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auto-detect same entity for non-ligands #251

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merged 2 commits into from
Dec 15, 2024
Merged

auto-detect same entity for non-ligands #251

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1fb7475
auto-detect same entity
arogozhnikov Dec 15, 2024
401d1e0
make all ligands as unique entities
arogozhnikov Dec 15, 2024
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27 changes: 17 additions & 10 deletions chai_lab/data/io/cif_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,7 @@ def get_chains_metadata(
token_res_names = context.token_res_names_to_string

asym_id2asym_unit = {}
entity_key2ihm_entity = {}

for asym_id, entity_type in context.asym_id2entity_type.items():
assert asym_id != 0, "zero is padding for asym_id"
Expand All @@ -96,27 +97,33 @@ def get_chains_metadata(
any_token_in_resi = residue_indices.new_zeros([max_res + 1]) - 99

any_token_in_resi[residue_indices] = torch.arange(
len(residue_indices),
dtype=residue_indices.dtype,
device=residue_indices.device,
len(residue_indices), dtype=any_token_in_resi.dtype
)

assert any_token_in_resi.min() >= 0

sequence = [chain_token_res_names[i] for i in any_token_in_resi]

chain_id_str = _get_chain_letter(asym_id)
if entity_type == EntityType.LIGAND.value:
entity_key = (entity_type, asym_id) # each ligand = separate entity.
else:
entity_key = (entity_type, *sequence)

asym_id2asym_unit[asym_id] = AsymUnit(
entity=Entity(
asym_entity_name = asymid2entity_name[asym_id]
if entity_key not in entity_key2ihm_entity:
entity_key2ihm_entity[entity_key] = Entity(
# sequence is a list of ChemComponents for aminoacids/bases
sequence=[
_to_chem_component(resi, entity_type, asym_id) for resi in sequence
],
description=asymid2entity_name[asym_id],
),
details=f"Chain {chain_id_str}",
id=chain_id_str,
# will be named same as first among replicas
description=f"Entity {asym_entity_name}",
)

asym_id2asym_unit[asym_id] = AsymUnit(
entity=entity_key2ihm_entity[entity_key],
details=f"Chain {asym_entity_name}",
id=asym_entity_name,
)

return asym_id2asym_unit
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