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Bio/Structure/SecStr/DSSP/Res.pm  view on Meta::CPAN

                residue as reported by the pdb entry.  Note, this DOES NOT
                uniquely specify a residue.  There may be an insertion code
                and/or chain identifier differences.
 Function     :
 Example      : $pdbNum = $self->_pdbNum( DSSP_ID );
 Returns      : a scalar
 Args         : DSSP_ID


=cut

sub _pdbNum {
    my $self = shift;
    my $dssp_key = shift;
    return $self->{ 'Res' }->[ $dssp_key ]->{ 'pdb_resnum' };
}

=head2 _pdbInsCo

 Title        : _pdbInsCo
 Usage        : fetches the Insertion Code for this residue, if it has one.
 Function     :
 Example      : $pdbNum = $self->_pdbInsCo( DSSP_ID );
 Returns      : a scalar
 Args         : DSSP_ID


=cut

sub _pdbInsCo {
    my $self = shift;
    my $dssp_key = shift;
    return $self->{ 'Res' }->[ $dssp_key ]->{ 'insertionco' };
}

=head2 _toPdbId

 Title        : _toPdbId
 Usage        : Takes a dssp key and builds the corresponding
                PDB identifier string
 Function     :
 Example      : $pdbId = $self->_toPdbId( DSSP_ID );
 Returns      : scalar
 Args         : DSSP_ID

=cut

sub _toPdbId {
    my $self = shift;
    my $dssp_key = shift;
    my $pdbId = ( $self->_pdbNum( $dssp_key ).
		  $self->_pdbInsCo( $dssp_key ) );
    my $chain = $self->_pdbChain( $dssp_key );
    $pdbId = "$pdbId:$chain" if $chain;
    return $pdbId;
}

=head2 _contSegs

 Title         : _contSegs
 Usage         : find the endpoints of continuous regions of this structure
 Function      : returns pointer to array of 3 element array.
                 Elements are the dssp keys of the start and end points of each
                 continuous element and its PDB chain id (may be blank).
                 Note that it is common to have several
                 continuous elements with the same chain id.  This occurs
                 when an internal region is disordered and no structural
                 information is available.
 Example       : $cont_seg_ptr = $dssp_obj->_contSegs();
 Returns       : pointer to array of arrays
 Args          : none


=cut

sub _contSegs {
    my $self = shift;
    if ( $self->{ 'contSegs' } ) {
	return $self->{ 'contSegs' };
    }
    else {
	# first time, so make contSegs
	my ( $cur_chain, $i, $beg );
	my @contSegs;
	#initialize
	$cur_chain = $self->_pdbChain( 1 );
	$beg = 1;
	#internal residues
	for ( $i = 2; $i <= $self->_numResLines() - 1; $i++ ) {
	    if ( $self->{ 'Res' }->[ $i ]->{ 'amino_acid' } eq '!' ) {
		push( @contSegs, [ $beg, $i - 1, $cur_chain ] );
		$beg = $i + 1;
		$cur_chain = $self->_pdbChain( $i + 1 );
	    }
	}
	# last residue must be the end of a chain
	push( @contSegs, [ $beg, $i, $cur_chain ] );

	$self->{ 'contSegs' } = \@contSegs;
	return $self->{ 'contSegs' };
    }
}

=head2 _numResLines

 Title         : _numResLines
 Usage         : returns the total number of residue lines in this
                 dssp file.
                 This number is DIFFERENT than the number of residues in
                 the pdb file because dssp has chain termination and chain
                 discontinuity 'residues'.
 Function      :
 Example       : $num_res = $dssp_obj->_numResLines();
 Returns       : scalar int
 Args          : none


=cut

sub _numResLines {
    my $self = shift;