-
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_label_from_fasta
(fasta_path)[source]¶ Gets the first chainID found - Should be a single chain fasta file.
-
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
(alignment_path, outdir, outname, tag='Dunbrack Lab - Antibody Database Team')[source]¶
-
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]