/ 
Bio-Prospect-1.04
River stage zero No dependents
/ Bio::Prospect::Thread

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