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components
component
Component
explicitmoleculecomponent
ExplicitMoleculeComponent
proteincomponent
ProteinComponent
negative_ions
positive_ions
smallmoleculecomponent
SmallMoleculeComponent
solventcomponent
SolventComponent
mapping
atom_mapper
AtomMapper
atom_mapping
AtomMapping
componentmapping
ComponentMapping
errors
AtomMappingError
ligandatommapping
LigandAtomMapping
protocols
GufeProtocolError
MissingUnitResultError
ProtocolDAGResultError
ProtocolUnitExecutionError
ProtocolUnitFailureError
ProtocolValidationError
protocol
Protocol
ProtocolResult
protocoldag
execute_DAG
DAGMixin
ProtocolDAG
ProtocolDAGResult
protocolunit
Context
ProtocolUnit
ProtocolUnitFailure
ProtocolUnitResult
settings
models
BaseForceFieldSettings
OpenMMSystemGeneratorFFSettings
Settings
SettingsBaseModel
ThermoSettings
gufe.storage
ChangedExternalResourceError
ExternalResourceError
MissingExternalResourceError
externalresource
base
ExternalStorage
Metadata
filestorage
FileStorage
memorystorage
MemoryStorage
transformations
transformation
NonTransformation
Transformation
TransformationBase
visualization
mapping_visualization
draw_mapping
draw_one_molecule_mapping
draw_unhighlighted_molecule
BLUE
RED
chemicalsystem
ChemicalSystem
custom_codecs
default_from_dict
inherited_is_my_dict
is_npy_dtype_dict
is_openff_quantity_dict
is_openff_unit_dict
custom_json
custom_json_factory
JSONCodec
JSONSerializerDeserializer
custom_typing
ligandnetwork
LigandNetwork
molhashing
deserialize_numpy
serialize_numpy
network
AlchemicalNetwork
tokenization
TOKENIZABLE_CLASS_REGISTRY
REMAPPED_CLASSES
TOKENIZABLE_REGISTRY
dict_decode_dependencies
dict_encode_dependencies
from_dict
get_all_gufe_objs
get_class
gufe_objects_from_shallow_dict
gufe_to_digraph
import_qualname
is_gufe_dict
is_gufe_key_dict
is_gufe_obj
key_decode_dependencies
key_encode_dependencies
key_renamed
modify_dependencies
module_qualname
nested_key_moved
new_key_added
old_key_removed
register_tokenizable_class
to_dict
tokenize
GufeKey
GufeTokenizable
KeyedChain
utils
ensure_filelike
Exceptions
Error when an atom mapping could not be created.