cocoatree.msa.map_to_pdb

cocoatree.msa.map_to_pdb(pdb_seq, pdb_pos, sequences, sequences_id, ref_seq_id)

Mapping of the unfiltered MSA positions on a PDB structure.

Parameters

pdb_seq: str,

amino acid sequence of the reference PDB file

pdb_pos: list,

Residue positions as found in the PDB file

sequences: list,

List of sequences of the unfiltered MSA

sequences_id: list,

List of sequence identifiers in the unfiltered MSA

ref_seq_id: str,

identifier of the sequence the positions are mapped onto. Should be included in seq_list.

Returns

mapping: numpy.ndarray of shape (3, len(pdb_seq)),

the first element is an array of the residues found in the PDB sequence the second element is an array of the PDB position of each amino acid the third element is an array of the positions of those same amino acids in the unfiltered MSA

Examples using cocoatree.msa.map_to_pdb

Perform full SCA analysis on the S1A serine protease dataset

Perform full SCA analysis on the S1A serine protease dataset