SYNOPSIS
my $stride_obj = Bio::Structure::SecStr::STRIDE::Res->new( '-file' => 'filename.stride' );
# or
my $stride_obj = Bio::Structure::SecStr::STRIDE::Res->new( '-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' )
DESCRIPTION
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://webclu.bio.wzw.tum.de/stride/
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
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.
FEEDBACK
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AUTHOR - Ed Green
Email [email protected]APPENDIX
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
pdbAuthor
Title : pdbAuthor Usage : returns author of this PDB entry Function : Example : $auth = $stride_obj->pdbAuthor() 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.
INTERNAL METHODS
_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 :