Domain

class chamois.model.Domain

A domain from a protein.

name

The name of the domain.

Type:

str

accession

The name of the domain, if any.

Type:

str or None

description

The description of the domain, if any.

Type:

str or None

kind

The kind of domain.

Type:

str

protein

The protein this domain belongs to.

Type:

Protein

__init__(name, accession, description, kind, protein)

class chamois.model.PfamDomain(Domain)

A protein domain that was found with a Pfam HMM.

name

The name of the domain.

Type:

str

accession

The name of the domain, if any.

Type:

str or None

description

The description of the domain, if any.

Type:

str or None

kind

The kind of domain.

Type:

str

protein

The protein this domain belongs to.

Type:

Protein

start

The start coordinate of the domain in the protein sequence.

Type:

int

end

The end coordinate of the domain in the protein sequence.

Type:

int

score

The raw bitscore for the domain, given by hmmsearch.

Type:

float

pvalue

The p-value for the domain, given by hmmsearch.

Type:

float

evalue

The database-corrected E-value for the domain, given by hmmsearch.

Type:

float

See also

PfamAnnotator: The domain annotator used for searching Pfam domains with HMMER.

__init__(name, accession, description, kind, protein, start, end, score, pvalue, evalue)

overlaps(other)

bool: Returns whether two domains overlap in the same protein.