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from dataclasses import dataclass, replace
from typing import Optional
import gemmi
import numpy as np
from rdkit import rdBase
from rdkit.Chem import AllChem
from rdkit.Chem.rdchem import Conformer, Mol
from sklearn.neighbors import KDTree
from boltz.data import const
from boltz.data.types import (
Atom,
Bond,
Chain,
Connection,
Interface,
Residue,
Structure,
StructureInfo,
)
####################################################################################################
# DATACLASSES
####################################################################################################
@dataclass(frozen=True, slots=True)
class ParsedAtom:
"""A parsed atom object."""
name: str
element: int
charge: int
coords: tuple[float, float, float]
conformer: tuple[float, float, float]
is_present: bool
chirality: int
@dataclass(frozen=True, slots=True)
class ParsedBond:
"""A parsed bond object."""
atom_1: int
atom_2: int
type: int
@dataclass(frozen=True, slots=True)
class ParsedResidue:
"""A parsed residue object."""
name: str
type: int
idx: int
atoms: list[ParsedAtom]
bonds: list[ParsedBond]
orig_idx: Optional[int]
atom_center: int
atom_disto: int
is_standard: bool
is_present: bool
@dataclass(frozen=True, slots=True)
class ParsedChain:
"""A parsed chain object."""
name: str
entity: str
type: str
residues: list[ParsedResidue]
sequence: list[str]
@dataclass(frozen=True, slots=True)
class ParsedConnection:
"""A parsed connection object."""
chain_1: str
chain_2: str
residue_index_1: int
residue_index_2: int
atom_index_1: str
atom_index_2: str
@dataclass(frozen=True, slots=True)
class ParsedStructure:
"""A parsed structure object."""
data: Structure
info: StructureInfo
covalents: list[int]
####################################################################################################
# HELPERS
####################################################################################################
def get_dates(block: gemmi.cif.Block) -> tuple[str, str, str]:
"""Get the deposited, released, and last revision dates.
Parameters
----------
block : gemmi.cif.Block
The block to process.
Returns
-------
str
The deposited date.
str
The released date.
str
The last revision date.
"""
deposited = "_pdbx_database_status.recvd_initial_deposition_date"
revision = "_pdbx_audit_revision_history.revision_date"
deposit_date = revision_date = release_date = ""
with contextlib.suppress(Exception):
deposit_date = block.find([deposited])[0][0]
release_date = block.find([revision])[0][0]
revision_date = block.find([revision])[-1][0]
return deposit_date, release_date, revision_date
def get_resolution(block: gemmi.cif.Block) -> float:
"""Get the resolution from a gemmi structure.
Parameters
----------
block : gemmi.cif.Block
The block to process.
Returns
-------
float
The resolution.
"""
resolution = 0.0
for res_key in (
"_refine.ls_d_res_high",
"_em_3d_reconstruction.resolution",
"_reflns.d_resolution_high",
):
with contextlib.suppress(Exception):
resolution = float(block.find([res_key])[0].str(0))
break
return resolution
def get_method(block: gemmi.cif.Block) -> str:
"""Get the method from a gemmi structure.
Parameters
----------
block : gemmi.cif.Block
The block to process.
Returns
-------
str
The method.
"""
method = ""
method_key = "_exptl.method"
with contextlib.suppress(Exception):
methods = block.find([method_key])
method = ",".join([m.str(0).lower() for m in methods])
return method
def convert_atom_name(name: str) -> tuple[int, int, int, int]:
"""Convert an atom name to a standard format.
Parameters
----------
name : str
The atom name.
Returns
-------
tuple[int, int, int, int]
The converted atom name.
"""
name = name.strip()
name = [ord(c) - 32 for c in name]
name = name + [0] * (4 - len(name))
return tuple(name)
def get_unk_token(dtype: gemmi.PolymerType) -> str:
"""Get the unknown token for a given entity type.
Parameters
----------
dtype : gemmi.EntityType
The entity type.
Returns
-------
str
The unknown token.
"""
if dtype == gemmi.PolymerType.PeptideL:
unk = const.unk_token["PROTEIN"]
elif dtype == gemmi.PolymerType.Dna:
unk = const.unk_token["DNA"]
elif dtype == gemmi.PolymerType.Rna:
unk = const.unk_token["RNA"]
else:
msg = f"Unknown polymer type: {dtype}"
raise ValueError(msg)
return unk
def get_conformer(mol: Mol) -> Conformer:
"""Retrieve an rdkit object for a deemed conformer.
Inspired by `pdbeccdutils.core.component.Component`.
Parameters
----------
mol: Mol
The molecule to process.
Returns
-------
Conformer
The desired conformer, if any.
Raises
------
ValueError
If there are no conformers of the given tyoe.
"""
for c in mol.GetConformers():
try:
if c.GetProp("name") == "Computed":
return c
except KeyError: # noqa: PERF203
pass
for c in mol.GetConformers():
try:
if c.GetProp("name") == "Ideal":
return c
except KeyError: # noqa: PERF203
pass
msg = "Conformer does not exist."
raise ValueError(msg)
def compute_covalent_ligands(
connections: list[gemmi.Connection],
subchain_map: dict[tuple[str, int], str],
entities: dict[str, gemmi.Entity],
) -> set[str]:
"""Compute the covalent ligands from a list of connections.
Parameters
----------
connections: List[gemmi.Connection]
The connections to process.
subchain_map: dict[tuple[str, int], str]
The mapping from chain, residue index to subchain name.
entities: dict[str, gemmi.Entity]
The entities in the structure.
Returns
-------
set
The covalent ligand subchains.
"""
# Get covalent chain ids
covalent_chain_ids = set()
for connection in connections:
if connection.type.name != "Covale":
continue
# Map to correct subchain
chain_1_name = connection.partner1.chain_name
chain_2_name = connection.partner2.chain_name
res_1_id = connection.partner1.res_id.seqid
res_1_id = str(res_1_id.num) + str(res_1_id.icode).strip()
res_2_id = connection.partner2.res_id.seqid
res_2_id = str(res_2_id.num) + str(res_2_id.icode).strip()
subchain_1 = subchain_map[(chain_1_name, res_1_id)]
subchain_2 = subchain_map[(chain_2_name, res_2_id)]
# If non-polymer or branched, add to set
entity_1 = entities[subchain_1].entity_type.name
entity_2 = entities[subchain_2].entity_type.name
if entity_1 in {"NonPolymer", "Branched"}:
covalent_chain_ids.add(subchain_1)
if entity_2 in {"NonPolymer", "Branched"}:
covalent_chain_ids.add(subchain_2)
return covalent_chain_ids
def compute_interfaces(atom_data: np.ndarray, chain_data: np.ndarray) -> np.ndarray:
"""Compute the chain-chain interfaces from a gemmi structure.
Parameters
----------
atom_data : List[tuple]
The atom data.
chain_data : List[tuple]
The chain data.
Returns
-------
List[tuple[int, int]]
The interfaces.
"""
# Compute chain_id per atom
chain_ids = []
for idx, chain in enumerate(chain_data):
chain_ids.extend([idx] * chain["atom_num"])
chain_ids = np.array(chain_ids)
# Filte to present atoms
coords = atom_data["coords"]
mask = atom_data["is_present"]
coords = coords[mask]
chain_ids = chain_ids[mask]
# Compute the distance matrix
tree = KDTree(coords, metric="euclidean")
query = tree.query_radius(coords, const.atom_interface_cutoff)
# Get unique chain pairs
interfaces = set()
for c1, pairs in zip(chain_ids, query):
chains = np.unique(chain_ids[pairs])
chains = chains[chains != c1]
interfaces.update((c1, c2) for c2 in chains)
# Get unique chain pairs
interfaces = [(min(i, j), max(i, j)) for i, j in interfaces]
interfaces = list({(int(i), int(j)) for i, j in interfaces})
interfaces = np.array(interfaces, dtype=Interface)
return interfaces
####################################################################################################
# PARSING
####################################################################################################
def parse_ccd_residue( # noqa: PLR0915, C901
name: str,
components: dict[str, Mol],
res_idx: int,
gemmi_mol: Optional[gemmi.Residue] = None,
is_covalent: bool = False,
) -> Optional[ParsedResidue]:
"""Parse an MMCIF ligand.
First tries to get the SMILES string from the RCSB.
Then, tries to infer atom ordering using RDKit.
Parameters
----------
name: str
The name of the molecule to parse.
components : dict
The preprocessed PDB components dictionary.
res_idx : int
The residue index.
gemmi_mol : Optional[gemmi.Residue]
The PDB molecule, as a gemmi Residue object, if any.
Returns
-------
ParsedResidue, optional
The output ParsedResidue, if successful.
"""
unk_chirality = const.chirality_type_ids[const.unk_chirality_type]
# Check if we have a PDB structure for this residue,
# it could be a missing residue from the sequence
is_present = gemmi_mol is not None
# Save original index (required for parsing connections)
if is_present:
orig_idx = gemmi_mol.seqid
orig_idx = str(orig_idx.num) + str(orig_idx.icode).strip()
else:
orig_idx = None
# Get reference component
ref_mol = components[name]
# Remove hydrogens
ref_mol = AllChem.RemoveHs(ref_mol, sanitize=False)
# Check if this is a single atom CCD residue
if ref_mol.GetNumAtoms() == 1:
pos = (0, 0, 0)
if is_present:
pos = (
gemmi_mol[0].pos.x,
gemmi_mol[0].pos.y,
gemmi_mol[0].pos.z,
)
ref_atom = ref_mol.GetAtoms()[0]
chirality_type = const.chirality_type_ids.get(
str(ref_atom.GetChiralTag()), unk_chirality
)
atom = ParsedAtom(
name=ref_atom.GetProp("name"),
element=ref_atom.GetAtomicNum(),
charge=ref_atom.GetFormalCharge(),
coords=pos,
conformer=(0, 0, 0),
is_present=is_present,
chirality=chirality_type,
)
unk_prot_id = const.unk_token_ids["PROTEIN"]
residue = ParsedResidue(
name=name,
type=unk_prot_id,
atoms=[atom],
bonds=[],
idx=res_idx,
orig_idx=orig_idx,
atom_center=0, # Placeholder, no center
atom_disto=0, # Placeholder, no center
is_standard=False,
is_present=is_present,
)
return residue
# If multi-atom, start by getting the PDB coordinates
pdb_pos = {}
if is_present:
# Match atoms based on names
for atom in gemmi_mol:
atom: gemmi.Atom
pos = (atom.pos.x, atom.pos.y, atom.pos.z)
pdb_pos[atom.name] = pos
# Get reference conformer coordinates
conformer = get_conformer(ref_mol)
# Parse each atom in order of the reference mol
atoms = []
atom_idx = 0
idx_map = {} # Used for bonds later
for i, atom in enumerate(ref_mol.GetAtoms()):
# Get atom name, charge, element and reference coordinates
atom_name = atom.GetProp("name")
charge = atom.GetFormalCharge()
element = atom.GetAtomicNum()
ref_coords = conformer.GetAtomPosition(atom.GetIdx())
ref_coords = (ref_coords.x, ref_coords.y, ref_coords.z)
chirality_type = const.chirality_type_ids.get(
str(atom.GetChiralTag()), unk_chirality
)
# If the atom is a leaving atom, skip if not in the PDB and is_covalent
if (
int(atom.GetProp("leaving_atom")) == 1
and is_covalent
and (atom_name not in pdb_pos)
):
continue
# Get PDB coordinates, if any
coords = pdb_pos.get(atom_name)
if coords is None:
atom_is_present = False
coords = (0, 0, 0)
else:
atom_is_present = True
# Add atom to list
atoms.append(
ParsedAtom(
name=atom_name,
element=element,
charge=charge,
coords=coords,
conformer=ref_coords,
is_present=atom_is_present,
chirality=chirality_type,
)
)
idx_map[i] = atom_idx
atom_idx += 1
# Load bonds
bonds = []
unk_bond = const.bond_type_ids[const.unk_bond_type]
for bond in ref_mol.GetBonds():
idx_1 = bond.GetBeginAtomIdx()
idx_2 = bond.GetEndAtomIdx()
# Skip bonds with atoms ignored
if (idx_1 not in idx_map) or (idx_2 not in idx_map):
continue
idx_1 = idx_map[idx_1]
idx_2 = idx_map[idx_2]
start = min(idx_1, idx_2)
end = max(idx_1, idx_2)
bond_type = bond.GetBondType().name
bond_type = const.bond_type_ids.get(bond_type, unk_bond)
bonds.append(ParsedBond(start, end, bond_type))
unk_prot_id = const.unk_token_ids["PROTEIN"]
return ParsedResidue(
name=name,
type=unk_prot_id,
atoms=atoms,
bonds=bonds,
idx=res_idx,
atom_center=0,
atom_disto=0,
orig_idx=orig_idx,
is_standard=False,
is_present=is_present,
)
def parse_polymer( # noqa: C901, PLR0915, PLR0912
polymer: gemmi.ResidueSpan,
polymer_type: gemmi.PolymerType,
sequence: list[str],
chain_id: str,
entity: str,
components: dict[str, Mol],
) -> Optional[ParsedChain]:
"""Process a gemmi Polymer into a chain object.
Performs alignment of the full sequence to the polymer
residues. Loads coordinates and masks for the atoms in
the polymer, following the ordering in const.atom_order.
Parameters
----------
polymer : gemmi.ResidueSpan
The polymer to process.
polymer_type : gemmi.PolymerType
The polymer type.
sequence : str
The full sequence of the polymer.
chain_id : str
The chain identifier.
entity : str
The entity name.
components : dict[str, Mol]
The preprocessed PDB components dictionary.
Returns
-------
ParsedChain, optional
The output chain, if successful.
Raises
------
ValueError
If the alignment fails.
"""
# Get unknown chirality token
unk_chirality = const.chirality_type_ids[const.unk_chirality_type]
# Ignore microheterogenities (pick first)
sequence = [gemmi.Entity.first_mon(item) for item in sequence]
# Align full sequence to polymer residues
# This is a simple way to handle all the different numbering schemes
result = gemmi.align_sequence_to_polymer(
sequence,
polymer,
polymer_type,
gemmi.AlignmentScoring(),
)
# Get coordinates and masks
i = 0
ref_res = set(const.tokens)
parsed = []
for j, match in enumerate(result.match_string):
# Get residue name from sequence
res_name = sequence[j]
# Check if we have a match in the structure
res = None
name_to_atom = {}
if match == "|":
# Get pdb residue
res = polymer[i]
name_to_atom = {a.name.upper(): a for a in res}
# Double check the match
if res.name != res_name:
msg = "Alignment mismatch!"
raise ValueError(msg)
# Increment polymer index
i += 1
# Map MSE to MET, put the selenium atom in the sulphur column
if res_name == "MSE":
res_name = "MET"
if "SE" in name_to_atom:
name_to_atom["SD"] = name_to_atom["SE"]
# Handle non-standard residues
elif res_name not in ref_res:
residue = parse_ccd_residue(
name=res_name,
components=components,
res_idx=j,
gemmi_mol=res,
is_covalent=True,
)
parsed.append(residue)
continue
# Load regular residues
ref_mol = components[res_name]
ref_mol = AllChem.RemoveHs(ref_mol, sanitize=False)
ref_conformer = get_conformer(ref_mol)
# Only use reference atoms set in constants
ref_name_to_atom = {a.GetProp("name"): a for a in ref_mol.GetAtoms()}
ref_atoms = [ref_name_to_atom[a] for a in const.ref_atoms[res_name]]
# Iterate, always in the same order
atoms: list[ParsedAtom] = []
for ref_atom in ref_atoms:
# Get atom name
atom_name = ref_atom.GetProp("name")
idx = ref_atom.GetIdx()
# Get conformer coordinates
ref_coords = ref_conformer.GetAtomPosition(idx)
ref_coords = (ref_coords.x, ref_coords.y, ref_coords.z)
# Get coordinated from PDB
if atom_name in name_to_atom:
atom = name_to_atom[atom_name]
atom_is_present = True
coords = (atom.pos.x, atom.pos.y, atom.pos.z)
else:
atom_is_present = False
coords = (0, 0, 0)
# Add atom to list
atoms.append(
ParsedAtom(
name=atom_name,
element=ref_atom.GetAtomicNum(),
charge=ref_atom.GetFormalCharge(),
coords=coords,
conformer=ref_coords,
is_present=atom_is_present,
chirality=const.chirality_type_ids.get(
str(ref_atom.GetChiralTag()), unk_chirality
),
)
)
# Fix naming errors in arginine residues where NH2 is
# incorrectly assigned to be closer to CD than NH1
if (res is not None) and (res_name == "ARG"):
ref_atoms: list[str] = const.ref_atoms["ARG"]
cd = atoms[ref_atoms.index("CD")]
nh1 = atoms[ref_atoms.index("NH1")]
nh2 = atoms[ref_atoms.index("NH2")]
cd_coords = np.array(cd.coords)
nh1_coords = np.array(nh1.coords)
nh2_coords = np.array(nh2.coords)
if all(atom.is_present for atom in (cd, nh1, nh2)) and (
np.linalg.norm(nh1_coords - cd_coords)
> np.linalg.norm(nh2_coords - cd_coords)
):
atoms[ref_atoms.index("NH1")] = replace(nh1, coords=nh2.coords)
atoms[ref_atoms.index("NH2")] = replace(nh2, coords=nh1.coords)
# Add residue to parsed list
if res is not None:
orig_idx = res.seqid
orig_idx = str(orig_idx.num) + str(orig_idx.icode).strip()
else:
orig_idx = None
atom_center = const.res_to_center_atom_id[res_name]
atom_disto = const.res_to_disto_atom_id[res_name]
parsed.append(
ParsedResidue(
name=res_name,
type=const.token_ids[res_name],
atoms=atoms,
bonds=[],
idx=j,
atom_center=atom_center,
atom_disto=atom_disto,
is_standard=True,
is_present=res is not None,
orig_idx=orig_idx,
)
)
# Get polymer class
if polymer_type == gemmi.PolymerType.PeptideL:
chain_type = const.chain_type_ids["PROTEIN"]
elif polymer_type == gemmi.PolymerType.Dna:
chain_type = const.chain_type_ids["DNA"]
elif polymer_type == gemmi.PolymerType.Rna:
chain_type = const.chain_type_ids["RNA"]
# Return polymer object
return ParsedChain(
name=chain_id,
entity=entity,
residues=parsed,
type=chain_type,
sequence=gemmi.one_letter_code(sequence),
)
def parse_connection(
connection: gemmi.Connection,
chains: list[ParsedChain],
subchain_map: dict[tuple[str, int], str],
) -> ParsedConnection:
"""Parse (covalent) connection from a gemmi Connection.
Parameters
----------
connections : gemmi.ConnectionList
The connection list to parse.
chains : List[Chain]
The parsed chains.
subchain_map : dict[tuple[str, int], str]
The mapping from chain, residue index to subchain name.
Returns
-------
List[Connection]
The parsed connections.
"""
# Map to correct subchains
chain_1_name = connection.partner1.chain_name
chain_2_name = connection.partner2.chain_name
res_1_id = connection.partner1.res_id.seqid
res_1_id = str(res_1_id.num) + str(res_1_id.icode).strip()
res_2_id = connection.partner2.res_id.seqid
res_2_id = str(res_2_id.num) + str(res_2_id.icode).strip()
subchain_1 = subchain_map[(chain_1_name, res_1_id)]
subchain_2 = subchain_map[(chain_2_name, res_2_id)]
# Get chain indices
chain_1 = next(chain for chain in chains if (chain.name == subchain_1))
chain_2 = next(chain for chain in chains if (chain.name == subchain_2))
# Get residue indices
res_1_idx, res_1 = next(
(idx, res)
for idx, res in enumerate(chain_1.residues)
if (res.orig_idx == res_1_id)
)
res_2_idx, res_2 = next(
(idx, res)
for idx, res in enumerate(chain_2.residues)
if (res.orig_idx == res_2_id)
)
# Get atom indices
atom_index_1 = next(
idx
for idx, atom in enumerate(res_1.atoms)
if atom.name == connection.partner1.atom_name
)
atom_index_2 = next(
idx
for idx, atom in enumerate(res_2.atoms)
if atom.name == connection.partner2.atom_name
)
conn = ParsedConnection(
chain_1=subchain_1,
chain_2=subchain_2,
residue_index_1=res_1_idx,
residue_index_2=res_2_idx,
atom_index_1=atom_index_1,
atom_index_2=atom_index_2,
)
return conn
def parse_mmcif( # noqa: C901, PLR0915, PLR0912
path: str,
components: dict[str, Mol],
use_assembly: bool = True,
) -> ParsedStructure:
"""Parse a structure in MMCIF format.
Parameters
----------
mmcif_file : PathLike
Path to the MMCIF file.
components: dict[str, Mol]
The preprocessed PDB components dictionary.
use_assembly: bool
Whether to use the first assembly.
Returns
-------
ParsedStructure
The parsed structure.
"""
# Disable rdkit warnings
blocker = rdBase.BlockLogs() # noqa: F841
# Parse MMCIF input file
block = gemmi.cif.read(str(path))[0]
# Extract medatadata
deposit_date, release_date, revision_date = get_dates(block)
resolution = get_resolution(block)
method = get_method(block)
# Load structure object
structure = gemmi.make_structure_from_block(block)
# Clean up the structure
structure.merge_chain_parts()
structure.remove_waters()
structure.remove_hydrogens()
structure.remove_alternative_conformations()
structure.remove_empty_chains()
# Expand assembly 1
if use_assembly and structure.assemblies:
how = gemmi.HowToNameCopiedChain.AddNumber
assembly_name = structure.assemblies[0].name
structure.transform_to_assembly(assembly_name, how=how)
# Parse entities
# Create mapping from subchain id to entity
entities: dict[str, gemmi.Entity] = {}
entity_ids: dict[str, int] = {}
for entity_id, entity in enumerate(structure.entities):
entity: gemmi.Entity
if entity.entity_type.name == "Water":
continue
for subchain_id in entity.subchains:
entities[subchain_id] = entity
entity_ids[subchain_id] = entity_id
# Create mapping from chain, residue to subchains
# since a Connection uses the chains and not subchins
subchain_map = {}
for chain in structure[0]:
for residue in chain:
seq_id = residue.seqid
seq_id = str(seq_id.num) + str(seq_id.icode).strip()
subchain_map[(chain.name, seq_id)] = residue.subchain
# Find covalent ligands
covalent_chain_ids = compute_covalent_ligands(
connections=structure.connections,
subchain_map=subchain_map,
entities=entities,
)
# Parse chains
chains: list[ParsedChain] = []
chain_seqs = []
for raw_chain in structure[0].subchains():
# Check chain type
subchain_id = raw_chain.subchain_id()
entity: gemmi.Entity = entities[subchain_id]
entity_type = entity.entity_type.name
# Parse a polymer
if entity_type == "Polymer":
# Skip PeptideD, DnaRnaHybrid, Pna, Other
if entity.polymer_type.name not in {
"PeptideL",
"Dna",
"Rna",
}:
continue
# Add polymer if successful
parsed_polymer = parse_polymer(
polymer=raw_chain,
polymer_type=entity.polymer_type,
sequence=entity.full_sequence,
chain_id=subchain_id,
entity=entity.name,
components=components,
)
if parsed_polymer is not None:
chains.append(parsed_polymer)
chain_seqs.append(parsed_polymer.sequence)
# Parse a non-polymer
elif entity_type in {"NonPolymer", "Branched"}:
# Skip UNL or other missing ligands
if any(components.get(lig.name) is None for lig in raw_chain):
continue
residues = []
for lig_idx, ligand in enumerate(raw_chain):
# Check if ligand is covalent
if entity_type == "Branched":
is_covalent = True
else:
is_covalent = subchain_id in covalent_chain_ids
ligand: gemmi.Residue
residue = parse_ccd_residue(
name=ligand.name,
components=components,
res_idx=lig_idx,
gemmi_mol=ligand,
is_covalent=is_covalent,
)
residues.append(residue)
if residues:
chains.append(
ParsedChain(
name=subchain_id,
entity=entity.name,
residues=residues,
type=const.chain_type_ids["NONPOLYMER"],
sequence=None,
)
)
# If no chains parsed fail
if not chains:
msg = "No chains parsed!"
raise ValueError(msg)
# Parse covalent connections
connections: list[ParsedConnection] = []
for connection in structure.connections:
# Skip non-covalent connections
connection: gemmi.Connection
if connection.type.name != "Covale":
continue
parsed_connection = parse_connection(
connection=connection,
chains=chains,
subchain_map=subchain_map,
)
connections.append(parsed_connection)
# Create tables
atom_data = []
bond_data = []
res_data = []
chain_data = []
connection_data = []
# Convert parsed chains to tables
atom_idx = 0
res_idx = 0
asym_id = 0
sym_count = {}
chain_to_idx = {}
res_to_idx = {}
for asym_id, chain in enumerate(chains):
# Compute number of atoms and residues
res_num = len(chain.residues)
atom_num = sum(len(res.atoms) for res in chain.residues)
# Find all copies of this chain in the assembly
entity_id = entity_ids[chain.name]
sym_id = sym_count.get(entity_id, 0)
chain_data.append(
(
chain.name,
chain.type,
entity_id,
sym_id,
asym_id,
atom_idx,
atom_num,
res_idx,
res_num,
)
)
chain_to_idx[chain.name] = asym_id
sym_count[entity_id] = sym_id + 1
# Add residue, atom, bond, data
for i, res in enumerate(chain.residues):
atom_center = atom_idx + res.atom_center
atom_disto = atom_idx + res.atom_disto
res_data.append(
(
res.name,
res.type,
res.idx,
atom_idx,
len(res.atoms),
atom_center,
atom_disto,
res.is_standard,
res.is_present,
)
)
res_to_idx[(chain.name, i)] = (res_idx, atom_idx)
for bond in res.bonds:
atom_1 = atom_idx + bond.atom_1
atom_2 = atom_idx + bond.atom_2
bond_data.append((atom_1, atom_2, bond.type))
for atom in res.atoms:
atom_data.append(
(
convert_atom_name(atom.name),
atom.element,
atom.charge,
atom.coords,
atom.conformer,
atom.is_present,
atom.chirality,
)
)
atom_idx += 1
res_idx += 1
# Convert connections to tables
for conn in connections:
chain_1_idx = chain_to_idx[conn.chain_1]
chain_2_idx = chain_to_idx[conn.chain_2]
res_1_idx, atom_1_offset = res_to_idx[(conn.chain_1, conn.residue_index_1)]
res_2_idx, atom_2_offset = res_to_idx[(conn.chain_2, conn.residue_index_2)]
atom_1_idx = atom_1_offset + conn.atom_index_1
atom_2_idx = atom_2_offset + conn.atom_index_2
connection_data.append(
(
chain_1_idx,
chain_2_idx,
res_1_idx,
res_2_idx,
atom_1_idx,
atom_2_idx,
)
)
# Convert into datatypes
atoms = np.array(atom_data, dtype=Atom)
bonds = np.array(bond_data, dtype=Bond)
residues = np.array(res_data, dtype=Residue)
chains = np.array(chain_data, dtype=Chain)
connections = np.array(connection_data, dtype=Connection)
mask = np.ones(len(chain_data), dtype=bool)
# Compute interface chains (find chains with a heavy atom within 5A)
interfaces = compute_interfaces(atoms, chains)
# Return parsed structure
info = StructureInfo(
deposited=deposit_date,
revised=revision_date,
released=release_date,
resolution=resolution,
method=method,
num_chains=len(chains),
num_interfaces=len(interfaces),
)
data = Structure(
atoms=atoms,
bonds=bonds,
residues=residues,
chains=chains,
connections=connections,
interfaces=interfaces,
mask=mask,
)
return ParsedStructure(data=data, info=info, covalents=[])
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