Bio::Structure::SecStrUserSContributed PerBio::Structure::SecStr::DSSP::Res(3)NAMEBio::Structure::SecStr::DSSP::Res - Module for parsing/accessing dssp
output
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' );
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
arguement. 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.
FEEDBACK
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
Support
Please direct usage questions or support issues to the mailing list:
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.
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:
http://bugzilla.open-bio.org/
AUTHOR - Ed Green
Email ed@compbio.berkeley.edu
APPENDIX
The rest of the documentation details each method. Internal methods
are preceded with a _
CONSTRUCTOR
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 )
ACCESSORS
totSurfArea
Title : totSurfArea
Usage : returns total accessible surface area in square Ang.
Function :
Example : $surArea = $dssp_obj->totSurfArea();
Returns : scalar
Args : none
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
pdbID
Title : pdbID
Usage : returns pdb identifier ( 1FJM, e.g.)
Function :
Example : $pdb_id = $dssp_obj->pdbID();
Returns : scalar string
Args : none
pdbAuthor
Title : pdbAuthor
Usage : returns author field
Function :
Example : $auth = $dssp_obj->pdbAuthor()
Returns : scalar string
Args : none
pdbCompound
Title : pdbCompound
Usage : returns pdbCompound given in PDB file
Function :
Example : $cmpd = $dssp_obj->pdbCompound();
Returns : scalar string
Args : none
pdbDate
Title : pdbDate
Usage : returns date given in PDB file
Function :
Example : $pdb_date = $dssp_obj->pdbDate();
Returns : scalar
Args : none
pdbHeader
Title : pdbHeader
Usage : returns header info from PDB file
Function :
Example : $header = $dssp_obj->pdbHeader();
Returns : scalar
Args : none
pdbSource
Title : pdbSource
Usage : returns pdbSource information from PDBSOURCE line
Function :
Example : $pdbSource = $dssp_obj->pdbSource();
Returns : scalar
Args : none
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
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
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
resSolvAcc
Title : resSolvAcc
Usage : returns solvent exposed area of this residue in
square Angstroms
Function :
Example : $solv_acc = $dssp_obj->resSolvAcc( RESIDUE_ID );
Returns : scalar
Args : RESIDUE_ID
resSurfArea
Title : resSurfArea
Usage : returns solvent exposed area of this residue in
square Angstroms
Function :
Example : $solv_acc = $dssp_obj->resSurfArea( RESIDUE_ID );
Returns : scalar
Args : RESIDUE_ID
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.
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
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)
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
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
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
resTco
Title : resTco
Usage : returns tco angle around this residue
Function : accessor
Example : resTco = $dssp_obj->resTco( RESIDUE_ID )
Returns : scalar
Args : RESIDUE_ID
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 )
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 )
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
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
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
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.
INTERNAL METHODS
_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 )
_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
_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
_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
_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
_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
_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
_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]
_parse
Title : _parse
Usage : parses dssp output
Function :
Example : used by the constructor
Returns :
Args : input source ( handled by Bio::Root:IO )
_parseResLine
Title : _parseResLine
Usage : parses a single residue line
Function :
Example : used internally
Returns :
Args : residue line ( string )
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