NAME
Prospect::Thread - Representation of a Prospect thread.
$Id: Thread.pm,v 1.26 2003/11/04 01:01:32 cavs 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 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);
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DESCRIPTION
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: Prospect::Thread
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qname()
Name: qname()
Purpose: return the name of the query sequence
Arguments: none
Returns: string
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qseq()
Name: qseq()
Purpose: return the query sequence
Arguments: none
Returns: string
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qseq_align()
Name: qseq_align()
Purpose: return the aligned query sequence
Arguments: none
Returns: string
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qss()
Name: qss()
Purpose: return the secondary structure of the aligned query sequence
Arguments: none
Returns: string
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qlen()
Name: qlen()
Purpose: return the length of the query sequence
Arguments: none
Returns: integer
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qstart()
Name: qstart()
Purpose: return the start of the alignment on the query sequence
Arguments: none
Returns: integer
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qend()
Name: qend()
Purpose: return the end of the alignment on the query sequence
Arguments: none
Returns: integer
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target_start()
Name: target_start()
Purpose: return the start position of the query sequence
Arguments: none
Returns: integer
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target_end()
Name: target_end()
Purpose: return the end position of the query sequence
Arguments: none
Returns: integer
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tname()
Name: tname()
Purpose: return the name of the template sequence
Arguments: none
Returns: string
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pdbcode()
Name: pdbcode()
Purpose: return the PDB id
Arguments: none
Returns: string
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tseq()
Name: tseq()
Purpose: return the template sequence
Arguments: none
Returns: string
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tseq_align()
Name: tseq_align()
Purpose: return the aligned template sequence
Arguments: none
Returns: string
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tss()
Name: tss()
Purpose: return the secondary structure of the aligned template sequence
Arguments: none
Returns: string
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tlen()
Name: tlen()
Purpose: return the length of the template sequence
Arguments: none
Returns: integer
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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
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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
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template_start()
Name: template_start()
Purpose: return the start position of the template sequence
Arguments: none
Returns: integer
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target_end()
Name: target_end()
Purpose: return the end position of the template sequence
Arguments: none
Returns: integer
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isGlobal()
Name: isGlobal()
Purpose: return whether the alignment is global (1) or local (0)
Arguments: none
Returns: integer
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raw_align()
Name: align()
Purpose: return the raw alignment from the prospect output
Arguments: none
Returns: string
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align_len()
Name: align_len()
Purpose: return the alignment length
Arguments: none
Returns: float
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identities()
Name: identities()
Purpose: return the number of identities
Arguments: none
Returns: float
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svm_score()
Name: svm_score()
Purpose: get/set the svm score
Arguments: none
Returns: float
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raw_score()
Name: raw_score()
Purpose: return the raw score
Arguments: none
Returns: float
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gap_score()
Name: gap_score()
Purpose: return the gap score
Arguments: none
Returns: float
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mutation_score()
Name: mutation_score()
Purpose: return the mutation score
Arguments: none
Returns: float
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ssfit_score()
Name: ssfit_score()
Purpose: return the ssfit score
Arguments: none
Returns: float
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pair_score()
Name: pair_score()
Purpose: return the pairwise score
Arguments: none
Returns: float
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singleton_score()
Name: singleton_score()
Purpose: return the singletonwise score
Arguments: none
Returns: float
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rgyr()
Name: rgyr()
Purpose: return the radius of gyration
Arguments: none
Returns: float
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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
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write_xml()
Name: write_xml()
Purpose: output the xml to a file
Arguments: IO::File object
Returns: none
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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
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thread_structure()
Name: thread_structure
Purpose: modify a Bio::Structure::IO::Entry object to reflect a prospect
threading alignment
Arguments: Prospect::Thread object, Bio::Structure::IO::Entry object
Returns: nada
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get_mismatches()
Name: get_mismatches
Purpose: return array of mismatches
Argument: nada
Returns: array of residue ids
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get_similarities()
Name: get_similarities
Purpose: return array of similarities
Argument: nada
Returns: array of residue ids
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get_deletions()
Name: get_deletions
Purpose: return array of deletions
Argument: nada
Returns: array of residue ids
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get_inserts()
Name: get_inserts
Purpose: return array of inserts
Argument: nada
Returns: array of residue ids
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get_inserts()
Name: get_inserted_residues
Purpose: return identities of inserted residues
Argument: position of insert
Returns: array of residue ids
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get_identities()
Name: get_identities
Purpose: return array of identities
Argument: nada
Returns: array of residue ids
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_add_similarity()
Name: _add_similarity
Purpose: add residue id to list of similarities
Arguments: residue id
Returns: nada
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_add_mismatch()
Name: _add_mismatch
Purpose: add residue id to list of mismatches
Arguments: residue id
Returns: nada
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_add_deletion()
Name: _add_deletion
Purpose: add residue id to list of deletions
Arguments: residue id
Returns: nada
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_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
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_add_identity()
Name: _add_identity
Purpose: add residue id to list of identities
Arguments: residue id
Returns: nada
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_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
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Name: _format_select
Purpose: handle the rasmol buffer limit
Arguments: array of ids to select
Returns: rasmol select statement
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_parse_xml_file()
Name: _parse_xml_file()
Purpose: parse the input XML file.
Arguments: [self]
Returns: self
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