OptimizationEntry

class openff.qcsubmit.datasets.OptimizationEntry(off_molecule=None, *, index, initial_molecules, attributes, extras={}, keywords={}, constraints=Constraints(freeze=[], set=[]))[source]

An optimization dataset specific entry class which can handle constraints.

Parameters:
__init__(off_molecule=None, **kwargs)[source]

Here we handle the constraints before calling the super.

Parameters:

off_molecule (Molecule | None) –

Methods

__init__([off_molecule])

Here we handle the constraints before calling the super.

add_constraint(constraint, constraint_type, ...)

Add new constraint of the given type.

construct([_fields_set])

Creates a new model setting __dict__ and __fields_set__ from trusted or pre-validated data.

copy(*[, include, exclude, update, deep])

Duplicate a model, optionally choose which fields to include, exclude and change.

dict(*[, include, exclude, by_alias, ...])

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

from_orm(obj)

get_off_molecule([include_conformers])

Build and openforcefield.topology.Molecule representation of the input molecule.

json(*[, include, exclude, by_alias, ...])

Generate a JSON representation of the model, include and exclude arguments as per dict().

parse_file(path, *[, content_type, ...])

parse_obj(obj)

parse_raw(b, *[, content_type, encoding, ...])

schema([by_alias, ref_template])

schema_json(*[, by_alias, ref_template])

update_forward_refs(**localns)

Try to update ForwardRefs on fields based on this Model, globalns and localns.

validate(value)

Attributes

formatted_keywords

Format the keywords with the constraints values.

constraints

index

initial_molecules

attributes

extras

keywords

add_constraint(constraint, constraint_type, indices, bonded=True, **kwargs)[source]

Add new constraint of the given type.

Parameters:

  • constraint (Literal['set', 'freeze']) – The major type of constraint, freeze or set

  • constraint_type (Literal['distance', 'angle', 'dihedral', 'xyz']) – the constraint sub type, angle, distance etc

  • indices (List[int]) – The atom indices the constraint should be placed on

  • bonded (bool) – If the constraint is intended to be put a bonded set of atoms

  • kwargs – Any extra information needed by the constraint, for the set class they need a value value=float

Return type:

None

property formatted_keywords: Dict[str, Any]

Format the keywords with the constraints values.

get_off_molecule(include_conformers=True)

Build and openforcefield.topology.Molecule representation of the input molecule.

Parameters:

include_conformers (bool) – If True all of the input conformers are included else they are dropped.

Return type:

Molecule