jade.basic.sequence.fasta.chain_fasta_files_from_biostructure(structure, prefix, outdir)[source]
jade.basic.sequence.fasta.chain_fasta_files_from_pose(pose, prefix, outdir)[source]

Creates fasta for each chain in the pose. Returns a list of paths for each fasta.

jade.basic.sequence.fasta.chain_fasta_from_biostructure(structure, outname, outdir)[source]

Creates a single fasta from biopython structure, split by individual chains.

jade.basic.sequence.fasta.chain_fasta_from_pose(pose, outname, outdir)[source]

Creates a single fasta from pose, split by individual chains.

jade.basic.sequence.fasta.fasta_from_pose(pose, fasta_label, outname, outdir)[source]

Creates a fasta from the pose.

jade.basic.sequence.fasta.fasta_from_sequences(sequences, outdir, outname)[source]

Output a general fasta, with tag being 1_outname etc. Use write_fasta for more control. Returns path to Fasta File written

jade.basic.sequence.fasta.get_biochain_sequence(bio_chain)[source]
jade.basic.sequence.fasta.get_label_from_fasta(fasta_path)[source]

Gets the first chainID found - Should be a single chain fasta file.

jade.basic.sequence.fasta.get_sequence_from_fasta(fasta_path, label)[source]
jade.basic.sequence.fasta.output_fasta_from_pdbs_biopython(path_header_dict, out_path, native_path=None, native_label='native', is_camelid=False)[source]

Used only for L and H chains! Concatonates the L and H in order if present, otherwise assumes camelid at H.

jade.basic.sequence.fasta.output_weblogo_for_sequences(sequences, outdir, outname, tag='Dunbrack Lab - Antibody Database Team')[source]
jade.basic.sequence.fasta.read_header_data_from_fasta(fasta_path)[source]

Reads > from fasta (PDBAA) and returns a defaultdict of pdb_chain: [method, residues, resolution, R factor]

jade.basic.sequence.fasta.split_fasta_from_fasta(fasta_path, prefix, outdir)[source]

If we have a multiple fasta sequence, we split it into idividual files. Makes analysis easier. Returns list of paths for each fasta

jade.basic.sequence.fasta.write_fasta(sequence, label, HANDLE)[source]

Writes a fasta with a sequence, chain, and open FILE handle. FULL Sequence on one line seems to be fine with HMMER3.