def pdb_to_fasta(pdb_filename, fasta_filename, id_filename, separate):
"""Write a pdb file as a fasta file."""
flat_map = {}
pdb_name = db.get_pdb_name(pdb_filename)
structure = pd.read_pickle(pdb_filename)
fasta_name_to_chain = {}
for (chain, residues) in struct.get_chain_to_valid_residues(structure):
fasta_name = pdb_name + '-' + chain[-2] + '-' + chain[-1]
flat_map[fasta_name] = residues
fasta_name_to_chain[fasta_name] = chain
names = []
filenames = []
id_filenames = []
if not separate:
write_fasta(flat_map, fasta_filename, id_out=id_filename)
filenames.append(fasta_filename)
id_filenames.append(id_filename)
names.append('all')
else:
for (name, seq) in flat_map.items():
new_dict = {}
new_dict[name] = seq
filename = fasta_filename.format(name)
filename2 = id_filename.format(name)
write_fasta(new_dict, filename, id_out=filename2)
names.append(fasta_name_to_chain[name])
filenames.append(filename)
id_filenames.append(filename2)
return (names, filenames, id_filenames)
def _get_seq_and_atoms(filename):
"""Form dictionaries mapping from chain to their sequence and atoms."""
seqs = {}
all_atoms = {}
structure = struct.parse_structure(filename)
pdb_name = db.get_pdb_name(filename)
for (chain, residues) in \
struct.get_chain_to_valid_residues(structure, pdb_name):
atoms = []
for residue in residues:
atoms.append(np.array(residue[['x', 'y', 'z']], dtype='f4'))
if len(residues) != 0:
# Ignore zero-length peptides.
seqs[chain] = residues
all_atoms[chain] = np.array(atoms)
return all_atoms, seqs
def _generate_reference(pdb_filename, s2r_chain, s2r_res, output_filename,
style):
"""Transform PDB structure to a reference structure."""
biopy_structure = db.parse_biopython_structure(pdb_filename)
pdb_name = db.get_pdb_name(pdb_filename)
new_model = Bio.PDB.Model.Model('0')
new_structure = Bio.PDB.Structure.Structure('')
for (chain, residues) in \
struct.get_chain_to_valid_residues(biopy_structure, pdb_name):
if style == 'dockground' and chain not in s2r_chain:
# If we are in dockground, we allow ourselves to remove unmapped
# chains.
continue
ref_chain = s2r_chain[chain]
if chain in s2r_res:
# If we have an alignment for this chain.
new_chain = Bio.PDB.Chain.Chain(ref_chain)
for i, residue in enumerate(residues):
if residue.id[0] != ' ':
continue
residue.segid = ""
residue.id = (' ', s2r_res[chain][i], residue.id[2])
new_chain.add(residue)
else:
# Else, just remove segment ID.
new_chain = Bio.PDB.Chain.Chain(ref_chain)
for i, residue in enumerate(residues):
residue.segid = ""
new_model.add(new_chain)
new_structure.add(new_model)
w = Bio.PDB.PDBIO()
w.set_structure(new_structure)
w.save(output_filename)