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better "extras" passing in Molecule for EFP #124

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better "extras" passing in Molecule for EFP #124

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4b18220
better "extras" passing in Molecule for EFP
loriab Sep 3, 2019
b4e61e0
allow empty models.Molecule
loriab Sep 3, 2019
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allow empty models.Molecule
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@loriab
loriab committed Sep 3, 2019
commit b4e61e0594008b0bbd60a666eaa0e39d37497573
5 changes: 4 additions & 1 deletion qcelemental/models/molecule.py
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Original file line number Diff line number Diff line change
Expand Up @@ -235,7 +235,10 @@ def __init__(self, orient: bool = False, validate: Optional[bool] = None, **kwar
kwargs["schema_version"] = kwargs.pop("schema_version", 2)
# original_keys = set(kwargs.keys()) # revive when ready to revisit sparsity

schema = to_schema(from_schema(kwargs), dtype=kwargs["schema_version"], copy=False, np_out=True)
schema = to_schema(from_schema(kwargs, missing_enabled_return='minimal'),
dtype=kwargs["schema_version"],
copy=False,
np_out=True)

kwargs["validated"] = True
kwargs = {**kwargs, **schema} # Allow any extra fields
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4 changes: 2 additions & 2 deletions qcelemental/molparse/from_schema.py
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Expand Up @@ -7,7 +7,7 @@
from .from_arrays import from_arrays


def from_schema(molschema, *, verbose: int = 1) -> Dict:
def from_schema(molschema, *, missing_enabled_return: str = 'error', verbose: int = 1) -> Dict:
"""Construct molecule dictionary representation from non-Psi4 schema.

Parameters
Expand Down Expand Up @@ -71,7 +71,7 @@ def from_schema(molschema, *, verbose: int = 1) -> Dict:
provenance=ms.get('provenance', None),
connectivity=ms.get('connectivity', None),
domain='qm',
#missing_enabled_return=missing_enabled_return,
missing_enabled_return=missing_enabled_return,
speclabel=False,
#tooclose=tooclose,
#zero_ghost_fragments=zero_ghost_fragments,
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