# $Header$
#
# bioperl module for Bio::Structure::SecStr::DSSP::Res.pm
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Ed Green <ed@compbio.berkeley.edu>
#
# Copyright Univ. of California
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Structure::SecStr::DSSP::Res - Module for parsing/accessing dssp output
=head1 SYNOPSIS
my $dssp_obj = Bio::Structure::SecStr::DSSP::Res->new('-file'=>'filename.dssp');
# or
my $dssp_obj = Bio::Structure::SecStr::DSSP::Res->new('-fh'=>\*STDOUT);
# get DSSP defined Secondary Structure for residue 20
$sec_str = $dssp_obj->resSecStr( 20 );
# get dssp defined sec. structure summary for PDB residue # 10 of chain A
$sec_str = $dssp_obj->resSecStrSum( '10:A' );
=head1 DESCRIPTION
DSSP::Res is a module for objectifying DSSP output. Methods are then
available for extracting all the information within the output file
and convenient subsets of it.
The principal purpose of DSSP is to determine secondary structural
elements of a given structure.
( Dictionary of protein secondary structure: pattern recognition
of hydrogen-bonded and geometrical features.
Biopolymers. 1983 Dec;22(12):2577-637. )
The DSSP program is available from:
http://www.cmbi.kun.nl/swift/dssp
This information is available on a per residue basis ( see resSecStr
and resSecStrSum methods ) or on a per chain basis ( see secBounds
method ).
resSecStr() & secBounds() return one of the following:
'H' = alpha helix
'B' = residue in isolated beta-bridge
'E' = extended strand, participates in beta ladder
'G' = 3-helix (3/10 helix)
'I' = 5 helix (pi helix)
'T' = hydrogen bonded turn
'S' = bend
'' = no assignment
A more general classification is returned using the resSecStrSum()
method. The purpose of this is to have a method for DSSP and STRIDE
derived output whose range is the same.
Its output is one of the following:
'H' = helix ( => 'H', 'G', or 'I' from above )
'B' = beta ( => 'B' or 'E' from above )
'T' = turn ( => 'T' or 'S' from above )
' ' = no assignment ( => ' ' from above )
The methods are roughly divided into 3 sections:
1. Global features of this structure (PDB ID, total surface area,
etc.). These methods do not require an argument.
2. Residue specific features ( amino acid, secondary structure,
solvent exposed surface area, etc. ). These methods do require an
argument. The argument is supposed to uniquely identify a
residue described within the structure. It can be of any of the
following forms:
('#A:B') or ( #, 'A', 'B' )
|| |
|| - Chain ID (blank for single chain)
|--- Insertion code for this residue. Blank for most residues.
|--- Numeric portion of residue ID.
(#)
|
--- Numeric portion of residue ID. If there is only one chain and
it has no ID AND there is no residue with an insertion code at this
number, then this can uniquely specify a residue.
('#:C') or ( #, 'C' )
| |
| -Chain ID
---Numeric portion of residue ID.
If a residue is incompletely specified then the first residue that
fits the arguments is returned. For example, if 19 is the argument
and there are three chains, A, B, and C with a residue whose number
is 19, then 19:A will be returned (assuming its listed first).
Since neither DSSP nor STRIDE correctly handle alt-loc codes, they
are not supported by these modules.
3. Value-added methods. Return values are not verbatem strings
parsed from DSSP or STRIDE output.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Ed Green
Email ed@compbio.berkeley.edu
=head1 APPENDIX
The rest of the documentation details each method.
Internal methods are preceded with a _
=cut
package Bio::Structure::SecStr::DSSP::Res;
use strict;
use Bio::Root::IO;
use Bio::PrimarySeq;
use base qw(Bio::Root::Root);
# Would be a class variable if Perl had them
#attribute begin col # columns
our %lookUp = ( 'pdb_resnum' => [ 5, 5 ],
'insertionco' => [ 10, 1 ],
'pdb_chain' => [ 11, 1 ],
'amino_acid' => [ 13, 1 ],
'term_sig' => [ 14, 1 ],
'ss_summary' => [ 16, 1 ],
'3tph' => [ 18, 1 ],
'4tph' => [ 19, 1 ],
'5tph' => [ 20, 1 ],
'geo_bend' => [ 21, 1 ],
'chirality' => [ 22, 1 ],
'beta_br1la' => [ 23, 1 ],
'beta_br2la' => [ 24, 1 ],
'bb_part1nu' => [ 25, 4 ],
'bb_part2nu' => [ 29, 4 ],
'betash_lab' => [ 33, 1 ],
'solv_acces' => [ 34, 4 ],
'hb1_nh_o_p' => [ 39, 6 ],
'hb1_nh_o_e' => [ 46, 4 ],
'hb1_o_hn_p' => [ 50, 6 ],
'hb1_o_hn_e' => [ 57, 4 ],
'hb2_nh_o_p' => [ 61, 6 ],
'hb2_nh_o_e' => [ 68, 4 ],
'hb2_o_hn_p' => [ 72, 6 ],
'hb2_o_hn_e' => [ 79, 4 ],
'tco' => [ 85, 6 ],
'kappa' => [ 91, 6 ],
'alpha' => [ 97, 6 ],
'phi' => [ 103, 6 ],
'psi' => [ 109, 6 ],
'x_ca' => [ 115, 7 ],
'y_ca' => [ 122, 7 ],
'z_ca' => [ 129, 7 ] );
=head1 CONSTRUCTOR
=cut
=head2 new
Title : new
Usage : makes new object of this class
Function : Constructor
Example : $dssp_obj = Bio::DSSP:Res->new( filename or FILEHANDLE )
Returns : object (ref)
Args : filename ( must be proper DSSP output file )
=cut
sub new {
my ( $class, @args ) = @_;
my $self = $class->SUPER::new( @args );
my $io = Bio::Root::IO->new( @args );
$self->_parse( $io->_fh() );
$io->close();
return $self;
}
=head1 ACCESSORS
=cut
# GLOBAL FEATURES / INFO / STATS
=head2 totSurfArea
Title : totSurfArea
Usage : returns total accessible surface area in square And.
Function :
Example : $surArea = $dssp_obj->totSurfArea();
Returns : scalar
Args : none
=cut
sub totSurfArea {
my $self = shift;
return $self->{ 'Head' }->{ 'ProAccSurf' };
}
=head2 numResidues
Title : numResidues
Usage : returns the total number of residues in all chains or
just the specified chain if a chain is specified
Function :
Example : $num_res = $dssp_obj->numResidues();
Returns : scalar int
Args : none
=cut
sub numResidues {
my $self = shift;
my $chain = shift;
if ( !( $chain ) ) {
return $self->{'Head'}->{'TotNumRes'};
}
else {
my ( $num_res,
$cont_seg );
my $cont_seg_pnt = $self->_contSegs();
foreach $cont_seg ( @{ $cont_seg_pnt } ) {
if ( $chain eq $cont_seg->[ 2 ] ) {
# this segment is part of the chain we want
$num_res += ( $self->_toDsspKey( $cont_seg->[ 1 ] )
- $self->_toDsspKey( $cont_seg->[ 0 ] )
+ 1 ); # this works because we know the
# the region between the start
# and end of a dssp key is
# continuous
}
}
return $num_res;
}
}
# STRAIGHT FROM PDB ENTRY
=head2 pdbID
Title : pdbID
Usage : returns pdb identifier ( 1FJM, e.g.)
Function :
Example : $pdb_id = $dssp_obj->pdbID();
Returns : scalar string
Args : none
=cut
sub pdbID {
my $self = shift;
return $self->{'Head'}->{'PDB'};
}
=head2 pdbAuthor
Title : pdbAuthor
Usage : returns author field
Function :
Example : $auth = $dssp_obj->pdbAuthor()
Returns : scalar string
Args : none
=cut
sub pdbAuthor {
my $self = shift;
return $self->{'Head'}->{'AUTHOR'};
}
=head2 pdbCompound
Title : pdbCompound
Usage : returns pdbCompound given in PDB file
Function :
Example : $cmpd = $dssp_obj->pdbCompound();
Returns : scalar string
Args : none
=cut
sub pdbCompound {
my $self = shift;
return $self->{'Head'}->{'COMPND'};
}
=head2 pdbDate
Title : pdbDate
Usage : returns date given in PDB file
Function :
Example : $pdb_date = $dssp_obj->pdbDate();
Returns : scalar
Args : none
=cut
sub pdbDate {
my $self = shift;
return $self->{'Head'}->{'DATE'};
}
=head2 pdbHeader
Title : pdbHeader
Usage : returns header info from PDB file
Function :
Example : $header = $dssp_obj->pdbHeader();
Returns : scalar
Args : none
=cut
sub pdbHeader {
my $self = shift;
return $self->{'Head'}->{'HEADER'};
}
=head2 pdbSource
Title : pdbSource
Usage : returns pdbSource information from PDBSOURCE line
Function :
Example : $pdbSource = $dssp_obj->pdbSource();
Returns : scalar
Args : none
=cut
sub pdbSource {
my $self = shift;
return $self->{'Head'}->{'SOURCE'};
}
# RESIDUE SPECIFIC ACCESSORS
=head2 resAA
Title : resAA
Usage : fetches the 1 char amino acid code, given an id
Function :
Example : $aa = $dssp_obj->resAA( '20:A' ); # pdb id as arg
Returns : 1 character scalar string
Args : RESIDUE_ID
=cut
sub resAA {
my $self = shift;
my @args = @_;
my $dssp_key = $self->_toDsspKey( @args );
return $self->{ 'Res' }->[ $dssp_key ]->{ 'amino_acid' };
}
=head2 resPhi
Title : resPhi
Usage : returns phi angle of a single residue
Function : accessor
Example : $phi = $dssp_obj->resPhi( RESIDUE_ID )
Returns : scalar
Args : RESIDUE_ID
=cut
sub resPhi {
my $self = shift;
my @args = @_;
my $dssp_key = $self->_toDsspKey( @args );
return $self->{ 'Res' }->[ $dssp_key ]->{ 'phi' };
}
=head2 resPsi
Title : resPsi
Usage : returns psi angle of a single residue
Function : accessor
Example : $psi = $dssp_obj->resPsi( RESIDUE_ID )
Returns : scalar
Args : RESIDUE_ID
=cut
sub resPsi {
my $self = shift;
my @args = @_;
my $dssp_key = $self->_toDsspKey( @args );
return $self->{ 'Res' }->[ $dssp_key ]->{ 'psi' };
}
=head2 resSolvAcc
Title : resSolvAcc
Usage : returns solvent exposed area of this residue in
square Andstroms
Function :
Example : $solv_acc = $dssp_obj->resSolvAcc( RESIDUE_ID );
Returns : scalar
Args : RESIDUE_ID
=cut
sub resSolvAcc {
my $self = shift;
my @args = @_;
my $dssp_key = $self->_toDsspKey( @args );
return $self->{ 'Res' }->[ $dssp_key ]->{ 'solv_acces' };
}
=head2 resSurfArea
Title : resSurfArea
Usage : returns solvent exposed area of this residue in
square Andstroms
Function :
Example : $solv_acc = $dssp_obj->resSurfArea( RESIDUE_ID );
Returns : scalar
Args : RESIDUE_ID
=cut
sub resSurfArea {
my $self = shift;
my @args = @_;
my $dssp_key = $self->_toDsspKey( @args );
return $self->{ 'Res' }->[ $dssp_key ]->{ 'solv_acces' };
}
=head2 resSecStr
Title : resSecStr
Usage : $ss = $dssp_obj->resSecStr( RESIDUE_ID );
Function : returns the DSSP secondary structural designation of this residue
Example :
Returns : a character ( 'B', 'E', 'G', 'H', 'I', 'S', 'T', or ' ' )
Args : RESIDUE_ID
NOTE : The range of this method differs from that of the
resSecStr method in the STRIDE SecStr parser. That is because of the
slightly different format for STRIDE and DSSP output. The resSecStrSum
method exists to map these different ranges onto an identical range.
=cut
sub resSecStr {
my $self = shift;
my @args = @_;
my $dssp_key = $self->_toDsspKey( @args );
my $ss_char = $self->{ 'Res' }->[ $dssp_key ]->{ 'ss_summary' };
return $ss_char if $ss_char;
return ' ';
}
=head2 resSecStrSum
Title : resSecStrSum
Usage : $ss = $dssp_obj->resSecStrSum( $id );
Function : returns what secondary structure group this residue belongs
to. One of: 'H': helix ( H, G, or I )
'B': beta ( B or E )
'T': turn ( T or S )
' ': none ( ' ' )
This method is similar to resSecStr, but the information
it returns is less specific.
Example :
Returns : a character ( 'H', 'B', 'T', or ' ' )
Args : dssp residue number of pdb residue identifier
=cut
sub resSecStrSum {
my $self = shift;
my @args = @_;
my $dssp_key = $self->_toDsspKey( @args );
my $ss_char = $self->{ 'Res' }->[ $dssp_key ]->{ 'ss_summary' };
if ( $ss_char eq 'H' || $ss_char eq 'G' || $ss_char eq 'I' ) {
return 'H';
}
if ( $ss_char eq ' ' || !( $ss_char ) ) {
return ' ';
}
if ( $ss_char eq 'B' || $ss_char eq 'E' ) {
return 'B';
}
else {
return 'T';
}
}
# DSSP SPECIFIC
=head2 hBonds
Title : hBonds
Usage : returns number of 14 different types of H Bonds
Function :
Example : $hb = $dssp_obj->hBonds
Returns : pointer to 14 element array of ints
Args : none
NOTE : The different type of H-Bonds reported are, in order:
TYPE O(I)-->H-N(J)
IN PARALLEL BRIDGES
IN ANTIPARALLEL BRIDGES
TYPE O(I)-->H-N(I-5)
TYPE O(I)-->H-N(I-4)
TYPE O(I)-->H-N(I-3)
TYPE O(I)-->H-N(I-2)
TYPE O(I)-->H-N(I-1)
TYPE O(I)-->H-N(I+0)
TYPE O(I)-->H-N(I+1)
TYPE O(I)-->H-N(I+2)
TYPE O(I)-->H-N(I+3)
TYPE O(I)-->H-N(I+4)
TYPE O(I)-->H-N(I+5)
=cut
sub hBonds {
my $self = shift;
return $self->{ 'HBond'};
}
=head2 numSSBr
Title : numSSBr
Usage : returns info about number of SS-bridges
Function :
Example : @SS_br = $dssp_obj->numSSbr();
Returns : 3 element scalar int array
Args : none
=cut
sub numSSBr {
my $self = shift;
return ( $self->{'Head'}->{'TotSSBr'},
$self->{'Head'}->{'TotIaSSBr'},
$self->{'Head'}->{'TotIeSSBr'} );
}
=head2 resHB_O_HN
Title : resHB_O_HN
Usage : returns pointer to a 4 element array
consisting of: relative position of binding
partner #1, energy of that bond (kcal/mol),
relative positionof binding partner #2,
energy of that bond (kcal/mol). If the bond
is not bifurcated, the second bond is reported
as 0, 0.0
Function : accessor
Example : $oBonds_ptr = $dssp_obj->resHB_O_HN( RESIDUE_ID )
Returns : pointer to 4 element array
Args : RESIDUE_ID
=cut
sub resHB_O_HN {
my $self = shift;
my @args = @_;
my $dssp_key = $self->_toDsspKey( @args );
return ( $self->{ 'Res' }->[ $dssp_key ]->{ 'hb1_o_hn_p' },
$self->{ 'Res' }->[ $dssp_key ]->{ 'hb1_o_hn_e' },
$self->{ 'Res' }->[ $dssp_key ]->{ 'hb2_o_hn_p' },
$self->{ 'Res' }->[ $dssp_key ]->{ 'hb2_o_hn_e' } );
}
=head2 resHB_NH_O
Title : resHB_NH_O
Usage : returns pointer to a 4 element array
consisting of: relative position of binding
partner #1, energy of that bond (kcal/mol),
relative positionof binding partner #2,
energy of that bond (kcal/mol). If the bond
is not bifurcated, the second bond is reported
as 0, 0.0
Function : accessor
Example : $nhBonds_ptr = $dssp_obj->resHB_NH_O( RESIDUE_ID )
Returns : pointer to 4 element array
Args : RESIDUE_ID
=cut
sub resHB_NH_O {
my $self = shift;
my @args = @_;
my $dssp_key = $self->_toDsspKey( @args );
return ( $self->{ 'Res' }->[ $dssp_key ]->{ 'hb1_nh_o_p' },
$self->{ 'Res' }->[ $dssp_key ]->{ 'hb1_nh_o_e' },
$self->{ 'Res' }->[ $dssp_key ]->{ 'hb2_nh_o_p' },
$self->{ 'Res' }->[ $dssp_key ]->{ 'hb2_nh_o_e' } );
}
=head2 resTco
Title : resTco
Usage : returns tco angle around this residue
Function : accessor
Example : resTco = $dssp_obj->resTco( RESIDUE_ID )
Returns : scalar
Args : RESIDUE_ID
=cut
sub resTco {
my $self = shift;
my @args = @_;
my $dssp_key = $self->_toDsspKey( @args );
return $self->{ 'Res' }->[ $dssp_key ]->{ 'tco' };
}
=head2 resKappa
Title : resKappa
Usage : returns kappa angle around this residue
Function : accessor
Example : $kappa = $dssp_obj->resKappa( RESIDUE_ID )
Returns : scalar
Args : RESIDUE_ID ( dssp or PDB )
=cut
sub resKappa {
my $self = shift;
my @args = @_;
my $dssp_key = $self->_toDsspKey( @args );
return $self->{ 'Res' }->[ $dssp_key ]->{ 'kappa' };
}
=head2 resAlpha
Title : resAlpha
Usage : returns alpha angle around this residue
Function : accessor
Example : $alpha = $dssp_obj->resAlpha( RESIDUE_ID )
Returns : scalar
Args : RESIDUE_ID ( dssp or PDB )
=cut
sub resAlpha {
my $self = shift;
my @args = @_;
my $dssp_key = $self->_toDsspKey( @args );
return $self->{ 'Res' }->[ $dssp_key ]->{ 'alpha' };
}
# VALUE ADDED METHODS (NOT JUST PARSE/REPORT)
=head2 secBounds
Title : secBounds
Usage : gets residue ids of boundary residues in each
contiguous secondary structural element of specified
chain
Function : returns pointer to array of 3 element arrays. First
two elements are the PDB IDs of the start and end points,
respectively and inclusively. The last element is the
DSSP secondary structural assignment code,
i.e. one of : ('B', 'E', 'G', 'H', 'I', 'S', 'T', or ' ')
Example : $ss_elements_pts = $dssp_obj->secBounds( 'A' );
Returns : pointer to array of arrays
Args : chain id ( 'A', for example ). No arg => no chain id
=cut
sub secBounds {
my $self = shift;
my $chain = shift;
my %sec_bounds;
$chain = '-' if ( !( $chain ) || $chain eq ' ' || $chain eq '-' );
# if we've memoized this chain, use that
if ( $self->{ 'SecBounds' } ) {
# check to make sure chain is valid
if ( !( $self->{ 'SecBounds' }->{ $chain } ) ) {
$self->throw( "No such chain: $chain\n" );
}
return $self->{ 'SecBounds' }->{ $chain };
}
my ( $cur_element, $i, $cur_chain, $beg, );
#initialize
$cur_element = $self->{ 'Res' }->[ 1 ]->{ 'ss_summary' };
$beg = 1;
for ( $i = 2; $i <= $self->_numResLines() - 1; $i++ ) {
if ( $self->{ 'Res' }->[ $i ]->{ 'amino_acid' } eq '!' ) {
# element is terminated by a chain discontinuity
push( @{ $sec_bounds{ $self->_pdbChain( $beg ) } },
[ $self->_toPdbId( $beg ),
$self->_toPdbId( $i - 1 ),
$cur_element ] );
$i++;
$beg = $i;
$cur_element = $self->{ 'Res' }->[ $i ]->{ 'ss_summary' };
}
elsif ( $self->{ 'Res' }->[ $i ]->{ 'ss_summary' } ne $cur_element ) {
# element is terminated by beginning of a new element
push( @{ $sec_bounds{ $self->_pdbChain( $beg ) } },
[ $self->_toPdbId( $beg ),
$self->_toPdbId( $i - 1 ),
$cur_element ] );
$beg = $i;
$cur_element = $self->{ 'Res' }->[ $i ]->{ 'ss_summary' };
}
}
#last residue
if ( $self->{ 'Res' }->[ $i ]->{ 'ss_summary' } eq $cur_element ) {
push( @{ $sec_bounds{ $self->_pdbChain( $beg ) } },
[ $self->_toPdbId( $beg ),
$self->_toPdbId( $i ),
$cur_element ] );
}
else {
push( @{ $sec_bounds{ $self->_pdbChain( $beg ) } },
[ $self->_toPdbId( $beg ),
$self->_toPdbId( $i - 1 ),
$cur_element ] );
push( @{ $sec_bounds{ $self->_pdbChain( $i ) } },
[ $self->_toPdbId( $i ),
$self->_toPdbId( $i ),
$self->{ 'Res' }->[ $i ]->{ 'ss_summary' } ] );
}
$self->{ 'SecBounds' } = \%sec_bounds;
# check to make sure chain is valid
if ( !( $self->{ 'SecBounds' }->{ $chain } ) ) {
$self->throw( "No such chain: $chain\n" );
}
return $self->{ 'SecBounds' }->{ $chain };
}
=head2 chains
Title : chains
Usage : returns pointer to array of chain I.D.s (characters)
Function :
Example : $chains_pnt = $dssp_obj->chains();
Returns : array of characters, one of which may be ' '
Args : none
=cut
sub chains {
my $self = shift;
my $cont_segs = $self->_contSegs();
my %chains;
my $seg;
foreach $seg ( @{ $cont_segs } ) {
$chains{ $seg->[ 2 ] } = 1;
}
my @chains = keys( %chains );
return \@chains;
}
=head2 residues
Title : residues
Usage : returns array of residue identifiers for all residues in
the output file, or in a specific chain
Function :
Example : @residues_ids = $dssp_obj->residues()
Returns : array of residue identifiers
Args : if none => returns residue ids of all residues of all
chains (in order); if chain id is given, returns just the residue
ids of residues in that chain
=cut
# Can't use the standard interface for getting the amino acid,
# pdb_resnum, etc. in this method because we don't *know* the residue
# indentifiers - we are building a list of them.
sub residues {
my $self = shift;
my $chain = shift;
my @residues;
my $num_res = $self->_numResLines();
my $aa;
for ( my $i = 1; $i <= $num_res; $i++ ) {
# find what character was in the slot for tha amino acid code,
# if it's a '!' we know this is not a *real* amino acid, it's
# a chain discontinuity marker
$aa = $self->{ 'Res' }->[ $i ]->{ 'amino_acid' };
if ( $aa ne '!' ) {
if ( !$chain ||
$chain eq $self->{ 'Res' }->[ $i ]->{ 'pdb_chain' } ) {
push( @residues,
$self->{ 'Res' }->[ $i ]->{ 'pdb_resnum' }.
$self->{ 'Res' }->[ $i ]->{ 'insertionco' }.
":".
$self->{ 'Res' }->[ $i ]->{ 'pdb_chain' } );
}
}
}
return @residues;
}
=head2 getSeq
Title : getSeq
Usage : returns a Bio::PrimarySeq object which represents a good
guess at the sequence of the given chain
Function : For most chains of most entries, the sequence returned by
this method will be very good. However, it is inherently
unsafe to rely on DSSP to extract sequence information about
a PDB entry. More reliable information can be obtained from
the PDB entry itself.
Example : $pso = $dssp_obj->getSeq( 'A' );
Returns : (pointer to) a PrimarySeq object
Args : Chain identifier. If none given, ' ' is assumed. If no ' '
chain, the first chain is used.
=cut
sub getSeq {
my $self = shift;
my $chain = shift;
my ( $pot_chain,
$seq,
$frag_num,
$frag,
$curPdbNum,
$lastPdbNum,
$gap_len,
$i,
$id,
);
my @frags;
if ( !( $chain ) ) {
$chain = ' ';
}
if ( $self->{ 'Seq' }->{ $chain } ) {
return $self->{ 'Seq' }->{ $chain };
}
my $contSegs_pnt = $self->_contSegs();
# load up specified chain
foreach $pot_chain ( @{ $contSegs_pnt } ) {
if ( $pot_chain->[ 2 ] eq $chain ) {
push( @frags, $pot_chain );
}
}
# if that didn't work, just get the first one
if ( !( @frags ) ) {
$chain = $contSegs_pnt->[ 0 ]->[ 2 ];
foreach $pot_chain ( @{ $contSegs_pnt } ) {
if ( $pot_chain->[ 2 ] eq $chain ) {
push( @frags, $pot_chain );
}
}
}
# now build the sequence string
$seq = "";
$frag_num = 0;
foreach $frag ( @frags ) {
$frag_num++;
if ( $frag_num > 1 ) { # we need to put in some gap seq
$curPdbNum = $self->_pdbNum( $frag->[ 0 ] );
$gap_len = $curPdbNum - $lastPdbNum - 1;
if ( $gap_len > 0 ) {
$seq .= 'u' x $gap_len;
}
else {
$seq .= 'u';
}
}
for ( $i = $frag->[ 0 ]; $i <= $frag->[ 1 ]; $i++ ) {
$seq .= $self->_resAA( $i );
}
$lastPdbNum = $self->_pdbNum( $i - 1 );
}
$id = $self->pdbID();
$id .= ":$chain";
$self->{ 'Seq' }->{ $chain } = Bio::PrimarySeq->new ( -seq => $seq,
-id => $id,
-moltype => 'protein'
);
return $self->{ 'Seq' }->{ $chain };
}
=head1 INTERNAL METHODS
=cut
=head2 _pdbChain
Title : _pdbChain
Usage : returns the pdb chain id of given residue
Function :
Example : $chain_id = $dssp_obj->pdbChain( DSSP_KEY );
Returns : scalar
Args : DSSP_KEY ( dssp or pdb )
=cut
sub _pdbChain {
my $self = shift;
my $dssp_key = shift;
return $self->{ 'Res' }->[ $dssp_key ]->{ 'pdb_chain' };
}
=head2 _resAA
Title : _resAA
Usage : fetches the 1 char amino acid code, given a dssp id
Function :
Example : $aa = $dssp_obj->_resAA( dssp_id );
Returns : 1 character scalar string
Args : dssp_id
=cut
sub _resAA {
my $self = shift;
my $dssp_key = shift;
return $self->{ 'Res' }->[ $dssp_key ]->{ 'amino_acid' };
}
=head2 _pdbNum
Title : _pdbNum
Usage : fetches the numeric portion of the identifier for a given
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;
return ( $#{$self->{ 'Res' }} );
}
=head2 _toDsspKey
Title : _toDsspKey
Usage : returns the unique dssp integer key given a pdb residue id.
All accessor methods require (internally)
the dssp key. This method is very useful in converting
pdb keys to dssp keys so the accessors can accept pdb keys
as argument. PDB Residue IDs are inherently
problematic since they have multiple parts of
overlapping function and ill-defined or observed
convention in form. Input can be in any of the formats
described in the DESCRIPTION section above.
Function :
Example : $dssp_id = $dssp_obj->_pdbKeyToDsspKey( '10B:A' )
Returns : scalar int
Args : pdb residue identifier: num[insertion code]:[chain]
=cut
sub _toDsspKey {
# Consider adding lookup table for 'common' name (like 20:A) for
# fast access. Could be built during parse of input.
my $self = shift;
my ( $key_num, $chain_id, $ins_code ) = @_;
if ( ! $chain_id) { # parse the lone argument
( $key_num, $chain_id, $ins_code )
= $key_num =~ m/([0-9]+)
([a-zA-z]?)
(?::([a-zA-Z]))?/xms
? ( $1, $2, $3 )
: $self->throw("Could not derive PDB key $key_num");
}
# Now find the residue which fits this description. Linear search is
# probably not the best way to do this, but oh well...
for ( my $i = 1; $i <= $self->_numResLines(); $i++ ) {
unless ( ($self->{'Res'}->[$i]->{'term_sig'} eq '*') ||
($self->{'Res'}->[$i]->{'amino_acid'} eq '!') ) {
# chain break 'residue', doesn't match anything
if ( $key_num == $self->{'Res'}->[$i]->{'pdb_resnum'} ) {
if ( $chain_id ) { # if a chain was specified
if ( $chain_id eq $self->{'Res'}->[$i]->{'pdb_chain'} ) {
# and it's the right one
if ( $ins_code ) { # if insertion code was specified
if ( $ins_code eq $self->{'Res'}->[$i]->{'insertionco'} ) {
# and it's the right one
return $i;
}
}
elsif ( $self->{'Res'}->[$i]->{'insertionco'} eq '' ) { # no isertion code specified, but need to check that the located residue doesn't have an insertion code E.g. pdb1aye fails on this
return $i;
}
}
}
else { # no chain was specified
return $i;
}
}
}
}
$self->throw( "PDB key not found." );
}
=head2 _parse
Title : _parse
Usage : parses dssp output
Function :
Example : used by the constructor
Returns :
Args : input source ( handled by Bio::Root:IO )
=cut
sub _parse {
my $self = shift;
my $file = shift;
my $cur;
my $current_chain;
my ( @elements, @hbond );
my ( %head, %his, );
my $element;
my $res_num;
$cur = <$file>;
unless ( $cur =~ /^==== Secondary Structure Definition/ ) {
$self->throw( "Not dssp output" );
return;
}
# REFERENCE line (always there)
$cur = <$file>;
( $element ) = ( $cur =~ /^REFERENCE\s+(.+?)\s+\./ );
$head{ 'REFERENCE' } = $element;
$cur = <$file>;
# Check for HEADER line (not always there)
if ( $cur =~ /^HEADER\s/ ) {
@elements = split( /\s+/, $cur );
pop( @elements ); # take off that annoying period
$head{ 'PDB' } = pop( @elements );
$head{ 'DATE' } = pop( @elements );
# now, everything else is "header" except for the word
# HEADER
shift( @elements );
$element = shift( @elements );
while ( @elements ) {
$element = $element." ".shift( @elements );
}
$head{ 'HEADER' } = $element;
$cur = <$file>;
}
# Check for COMPND line (not always there)
if ( $cur =~ /^COMPND\s/ ) {
($element) = ( $cur =~ /^COMPND\s+(.+?)\s+\./ );
$head{ 'COMPND' } = $element;
$cur = <$file>;
}
# Check for SOURCE or PDBSOURCE line (not always there)
if ( $cur =~ /^PDBSOURCE\s/ ) {
($element) = ( $cur =~ /^PDBSOURCE\s+(.+?)\s+\./ );
$head{ 'SOURCE' } = $element;
$cur = <$file>;
}
elsif ( $cur =~ /^SOURCE\s/ ) {
($element) = ( $cur =~ /^SOURCE\s+(.+?)\s+\./ );
$head{ 'SOURCE' } = $element;
$cur = <$file>;
}
# Check for AUTHOR line (not always there)
if ( $cur =~ /^AUTHOR/ ) {
($element) = ( $cur =~ /^AUTHOR\s+(.+?)\s+/ );
$head{ 'AUTHOR' } = $element;
$cur = <$file>;
}
# A B C D E TOTAL NUMBER OF RESIDUES, NUMBER ... line
@elements = split( /\s+/, $cur );
shift( @elements );
$head{ 'TotNumRes' } = shift( @elements );
$head{ 'NumChain' } = shift( @elements );
$head{ 'TotSSBr' } = shift( @elements );
$head{ 'TotIaSSBr' } = shift( @elements );
$head{ 'TotIeSSBr' } = shift( @elements );
$cur = <$file>;
( $element ) = ( $cur =~ /\s*(\d+\.\d*)\s+ACCESSIBLE SURFACE OF PROTEIN/ );
$head{ 'ProAccSurf' } = $element;
$self->{ 'Head' } = \%head;
for ( my $i = 1; $i <= 14; $i++ ) {
$cur = <$file>;
( $element ) =
$cur =~ /\s*(\d+)\s+\d+\.\d+\s+TOTAL NUMBER OF HYDROGEN/;
push( @hbond, $element );
# $hbond{ $hBondType } = $element;
}
$self->{ 'HBond' } = \@hbond;
my $histogram_finished = 0;
while ( !($histogram_finished) && chomp( $cur = <$file> ) ) {
if ( $cur =~ /RESIDUE AA STRUCTURE/ ) {
$histogram_finished = 1;
}
}
while ( $cur = <$file> ) {
if ( $cur =~ m/^\s*$/ ) {
next;
}
$res_num = substr( $cur, 0, 5 );
$res_num =~ s/\s//g;
$self->{ 'Res' }->[ $res_num ] = &_parseResLine( $cur );
}
}
=head2 _parseResLine
Title : _parseResLine
Usage : parses a single residue line
Function :
Example : used internally
Returns :
Args : residue line ( string )
=cut
sub _parseResLine() {
my $cur = shift;
my ( $feat, $value );
my %elements;
foreach $feat ( keys %lookUp ) {
$value = substr( $cur, $lookUp{ $feat }->[0],
$lookUp{ $feat }->[1] );
$value =~ s/\s//g;
$elements{$feat} = $value ;
}
# if no chain id, make it '-' (like STRIDE...very convenient)
if ( !( $elements{ 'pdb_chain' } ) || $elements{ 'pdb_chain'} eq ' ' ) {
$elements{ 'pdb_chain' } = '-';
}
return \%elements;
}
1;