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lib/Bio/ProteaseI.pm  view on Meta::CPAN

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

# ABSTRACT: A role to build your customized Protease

use Moose::Role;
use Carp 'croak';
use namespace::autoclean;

requires '_cuts';

sub cut {
    my ( $self, $substrate, $pos ) = @_;

    croak "Incorrect substrate argument"
        unless ( defined $substrate and _looks_like_string($substrate) );

    unless ( defined $pos and $pos > 0 and $pos <= length $substrate ) {

        croak "Incorrect position.";
    }

    $substrate = uc $substrate;
    $substrate = _cap_head($substrate);
    $pos += 3;

    my $pep = substr($substrate, $pos - 4, 8);

    if ( $self->_cuts($pep) ) {
        my $product = substr($substrate, 0, $pos);
        substr($substrate, 0, $pos) = '';

        _uncap($product, $substrate);

        return ($product, $substrate);
    }

    else { return }
}

sub digest {
    my ( $self, $substrate ) = @_;

    croak "Incorrect substrate argument"
        unless ( defined $substrate and _looks_like_string($substrate) );

    # Get the positions where the enzyme cuts
    my @sites = $self->cleavage_sites($substrate) or return $substrate;

    # Get the peptide products;
    my @products;
    my $start = 0;
    while ( my $site = shift @sites ) {
        my $length = $site - $start;
        my $product = substr($substrate, $start, $length);
        push @products, $product;
        $start += $length;
    }

    # Last peptide: cut from last position to the end.
    push @products, substr($substrate, $start);

    return @products;
}

sub is_substrate {
    my ($self, $substrate) = @_;