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Bio::Structure::SecStr::DSSP::Res.3pm

NAME

Bio::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 )