Bio::Structure::IO::pdb - PDB input/output stream
It is probably best not to use this object directly, but rather go through the Bio::Structure::IO handler system. Go:
$stream = Bio::Structure::IO->new(-file => $filename, -format => 'PDB'); while ( (my $structure = $stream->next_structure()) ) { # do something with $structure }
This object can transform Bio::Structure objects to and from PDB flat file databases. The working is similar to that of the Bio::SeqIO handlers.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_structure Usage : $struc = $stream->next_structure() Function: returns the next structure in the stream Returns : Bio::Structure object Args :
Title : write_structure Usage : $stream->write_structure($struc) Function: writes the $struc object (must be a Bio::Structure) to the stream Returns : 1 for success and 0 for error Args : Bio::Structure object
Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional)
Title : _noatom Usage : $obj->_noatom($newval) Function: Example : Returns : value of _noatom Args : newvalue (optional)
Title : _noheader Usage : $obj->_noheader($newval) Function: Example : Returns : value of _noheader Args : newvalue (optional)
Title : _read_PDB_singlecontline Usage : $obj->_read_PDB_singlecontline($record, $fromto, $buffer)) Function: read single continued record from PDB Returns : concatenated record entry (between $fromto columns) Args : record, colunm delimiters, buffer
Title : _read_PDB_jrnl Usage : $obj->_read_PDB_jrnl($\buffer)) Function: read jrnl record from PDB Returns : Bio::Annotation::Reference object Args :
Title : _read_PDB_remark_1 Usage : $obj->_read_PDB_remark_1($\buffer)) Function: read "remark 1" record from PDB Returns : array of Bio::Annotation::Reference objects Args :
Title : _read_PDB_coordinate_section Usage : $obj->_read_PDB_coordinate_section($\buffer)) Function: read one model from a PDB Returns : Bio::Structure::Model object Args :
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.