Bio::Structure::SecStr::DSSP::Res - Module for parsing/accessing dssp output my $dssp_obj = new Bio::Structure::SecStr::DSSP::Res('-file'=>'filename.dssp'); # or my $dssp_obj = new Bio::Structure::SecStr::DSSP::Res('-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' ); 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.

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email ed@compbio.berkeley.edu The rest of the documentation details each method. Internal methods are preceded with a _

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 )

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->aminoAcid( '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

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.

_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 )