Skip to content

Commit

Permalink
More work on portal updates
Browse files Browse the repository at this point in the history
  • Loading branch information
@bennybp
bennybp committed May 27, 2022
1 parent 7f520c0 commit 727c8f9
Showing 1 changed file with 101 additions and 79 deletions.
180 changes: 101 additions & 79 deletions openff/qcsubmit/results/results.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -293,35 +293,29 @@ def from_datasets(
for dataset in datasets:

client = dataset.client
dataset_specs = dataset.specifications

# Fetch all entries for use later
dataset.fetch_entries(include=['molecule'])

if spec_name not in dataset_specs:
if spec_name not in dataset.specifications:
raise KeyError(f"The {dataset.name} dataset does not contain a '{spec_name}' compute specification")

for entry_name, spec_name, record in dataset.iterate_records(specification_names=spec_name,
status=RecordStatusEnum.complete):
entry = dataset.get_entry(entry_name)
molecule = entry.molecule

br = BasicResult(
record_id=record.id,
cmiles=molecule.extras[
"canonical_isomeric_explicit_hydrogen_mapped_smiles"
],
inchi_key=Molecule.from_mapped_smiles(
molecule.extras[
"canonical_isomeric_explicit_hydrogen_mapped_smiles"
],
# Undefined stereochemistry is not expected however there
# may be some TK specific edge cases we don't want
# exceptions for such as OE and nitrogen stereochemistry.
allow_undefined_stereo=True,
).to_inchikey(fixed_hydrogens=True),
)
cmiles = molecule.extras["canonical_isomeric_explicit_hydrogen_mapped_smiles"]
inchi_key = molecule.attributes.get("fixed_hydrogen_inchi_key")

# Undefined stereochemistry is not expected however there
# may be some TK specific edge cases we don't want
# exceptions for such as OE and nitrogen stereochemistry.
if inchi_key is None:
tmp_mol=Molecule.from_mapped_smiles(cmiles, allow_undefined_stereo=True)
inchi_key=tmp_mol.to_inchikey(fixed_hydrogens=True)

br = BasicResult(record_id=record.id, cmiles=cmiles, inchi_key=inchi_key)
result_records[client.address][record.id] = br

return cls(
Expand Down Expand Up @@ -421,28 +415,29 @@ def from_datasets(
for dataset in datasets:

client = dataset.client
query = dataset.query(spec_name)

result_records[client.address].update(
{
query[entry.name].id: OptimizationResult(
record_id=query[entry.name].id,
cmiles=entry.attributes[
"canonical_isomeric_explicit_hydrogen_mapped_smiles"
],
inchi_key=entry.attributes.get("fixed_hydrogen_inchi_key")
or Molecule.from_mapped_smiles(
entry.attributes[
"canonical_isomeric_explicit_hydrogen_mapped_smiles"
],
allow_undefined_stereo=True,
).to_inchikey(fixed_hydrogens=True),
)
for entry in dataset.data.records.values()
if entry.name in query
and query[entry.name].status.value.upper() == "COMPLETE"
}
)

# Fetch all entries for use later
dataset.fetch_entries(include=['initial_molecule'])

if spec_name not in dataset.specifications:
raise KeyError(f"The {dataset.name} dataset does not contain a '{spec_name}' compute specification")


for entry_name, spec_name, record in dataset.iterate_records(specification_names=spec_name,
status=RecordStatusEnum.complete):

entry = dataset.get_entry(entry_name)
molecule = entry.initial_molecule

cmiles = molecule.extras["canonical_isomeric_explicit_hydrogen_mapped_smiles"]
inchi_key = molecule.attributes.get("fixed_hydrogen_inchi_key")

if inchi_key is None:
tmp_mol = Molecule.from_mapped_smiles(cmiles, allow_undefined_stereo=True)
inchi_key=tmp_mol.to_inchikey(fixed_hydrogens=True)

opt_rec = OptimizationResult(record_id=record.id, cmiles=cmiles, inchi_key=inchi_key)
result_records[client.address][record.id] = opt_rec

return cls(
entries={
Expand All @@ -465,7 +460,7 @@ def from_server(
# noinspection PyTypeChecker
return cls.from_datasets(
[
client.get_dataset("OptimizationDataset", dataset_name)
client.get_dataset("Optimization", dataset_name)
for dataset_name in datasets
],
spec_name,
Expand All @@ -479,23 +474,30 @@ def to_records(self) -> List[Tuple[OptimizationRecord, Molecule]]:
record.
"""

records_and_molecules = [
result
for client_address, entries in self.entries.items()
for result in cached_query_optimization_results(client_address, entries)
]
records_and_molecules = []

for client_address, records in self.entries.items():
client = cached_fractal_client(address=client_address)

for record in records:
rec = client.get_optimizations(record.record_id, include=['initial_molecule'])

records, _ = zip(*records_and_molecules)
# OpenFF molecule
molecule: Molecule = Molecule.from_mapped_smiles(
record.cmiles, allow_undefined_stereo=True
)

self._validate_record_types(records, OptimizationRecord)
molecule.add_conformer(
numpy.array(rec.initial_molecule.geometry, float).reshape(-1, 3) * unit.bohr
)

records_and_molecules.append((rec, molecule))

return records_and_molecules


# NOTE: no longer using `driver` here
def to_basic_result_collection(
self, driver: Optional[Union[str, List[str]]] = None
) -> BasicResultCollection:
def to_basic_result_collection(self) -> BasicResultCollection:
"""Returns a basic results collection which references results records which
were created from the *final* structure of one of the optimizations in this
collection, and used the same program, method, and basis as the parent
Expand Down Expand Up @@ -638,28 +640,27 @@ def from_datasets(
for dataset in datasets:

client = dataset.client
query = dataset.query(spec_name)

result_records[client.address].update(
{
query[entry.name].id: TorsionDriveResult(
record_id=query[entry.name].id,
cmiles=entry.attributes[
"canonical_isomeric_explicit_hydrogen_mapped_smiles"
],
inchi_key=entry.attributes.get("fixed_hydrogen_inchi_key")
or Molecule.from_mapped_smiles(
entry.attributes[
"canonical_isomeric_explicit_hydrogen_mapped_smiles"
],
allow_undefined_stereo=True,
).to_inchikey(fixed_hydrogens=True),
)
for entry in dataset.data.records.values()
if entry.name in query
and query[entry.name].status.value.upper() == "COMPLETE"
}
)

# Fetch all entries for use later
dataset.fetch_entries()

if spec_name not in dataset.specifications:
raise KeyError(f"The {dataset.name} dataset does not contain a '{spec_name}' compute specification")

for entry_name, spec_name, record in dataset.iterate_records(specification_names=spec_name,
status=RecordStatusEnum.complete):

entry = dataset.get_entry(entry_name)

cmiles = entry.attributes["canonical_isomeric_explicit_hydrogen_mapped_smiles"]
inchi_key = entry.attributes.get("fixed_hydrogen_inchi_key")

if inchi_key is None:
tmp_mol = Molecule.from_mapped_smiles(cmiles, allow_undefined_stereo=True)
inchi_key = tmp_mol.to_inchikey(fixed_hydrogens=True)

td_rec = TorsionDriveResult(record_id=record.id, cmiles=cmiles, inchi_key=inchi_key)
result_records[client.address][record.id] = td_rec

return cls(
entries={
Expand Down Expand Up @@ -697,18 +698,39 @@ def to_records(self) -> List[Tuple[TorsiondriveRecord, Molecule]]:
record.
"""

records_and_molecules = [
result
for client_address, entries in self.entries.items()
for result in cached_query_torsion_drive_results(client_address, entries)
]
records_and_molecules = []

records, _ = zip(*records_and_molecules)
for client_address, records in self.entries.items():
client = cached_fractal_client(address=client_address)

for record in records:
rec = client.get_torsiondrives(record.record_id)

self._validate_record_types(records, TorsiondriveRecord)
# OpenFF molecule
molecule: Molecule = Molecule.from_mapped_smiles(
record.cmiles, allow_undefined_stereo=True
)

# Map of torsion drive keys to minimum optimization
qc_grid_molecules = [(k, v.final_molecule) for k,v in rec.minimum_optimizations.items()]

# order the ids so the conformers follow the torsiondrive scan range
# x[0] is the torsiondrive key, ie "[90]"
# [1:-1] strips off brackets from the angle
qc_grid_molecules.sort(key=lambda x: float(x[0][1:-1]))

molecule._conformers = [
numpy.array(qc_molecule.geometry, float).reshape(-1, 3) * unit.bohr
for _, qc_molecule in qc_grid_molecules
]

molecule.properties["grid_ids"] = [x[0] for x in qc_grid_molecules]

records_and_molecules.append((rec, molecule))

return records_and_molecules


def create_optimization_dataset(
self,
dataset_name: str,
Expand Down

0 comments on commit 727c8f9

Please sign in to comment.