Bio::Structure::SecStr::STRIDE::Res - Module for parsing/accessing stride output my $stride_obj = new Bio::Structure::SecStr::STRIDE::Res( '-file' => 'filename.stride' ); # or my $stride_obj = new Bio::Structure::SecStr::STRIDE::Res( '-fh' => \*STDOUT ); # Get secondary structure assignment for PDB residue 20 of chain A $sec_str = $stride_obj->resSecStr( '20:A' ); # same $sec_str = $stride_obj->resSecStr( 20, 'A' ) STRIDE::Res is a module for objectifying STRIDE output. STRIDE is a program (similar to DSSP) for assigning secondary structure to individual residues of a pdb structure file. ( Knowledge-Based Protein Secondary Structure Assignment, PROTEINS: Structure, Function, and Genetics 23:566-579 (1995) ) STRIDE is available here: http://www.embl-heidelberg.de/argos/stride/down_stride.html Methods are then available for extracting all of the infomation present within the output or convenient subsets of it. Although they are very similar in function, DSSP and STRIDE differ somewhat in output format. Thes differences are reflected in the return value of some methods of these modules. For example, both the STRIDE and DSSP parsers have resSecStr() methods for returning the secondary structure of a given residue. However, the range of return values for DSSP is ( H, B, E, G, I, T, and S ) whereas the range of values for STRIDE is ( H, G, I, E, B, b, T, and C ). See individual methods for details. 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.

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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 : $stride_obj = Bio::Structure::SecStr::STRIDE:Res->new( '-file' => filename # or '-fh' => FILEHANDLE ) Returns : object (ref) Args : filename or filehandle( must be proper STRIDE output )

totSurfArea
Title : totSurfArea Usage : returns sum of surface areas of all residues of all chains considered. Result is memoized. Function : Example : $tot_SA = $stride_obj->totSurfArea(); Returns : scalar Args : none

numResidues
Title : numResidues Usage : returns total number of residues in all chains or just the specified chain Function : Example : $tot_res = $stride_obj->numResidues(); Returns : scalar int Args : none or chain id

pdbID
Title : pdbID Usage : returns pdb identifier ( 1FJM, e.g. ) Function : Example : $pdb_id = $stride_obj->pdbID(); Returns : scalar string Args : none

pdbCompound
Title : pdbCompound Usage : returns string of what was found on the CMP lines Function : Example : $cmp = $stride_obj->pdbCompound(); Returns : string Args : none

pdbDate
Title : pdbDate Usage : returns date given in PDB file Function : Example : $pdb_date = $stride_obj->pdbDate(); Returns : scalar Args : none

pdbHeader
Title : pdbHeader Usage : returns string of characters found on the PDB header line Function : Example : $head = $stride_obj->pdbHeader(); Returns : scalar Args : none

pdbSource
Title : pdbSource Usage : returns string of what was found on SRC lines Function : Example : $src = $stride_obj->pdbSource(); Returns : scalar Args : none

resAA
Title : resAA Usage : returns 1 letter abbr. of the amino acid specified by the arguments Function : Examples : $aa = $stride_obj->resAA( RESIDUE_ID ); Returns : scalar character Args : RESIDUE_ID

resPhi
Title : resPhi Usage : returns phi angle of specified residue Function : Example : $phi = $stride_obj->resPhi( RESIDUE_ID ); Returns : scaler Args : RESIDUE_ID

resPsi
Title : resPsi Usage : returns psi angle of specified residue Function : Example : $psi = $stride_obj->resPsi( RESIDUE_ID ); Returns : scalar Args : RESIDUE_ID

resSolvAcc
Title : resSolvAcc Usage : returns stride calculated surface area of specified residue Function : Example : $sa = $stride_obj->resSolvAcc( RESIDUE_ID ); Returns : scalar Args : RESIDUE_ID

resSurfArea
Title : resSurfArea Usage : returns stride calculated surface area of specified residue Function : Example : $sa = $stride_obj->resSurfArea( RESIDUE_ID ); Returns : scalar Args : RESIDUE_ID

resSecStr
Title : resSecStr Usage : gives one letter abbr. of stride determined secondary structure of specified residue Function : Example : $ss = $stride_obj->resSecStr( RESIDUE_ID ); Returns : one of: 'H' => Alpha Helix 'G' => 3-10 helix 'I' => PI-helix 'E' => Extended conformation 'B' or 'b' => Isolated bridge 'T' => Turn 'C' => Coil ' ' => None # NOTE: This range is slightly DIFFERENT from the # DSSP method of the same name Args : RESIDUE_ID

resSecStrSum
Title : resSecStrSum Usage : gives one letter summary of secondary structure of specified residue. More general than secStruc() Function : Example : $ss_sum = $stride_obj->resSecStrSum( RESIDUE_ID ); Returns : one of: 'H' (helix), 'B' (beta), 'T' (turn), or 'C' (coil) Args : residue identifier(s) ( SEE INTRO NOTE )

resSecStrName
Title : resSecStrName Usage : gives full name of the secondary structural element classification of the specified residue Function : Example : $ss_name = $stride_obj->resSecStrName( RESIDUE_ID ); Returns : scalar string Args : RESIDUE_ID

strideLocs
Title : strideLocs Usage : returns stride determined contiguous secondary structural elements as specified on the LOC lines Function : Example : $loc_pnt = $stride_obj->strideLocs(); Returns : pointer to array of 5 element arrays. 0 => stride name of structural element 1 => first residue pdb key (including insertion code, if app.) 2 => first residue chain id 3 => last residue pdb key (including insertion code, if app.) 4 => last residue chain id NOTE the differences between this range and the range of SecBounds() Args : none

secBounds
Title : secBounds Usage : gets residue ids of boundary residues in each contiguous secondary structural element of specified chain Function : Example : $ss_bound_pnt = $stride_obj->secBounds( 'A' ); 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 STRIDE secondary structural element code (same range as resSecStr). Args : chain identifier ( one character ). If none, '-' is assumed

chains
Title : chains Usage : gives array chain I.D.s (characters) Function : Example : @chains = $stride_obj->chains(); Returns : array of characters Args : none

getSeq
Title : getSeq Usage : returns a Bio::PrimarySeq object which represents an approximation at the sequence of the specified chain. Function : For most chain of most entries, the sequence returned by this method will be very good. However, it it inherently unsafe to rely on STRIDE to extract sequence information about a PDB entry. More reliable information can be obtained from the PDB entry itself. If a second option is given (and evaluates to true), the sequence generated will have 'X' in spaces where the pdb residue numbers are discontinuous. In some cases this results in a better sequence object (when the discontinuity is due to regions which were present, but could not be resolved). In other cases, it will result in a WORSE sequence object (when the discontinuity is due to historical sequence numbering and all sequence is actually resolved). Example : $pso = $dssp_obj->getSeq( 'A' ); Returns : (pointer to) a PrimarySeq object Args : Chain identifier. If none given, '-' is assumed.

_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( 3, 'A' ); Returns : a scalar Args : valid ordinal num / chain combination

_resAA
Title : _resAA Usage : returns 1 letter abbr. of the amino acid specified by the arguments Function : Examples : $aa = $stride_obj->_resAA( 3, '-' ); Returns : scalar character Args : ( ord. num, chain )

_pdbInsCo
Title : _pdbInsCo Usage : fetches the Insertion code for this residue. Function : Example : $pdb_ins_co = $self->_pdb_ins_co( 15, 'B' ); Returns : a scalar Args : ordinal number and chain

_toOrdChain
Title : _toOrdChain Usage : takes any set of residue identifying parameters and wrestles them into a two element array: the chain and the ordinal number of this residue. This two element array can then be efficiently used as keys in many of the above accessor methods ('#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). Function : Example : my ( $ord, $chain ) = $self->_toOrdChain( @args ); Returns : two element array Args : valid set of residue identifier(s) ( SEE NOTE ABOVE )

_parse
Title : _parse Usage : as name suggests, parses stride output, creating object Function : Example : $self->_parse( $io ); Returns : Args : valid Bio::Root::IO object

_parseTop
Title : _parseTop Usage : makes sure this looks like stride output Function : Example : Returns : Args :

_parseHead
Title : _parseHead Usage : parses Function : HDR, CMP, SRC, and AUT lines Example : Returns : Args :

_parseSummary
Title : _parseSummary Usage : parses LOC lines Function : Example : Returns : Args :

_parseASG
Title : _parseASG Usage : parses ASG lines Function : Example : Returns : Args :