Pfam Access Functions
This module defines functions for interfacing Pfam database.
- prody.database.pfam.fetchPfamMSA(acc, alignment='seed', compressed=False, **kwargs)[source]
Returns a path to the downloaded Pfam MSA file.
- Parameters:
acc (str) – Pfam ID or Accession Code
alignment – alignment type, one of
'full','seed'(default),'ncbi','metagenomics','rp15','rp35','rp55','rp75'or'uniprot'where rp stands for representative proteomes. InterPro Pfam seems to only have seed alignments easily accessible in most casescompressed – gzip the downloaded MSA file, default is False
timeout – timeout for blocking connection attempt in seconds, default is 60
outname (str) – out filename, default is input
'acc_alignment.format'folder (str) – output folder, default is
'.'
- prody.database.pfam.parsePfamPDBs(query, data=None, **kwargs)[source]
Returns a list of
AtomGroupobjects containing sections of chains that correspond to a particular PFAM domain family. These are defined by alignment start and end residue numbers.- Parameters:
query (str) – Pfam ID, UniProt ID or PDB ID If a PDB ID is provided the corresponding UniProt ID is used. If this returns multiple matches then start or end must also be provided. This query is also used for label refinement of the Pfam domain MSA.
data (list) – If given the data list from the Pfam mapping table will be output through this argument.
- Keyword Arguments:
start – Residue number for defining the start of the domain. The PFAM domain that starts closest to this will be selected. Default is 1
end – Residue number for defining the end of the domain. The PFAM domain that ends closest to this will be selected.
num_pdbs – Number of pdb chains to parse before stopping Default behaviour is to pass all of them