:   convert a single amino acid code (e.g. W) to its three letter
            amino acid code (e.g. TRP)
 Arguments: single amino acid code
 Returns:   triple amino acid code

_format_select()

 Name:      _format_select
 Purpose:   handle the rasmol buffer limit
 Arguments: array of ids to select
 Returns:   rasmol select statement

_parse_xml_file()

 Name:      _parse_xml_file()
 Purpose:   parse the input XML file.  
 Arguments: [self]
 Returns:   self

_parse_structure()

 Name:      _parse_structure
 Purpose:   parse the pdb model and determine identities, similarities, deletions
 Arguments: scalar containing coordinates in pdb format
 Returns:   nada