NAME
Bio::Structure::SecStr::STRIDE::Res - Module for parsing/accessing stride output
SYNOPSIS
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' )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://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. FEEDBACK
MailingLists
UsUser 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 listsReporting 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/AUTHOR - Ed Green
Email ed@compbio.berkeley.edu
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 : nonenumResidues
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 idpdbID
Title : pdbID
Usage : returns pdb identifier ( 1FJM, e.g. )
Function :
Example : $pdb_id = $stride_obj->pdbID();
Returns : scalar string
Args : nonepdbAuthor
Title : pdbAuthor
Usage : returns author of this PDB entry
Function :
Example : $auth = $stride_obj->pdbAuthor()
Returns : scalar string
Args : nonepdbCompound
Title : pdbCompound
Usage : returns string of what was found on the
CMP lines
Function :
Example : $cmp = $stride_obj->pdbCompound();
Returns : string
Args : nonepdbDate
Title : pdbDate
Usage : returns date given in PDB file
Function :
Example : $pdb_date = $stride_obj->pdbDate();
Returns : scalar
Args : nonepdbHeader
Title : pdbHeader
Usage : returns string of characters found on the PDB header line
Function :
Example : $head = $stride_obj->pdbHeader();
Returns : scalar
Args : nonepdbSource
Title : pdbSource
Usage : returns string of what was found on SRC lines
Function :
Example : $src = $stride_obj->pdbSource();
Returns : scalar
Args : noneresAA
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_IDresPhi
Title : resPhi
Usage : returns phi angle of specified residue
Function :
Example : $phi = $stride_obj->resPhi( RESIDUE_ID );
Returns : scaler
Args : RESIDUE_IDresPsi
Title : resPsi
Usage : returns psi angle of specified residue
Function :
Example : $psi = $stride_obj->resPsi( RESIDUE_ID );
Returns : scalar
Args : RESIDUE_IDresSolvAcc
Title : resSolvAcc
Usage : returns stride calculated surface area of specified residue
Function :
Example : $sa = $stride_obj->resSolvAcc( RESIDUE_ID );
Returns : scalar
Args : RESIDUE_IDresSurfArea
Title : resSurfArea
Usage : returns stride calculated surface area of specified residue
Function :
Example : $sa = $stride_obj->resSurfArea( RESIDUE_ID );
Returns : scalar
Args : RESIDUE_IDresSecStr
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_IDresSecStrSum
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_IDstrideLocs
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 : nonesecBounds
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 assumedchains
Title : chains
Usage : gives array chain I.D.s (characters)
Function :
Example : @chains = $stride_obj->chains();
Returns : array of characters
Args : nonegetSeq
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 :