| |
| |
| @@ -19,6 +19,9 @@ |
| from alphafold.common import residue_constants |
| from Bio.PDB import PDBParser |
| import numpy as np |
| +from string import ascii_uppercase,ascii_lowercase |
| + |
| +CHAIN_IDs = ascii_uppercase+ascii_lowercase |
| |
| FeatureDict = Mapping[str, np.ndarray] |
| ModelOutput = Mapping[str, Any] # Is a nested dict. |
| @@ -75,14 +78,15 @@ |
| |
| if chain_id is not None: |
| chain = model[chain_id] |
| + chains = [chain] |
| else: |
| chains = list(model.get_chains()) |
| - if len(chains) != 1: |
| - raise ValueError( |
| - 'Only single chain PDBs are supported when chain_id not specified. ' |
| - f'Found {len(chains)} chains.') |
| - else: |
| - chain = chains[0] |
| + # if len(chains) != 1: |
| + # raise ValueError( |
| + # 'Only single chain PDBs are supported when chain_id not specified. ' |
| + # f'Found {len(chains)} chains.') |
| + # else: |
| + # chain = chains[0] |
| |
| atom_positions = [] |
| aatype = [] |
| @@ -90,31 +94,35 @@ |
| residue_index = [] |
| b_factors = [] |
| |
| - for res in chain: |
| - if res.id[2] != ' ': |
| - raise ValueError( |
| - f'PDB contains an insertion code at chain {chain.id} and residue ' |
| - f'index {res.id[1]}. These are not supported.') |
| - res_shortname = residue_constants.restype_3to1.get(res.resname, 'X') |
| - restype_idx = residue_constants.restype_order.get( |
| - res_shortname, residue_constants.restype_num) |
| - pos = np.zeros((residue_constants.atom_type_num, 3)) |
| - mask = np.zeros((residue_constants.atom_type_num,)) |
| - res_b_factors = np.zeros((residue_constants.atom_type_num,)) |
| - for atom in res: |
| - if atom.name not in residue_constants.atom_types: |
| + PARAM_CHAIN_BREAK = 100 |
| + residue_index_prev = 0 |
| + for k,chain in enumerate(chains): |
| + for res in chain: |
| + if res.id[2] != ' ': |
| + raise ValueError( |
| + f'PDB contains an insertion code at chain {chain.id} and residue ' |
| + f'index {res.id[1]}. These are not supported.') |
| + res_shortname = residue_constants.restype_3to1.get(res.resname, 'X') |
| + restype_idx = residue_constants.restype_order.get( |
| + res_shortname, residue_constants.restype_num) |
| + pos = np.zeros((residue_constants.atom_type_num, 3)) |
| + mask = np.zeros((residue_constants.atom_type_num,)) |
| + res_b_factors = np.zeros((residue_constants.atom_type_num,)) |
| + for atom in res: |
| + if atom.name not in residue_constants.atom_types: |
| + continue |
| + pos[residue_constants.atom_order[atom.name]] = atom.coord |
| + mask[residue_constants.atom_order[atom.name]] = 1. |
| + res_b_factors[residue_constants.atom_order[atom.name]] = atom.bfactor |
| + if np.sum(mask) < 0.5: |
| + # If no known atom positions are reported for the residue then skip it. |
| continue |
| - pos[residue_constants.atom_order[atom.name]] = atom.coord |
| - mask[residue_constants.atom_order[atom.name]] = 1. |
| - res_b_factors[residue_constants.atom_order[atom.name]] = atom.bfactor |
| - if np.sum(mask) < 0.5: |
| - # If no known atom positions are reported for the residue then skip it. |
| - continue |
| - aatype.append(restype_idx) |
| - atom_positions.append(pos) |
| - atom_mask.append(mask) |
| - residue_index.append(res.id[1]) |
| - b_factors.append(res_b_factors) |
| + aatype.append(restype_idx) |
| + atom_positions.append(pos) |
| + atom_mask.append(mask) |
| + residue_index.append(res.id[1] + residue_index_prev + PARAM_CHAIN_BREAK*k) |
| + b_factors.append(res_b_factors) |
| + residue_index_prev = residue_index[-1] |
| |
| return Protein( |
| atom_positions=np.array(atom_positions), |
| @@ -150,10 +158,21 @@ |
| |
| pdb_lines.append('MODEL 1') |
| atom_index = 1 |
| - chain_id = 'A' |
| + chain_index = -1 |
| + residue_index_prev = residue_index[0]-100 |
| # Add all atom sites. |
| for i in range(aatype.shape[0]): |
| + if residue_index[i] - residue_index_prev > 1: # chain break |
| + chain_index += 1 |
| + res_num = 1 |
| + if chain_index > 0: |
| + pdb_lines.append("TER") |
| + elif residue_index[i] != residue_index_prev: |
| + res_num += 1 |
| + residue_index_prev = residue_index[i] |
| + chain_id = CHAIN_IDs[chain_index] |
| res_name_3 = res_1to3(aatype[i]) |
| + # |
| for atom_name, pos, mask, b_factor in zip( |
| atom_types, atom_positions[i], atom_mask[i], b_factors[i]): |
| if mask < 0.5: |
| @@ -169,7 +188,7 @@ |
| # PDB is a columnar format, every space matters here! |
| atom_line = (f'{record_type:<6}{atom_index:>5} {name:<4}{alt_loc:>1}' |
| f'{res_name_3:>3} {chain_id:>1}' |
| - f'{residue_index[i]:>4}{insertion_code:>1} ' |
| + f'{res_num:>4}{insertion_code:>1} ' |
| f'{pos[0]:>8.3f}{pos[1]:>8.3f}{pos[2]:>8.3f}' |
| f'{occupancy:>6.2f}{b_factor:>6.2f} ' |
| f'{element:>2}{charge:>2}') |
|
|
