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package Bio::Protease;
{
  $Bio::Protease::VERSION = '1.112980';
}

# ABSTRACT: Digest your protein substrates with customizable specificity

use Moose 1.23;
use MooseX::ClassAttribute;
use Bio::Protease::Types qw(ProteaseRegex ProteaseName);
use namespace::autoclean;

with qw(
    Bio::ProteaseI
    Bio::Protease::Role::Specificity::Regex
    Bio::Protease::Role::WithCache
);

has '+regex' => ( init_arg => 'specificity' );

has specificity => (
    is  => 'ro',
    isa => ProteaseName,
    required => 1,
    coerce   => 1
);

class_has Specificities => (
    is         => 'ro',
    lazy_build => 1,
);

sub _build_Specificities {

    my %specificity_of = (
        'alcalase'                   => [ '.{3}[MYFLIVW].{4}'],
        'arg-c_proteinase'           => [ '.{3}R.{4}' ],
        'asp-n_endopeptidase'        => [ '.{4}D.{3}' ],
        'asp-n_endopeptidase_glu'    => [ '.{4}[DE].{3}' ],
        'bnps_skatole'               => [ '.{3}W.{4}' ],
        'caspase_1'                  => [ '[FWYL].[HAT]D[^PEDQKR].{3}' ],
        'caspase_2'                  => [ 'DVAD[^PEDQKR].{3}' ],
        'caspase_3'                  => [ 'DMQD[^PEDQKR].{3}' ],
        'caspase_4'                  => [ 'LEVD[^PEDQKR].{3}' ],
        'caspase_5'                  => [ '[LW]EHD.{4}' ],
        'caspase_6'                  => [ 'VE[HI]D[^PEDQKR].{3}' ],
        'caspase_7'                  => [ 'DEVD[^PEDQKR].{3}' ],
        'caspase_8'                  => [ '[IL]ETD[^PEDQKR].{3}' ],
        'caspase_9'                  => [ 'LEHD.{4}' ],
        'caspase_10'                 => [ 'IEAD.{4}' ],
        'chymotrypsin'               => [ '.{3}[FY][^P].{3}|.{3}W[^MP].{3}' ],
        'chymotrypsin_low'           => [ '.{3}[FLY][^P].{3}|.{3}W[^MP].{3}|.{3}M[^PY].{3}|.{3}H[^DMPW].{3}' ],
        'clostripain'                => [ '.{3}R.{4}' ],
        'cnbr'                       => [ '.{3}M.{4}' ],
        'enterokinase'               => [ '[DN][DN][DN]K.{4}' ],
        'factor_xa'                  => [ '[AFGILTVM][DE]GR.{4}' ],
        'formic_acid'                => [ '.{3}D.{4}' ],
        'glutamyl_endopeptidase'     => [ '.{3}E.{4}' ],
        'granzymeb'                  => [ 'IEPD.{4}' ],
        'hydroxylamine'              => [ '.{3}NG.{3}' ],
        'hcl'                        => [ '.{8}' ],
        'iodosobenzoic_acid'         => [ '.{3}W.{4}' ],
        'lysc'                       => [ '.{3}K.{4}' ],
        'lysn'                       => [ '.{4}K.{3}' ],
        'ntcb'                       => [ '.{4}C.{3}' ],
        'pepsin_ph1.3'               => [ '.[^HKR][^P][^R][FLWY][^P].{2}|.[^HKR][^P][FLWY].[^P].{2}' ],
        'pepsin'                     => [ '.[^HKR][^P][^R][FL][^P].{2}|.[^HKR][^P][FL].[^P].{2}' ],
        'proline_endopeptidase'      => [ '.{2}[HKR]P[^P].{3}' ],
        'proteinase_k'               => [ '.{3}[AFILTVWY].{4}' ],
        'staphylococcal_peptidase_i' => [ '.{2}[^E]E.{4}' ],
        'thermolysin'                => [ '.{3}[^XDE][AFILMV][^P].{2}' ],