Cutters and Filters

This document introdues the various classes used for slicing proteins. See blow instractions to in order to add new methods of slicing and filtering. After implementing your Cutter or Filter do the following in pdbslicer.py:

Cutters

Cutters are classes which allow us to slice a protein data structure (model) into slices. For example: Use the ByAmino cutter to insert model and to get a list (Cut) of its amino acids data structure. Each item in this data structure is a list of atoms which represents one amino acid. An atom is represented by a hash references of the record components of atom line from the PDB file.

$line= 'ATOM    149  CD1ALEU A  18     -24.795  15.010  15.993  0.50 10.41           C';
$atom_record = $parser->_parse_atom($line);
# Will results:
 {
        'record_name' => 'ATOM',
        'chain_id' => 'A',
        'atom_serial_number' => '149',
        'atom_name' => 'CD1',
        'resname' => 'LEU',
        'altloc' => 'A',
        'resseq' => '18',
        'charge' => '',
        'occupancy' => '0.50',
        'X' => '-24.795',
        'Y' => '15.010',
        'Z' => '15.993',
        'tempfactor' => '10.41',
        'icode' => '',
        'element_symbol' => 'C',
        'line_index' => 'NOT_DEFINED',
        'orig_line' => 'ATOM    149  CD1ALEU A  18     -24.795  15.010  15.993  0.50 10.41           C',
 };

Cut.pm

This is the parent class of each Cut sub class Implements the following methods:

Implemented Cutters

We have already implemented the following cutters:

Filters

You can filter the results of a Cut after making the cut by running an object which implements Filter.pm methods.

Filter.pm

This is the parent class of each filter sub class Implements the following methods:

Implemented Filter

We implemented the following classes of filters: