OpenFF NAGL 0.3.7+9.g10c2555.dirty documentation

openff-nagl

Index

A

ActivationFunction (class in openff.nagl.nn) (class in openff.nagl.nn.activation) add_toolkit() (openff.nagl.toolkits.registry.NAGLToolkitRegistry method) allowed_elements (openff.nagl.domains.ChemicalDomain attribute) append_gcn_layer() (openff.nagl.nn.gcn.BaseGCNStack method)

assign_partial_charges() (openff.nagl.toolkits.NAGLRDKitToolkitWrapper method) (openff.nagl.toolkits.rdkit.NAGLRDKitToolkitWrapper method) available_aggregator_types (openff.nagl.nn.gcn.BaseGCNStack property) (openff.nagl.nn.gcn.GINConvStack attribute) (openff.nagl.nn.gcn.SAGEConvStack attribute)

B

BaseGCNStack (class in openff.nagl.nn.gcn)

C

calculate_circular_fingerprint_similarity() (in module openff.nagl.toolkits.openff) (openff.nagl.toolkits.NAGLRDKitToolkitWrapper method) (openff.nagl.toolkits.rdkit.NAGLRDKitToolkitWrapper method) call_toolkit_function() (in module openff.nagl.toolkits.openff) capture_oechem_warnings() (in module openff.nagl.toolkits.openff) capture_toolkit_warnings() (in module openff.nagl.toolkits.openff) categories (openff.nagl.features.atoms.AtomConnectivity attribute) (openff.nagl.features.atoms.AtomFormalCharge attribute) (openff.nagl.features.atoms.AtomHybridization attribute) (openff.nagl.features.atoms.AtomicElement attribute) charge_label (openff.nagl.training.loss.MultipleDipoleTarget attribute) (openff.nagl.training.loss.MultipleESPTarget attribute) (openff.nagl.training.loss.SingleDipoleTarget attribute) check_allowed_elements() (openff.nagl.domains.ChemicalDomain method) check_forbidden_patterns() (openff.nagl.domains.ChemicalDomain method) check_molecule() (openff.nagl.domains.ChemicalDomain method) compute() (openff.nagl.training.metrics.BaseMetric method) (openff.nagl.training.metrics.MAEMetric method) (openff.nagl.training.metrics.MSEMetric method) (openff.nagl.training.metrics.RMSEMetric method)

compute_properties() (openff.nagl.GNNModel method) compute_property() (openff.nagl.GNNModel method) ComputePartialCharges (class in openff.nagl.nn) (class in openff.nagl.nn.postprocess) configure_optimizers() (openff.nagl.training.training.TrainingGNNModel method) conformation_column (openff.nagl.training.loss.MultipleDipoleTarget attribute) (openff.nagl.training.loss.SingleDipoleTarget attribute) ConvolutionModule (class in openff.nagl.nn) copy() (openff.nagl.nn.ConvolutionModule method) (openff.nagl.nn.ReadoutModule method) (openff.nagl.nn.SequentialLayers method) create_atom_label_report() (in module openff.nagl.training.reporting) create_gcn_layer() (openff.nagl.nn.gcn.BaseGCNStack class method) create_molecule_label_report() (in module openff.nagl.training.reporting)

D

default_activation_function (openff.nagl.nn.gcn.BaseGCNStack property) (openff.nagl.nn.gcn.GINConvStack attribute) (openff.nagl.nn.gcn.SAGEConvStack attribute) (openff.nagl.nn.SequentialLayers attribute) default_aggregator_type (openff.nagl.nn.gcn.BaseGCNStack property) (openff.nagl.nn.gcn.GINConvStack attribute) (openff.nagl.nn.gcn.SAGEConvStack attribute) default_dropout (openff.nagl.nn.gcn.BaseGCNStack property) (openff.nagl.nn.gcn.GINConvStack attribute) (openff.nagl.nn.gcn.SAGEConvStack attribute) (openff.nagl.nn.SequentialLayers attribute)

deregister_toolkit() (openff.nagl.toolkits.registry.NAGLToolkitRegistry method) DGLMoleculeDataLoader (class in openff.nagl.nn) DGLMoleculeDataModule (class in openff.nagl.training.training) DGLMoleculeDataset (class in openff.nagl.nn) DGLMoleculeDatasetEntry (class in openff.nagl.nn) dict() (openff.nagl.features.atoms.AtomHybridization method)

E

ELU (openff.nagl.nn.activation.ActivationFunction attribute) (openff.nagl.nn.ActivationFunction attribute) encode() (openff.nagl.features.Feature method) enumerate_resonance_forms() (in module openff.nagl.utils.resonance) (openff.nagl.utils.resonance.ResonanceEnumerator method) enumerate_stereoisomers() (in module openff.nagl.toolkits.openff)

esp_length_column (openff.nagl.training.loss.MultipleESPTarget attribute) evaluate_target() (openff.nagl.training.loss.HeavyAtomReadoutTarget method) (openff.nagl.training.loss.MultipleDipoleTarget method) (openff.nagl.training.loss.MultipleESPTarget method) (openff.nagl.training.loss.ReadoutTarget method) (openff.nagl.training.loss.SingleDipoleTarget method)

F

forbidden_patterns (openff.nagl.domains.ChemicalDomain attribute) forward() (openff.nagl.nn.ComputePartialCharges method) (openff.nagl.nn.ConvolutionModule method) (openff.nagl.nn.gcn.BaseGCNStack method) (openff.nagl.nn.PoolAtomFeatures method) (openff.nagl.nn.PoolBondFeatures method) (openff.nagl.nn.postprocess.ComputePartialCharges method) (openff.nagl.nn.postprocess.PostprocessLayer method) (openff.nagl.nn.postprocess.RegularizedComputePartialCharges method) (openff.nagl.nn.ReadoutModule method) (openff.nagl.nn.RegularizedComputePartialCharges method) (openff.nagl.training.training.TrainingGNNModel method)

from_arrow_dataset() (openff.nagl.nn.DGLMoleculeDataset class method) from_config() (openff.nagl.nn.ConvolutionModule class method) (openff.nagl.nn.ReadoutModule class method) from_mapped_smiles() (openff.nagl.nn.DGLMoleculeDatasetEntry class method) from_openff() (openff.nagl.nn.DGLMoleculeDataset class method) (openff.nagl.nn.DGLMoleculeDatasetEntry class method) from_yaml() (openff.nagl.GNNModel class method) (openff.nagl.training.training.TrainingGNNModel class method)

G

get() (openff.nagl.nn.activation.ActivationFunction class method) (openff.nagl.nn.ActivationFunction class method) get_atoms_are_in_ring_size() (in module openff.nagl.toolkits.openff) (openff.nagl.toolkits.NAGLOpenEyeToolkitWrapper method) (openff.nagl.toolkits.NAGLRDKitToolkitWrapper method) (openff.nagl.toolkits.openeye.NAGLOpenEyeToolkitWrapper method) (openff.nagl.toolkits.rdkit.NAGLRDKitToolkitWrapper method) get_best_rmsd() (in module openff.nagl.toolkits.openff) (openff.nagl.toolkits.NAGLOpenEyeToolkitWrapper method) (openff.nagl.toolkits.NAGLRDKitToolkitWrapper method) (openff.nagl.toolkits.openeye.NAGLOpenEyeToolkitWrapper method) (openff.nagl.toolkits.rdkit.NAGLRDKitToolkitWrapper method) get_bonds_are_in_ring_size() (in module openff.nagl.toolkits.openff) (openff.nagl.toolkits.NAGLOpenEyeToolkitWrapper method) (openff.nagl.toolkits.NAGLRDKitToolkitWrapper method) (openff.nagl.toolkits.openeye.NAGLOpenEyeToolkitWrapper method) (openff.nagl.toolkits.rdkit.NAGLRDKitToolkitWrapper method) get_function() (openff.nagl.nn.activation.ActivationFunction class method) (openff.nagl.nn.ActivationFunction class method)

get_metric_type() (in module openff.nagl.training.metrics) get_molecule_hybridizations() (in module openff.nagl.toolkits.openff) (openff.nagl.toolkits.NAGLOpenEyeToolkitWrapper method) (openff.nagl.toolkits.NAGLRDKitToolkitWrapper method) (openff.nagl.toolkits.openeye.NAGLOpenEyeToolkitWrapper method) (openff.nagl.toolkits.rdkit.NAGLRDKitToolkitWrapper method) get_nvalues_per_molecule() (openff.nagl.nn.PoolAtomFeatures method) (openff.nagl.nn.PoolBondFeatures method) get_openff_molecule_bond_indices() (in module openff.nagl.toolkits.openff) get_required_columns() (openff.nagl.training.loss.HeavyAtomReadoutTarget method) (openff.nagl.training.loss.MultipleDipoleTarget method) (openff.nagl.training.loss.MultipleESPTarget method) (openff.nagl.training.loss.ReadoutTarget method) (openff.nagl.training.loss.SingleDipoleTarget method) get_value() (openff.nagl.nn.activation.ActivationFunction class method) (openff.nagl.nn.ActivationFunction class method) GINConvStack (class in openff.nagl.nn.gcn) GNNModel (class in openff.nagl) guess_file_format() (in module openff.nagl.toolkits.openff)

I

Identity (openff.nagl.nn.activation.ActivationFunction attribute) (openff.nagl.nn.ActivationFunction attribute)

inverse_distance_matrix_column (openff.nagl.training.loss.MultipleESPTarget attribute) is_conformer_identical() (in module openff.nagl.toolkits.openff)

L

labels (openff.nagl.nn.DGLMoleculeDatasetEntry attribute) LeakyReLU (openff.nagl.nn.activation.ActivationFunction attribute) (openff.nagl.nn.ActivationFunction attribute)

load() (openff.nagl.GNNModel class method)

M

map_indexed_smiles() (in module openff.nagl.toolkits.openff) mapped_smiles_to_smiles() (openff.nagl.toolkits.NAGLRDKitToolkitWrapper class method) (openff.nagl.toolkits.rdkit.NAGLRDKitToolkitWrapper class method) METRICS (in module openff.nagl.training.metrics) module openff.nagl openff.nagl.domains openff.nagl.features openff.nagl.features.atoms openff.nagl.features.bonds openff.nagl.molecule openff.nagl.nn openff.nagl.nn.activation openff.nagl.nn.gcn openff.nagl.nn.postprocess openff.nagl.toolkits openff.nagl.toolkits.openeye openff.nagl.toolkits.openff openff.nagl.toolkits.rdkit openff.nagl.toolkits.registry openff.nagl.training openff.nagl.training.loss openff.nagl.training.metrics openff.nagl.training.reporting openff.nagl.training.templates openff.nagl.training.templates.files openff.nagl.training.training openff.nagl.utils openff.nagl.utils.resonance

molecule (openff.nagl.nn.DGLMoleculeDatasetEntry attribute) molecule_from_networkx() (in module openff.nagl.toolkits.openff)

N

n_atom_features (openff.nagl.nn.DGLMoleculeDataset property) n_conformation_column (openff.nagl.training.loss.MultipleDipoleTarget attribute) n_esp_column (openff.nagl.training.loss.MultipleESPTarget attribute) n_feature_columns (openff.nagl.nn.PoolAtomFeatures attribute) (openff.nagl.nn.PoolBondFeatures attribute) n_features (openff.nagl.nn.ComputePartialCharges attribute) (openff.nagl.nn.postprocess.ComputePartialCharges attribute) (openff.nagl.nn.postprocess.PostprocessLayer attribute) (openff.nagl.nn.postprocess.RegularizedComputePartialCharges attribute) (openff.nagl.nn.RegularizedComputePartialCharges attribute) NAGL_TOOLKIT_REGISTRY (in module openff.nagl.toolkits) NAGLOpenEyeToolkitWrapper (class in openff.nagl.toolkits) (class in openff.nagl.toolkits.openeye) NAGLRDKitToolkitWrapper (class in openff.nagl.toolkits) (class in openff.nagl.toolkits.rdkit) NAGLToolkitRegistry (class in openff.nagl.toolkits.registry) name (openff.nagl.features.atoms.AtomAverageFormalCharge attribute) (openff.nagl.features.atoms.AtomConnectivity attribute) (openff.nagl.features.atoms.AtomFormalCharge attribute) (openff.nagl.features.atoms.AtomGasteigerCharge attribute) (openff.nagl.features.atoms.AtomHybridization attribute) (openff.nagl.features.atoms.AtomicElement attribute) (openff.nagl.features.atoms.AtomInRingOfSize attribute) (openff.nagl.features.atoms.AtomIsAromatic attribute) (openff.nagl.features.atoms.AtomIsInRing attribute) (openff.nagl.features.bonds.BondInRingOfSize attribute) (openff.nagl.features.bonds.BondIsAromatic attribute) (openff.nagl.features.bonds.BondIsInRing attribute) (openff.nagl.features.bonds.BondOrder attribute) (openff.nagl.features.bonds.WibergBondOrder attribute) (openff.nagl.features.Feature attribute) (openff.nagl.nn.ComputePartialCharges attribute) (openff.nagl.nn.gcn.BaseGCNStack property) (openff.nagl.nn.gcn.GINConvStack attribute) (openff.nagl.nn.gcn.SAGEConvStack attribute) (openff.nagl.nn.postprocess.ComputePartialCharges attribute) (openff.nagl.nn.postprocess.PostprocessLayer attribute) (openff.nagl.nn.postprocess.RegularizedComputePartialCharges attribute) (openff.nagl.nn.RegularizedComputePartialCharges attribute) (openff.nagl.toolkits.NAGLOpenEyeToolkitWrapper attribute) (openff.nagl.toolkits.NAGLRDKitToolkitWrapper attribute) (openff.nagl.toolkits.openeye.NAGLOpenEyeToolkitWrapper attribute) (openff.nagl.toolkits.rdkit.NAGLRDKitToolkitWrapper attribute) (openff.nagl.training.loss.HeavyAtomReadoutTarget attribute) (openff.nagl.training.loss.MultipleDipoleTarget attribute) (openff.nagl.training.loss.MultipleESPTarget attribute) (openff.nagl.training.loss.ReadoutTarget attribute) (openff.nagl.training.loss.SingleDipoleTarget attribute) (openff.nagl.training.metrics.BaseMetric attribute) (openff.nagl.training.metrics.MAEMetric attribute) (openff.nagl.training.metrics.MSEMetric attribute) (openff.nagl.training.metrics.RMSEMetric attribute)

normalize_molecule() (in module openff.nagl.toolkits.openff)

O

openff.nagl module openff.nagl.domains module openff.nagl.features module openff.nagl.features.atoms module openff.nagl.features.bonds module openff.nagl.molecule module openff.nagl.nn module openff.nagl.nn.activation module openff.nagl.nn.gcn module openff.nagl.nn.postprocess module openff.nagl.toolkits module openff.nagl.toolkits.openeye module

openff.nagl.toolkits.openff module openff.nagl.toolkits.rdkit module openff.nagl.toolkits.registry module openff.nagl.training module openff.nagl.training.loss module openff.nagl.training.metrics module openff.nagl.training.reporting module openff.nagl.training.templates module openff.nagl.training.templates.files module openff.nagl.training.training module openff.nagl.utils module openff.nagl.utils.resonance module

P

PoolAtomFeatures (class in openff.nagl.nn) PoolBondFeatures (class in openff.nagl.nn) PostprocessLayer (class in openff.nagl.nn.postprocess)

prediction_label (openff.nagl.training.loss.HeavyAtomReadoutTarget attribute) (openff.nagl.training.loss.ReadoutTarget attribute) prepare_data() (openff.nagl.training.training.DGLMoleculeDataModule method)

R

ReadoutModule (class in openff.nagl.nn) RegularizedComputePartialCharges (class in openff.nagl.nn) (class in openff.nagl.nn.postprocess) ReLU (openff.nagl.nn.activation.ActivationFunction attribute) (openff.nagl.nn.ActivationFunction attribute) report_artifact() (openff.nagl.training.loss.MultipleDipoleTarget method) (openff.nagl.training.loss.MultipleESPTarget method) (openff.nagl.training.loss.ReadoutTarget method)

reset_parameters() (openff.nagl.nn.gcn.BaseGCNStack method) ResonanceEnumerator (class in openff.nagl.utils.resonance) ring_size (openff.nagl.features.atoms.AtomInRingOfSize attribute) (openff.nagl.features.bonds.BondInRingOfSize attribute)

S

SAGEConvStack (class in openff.nagl.nn.gcn) save() (openff.nagl.GNNModel method) SequentialLayers (class in openff.nagl.nn) setup() (openff.nagl.training.training.DGLMoleculeDataModule method) Sigmoid (openff.nagl.nn.activation.ActivationFunction attribute) (openff.nagl.nn.ActivationFunction attribute) smiles_to_inchi_key() (in module openff.nagl.toolkits.openff) smiles_to_mapped_smiles() (openff.nagl.toolkits.NAGLRDKitToolkitWrapper class method) (openff.nagl.toolkits.rdkit.NAGLRDKitToolkitWrapper class method) stream_molecules_from_file() (in module openff.nagl.toolkits.openff)

stream_molecules_from_sdf_file() (in module openff.nagl.toolkits.openff) (openff.nagl.toolkits.NAGLOpenEyeToolkitWrapper method) (openff.nagl.toolkits.NAGLRDKitToolkitWrapper class method) (openff.nagl.toolkits.openeye.NAGLOpenEyeToolkitWrapper method) (openff.nagl.toolkits.rdkit.NAGLRDKitToolkitWrapper class method) stream_molecules_from_smiles_file() (in module openff.nagl.toolkits.openff) stream_molecules_to_file() (in module openff.nagl.toolkits.openff) (openff.nagl.toolkits.NAGLOpenEyeToolkitWrapper method) (openff.nagl.toolkits.NAGLRDKitToolkitWrapper method) (openff.nagl.toolkits.openeye.NAGLOpenEyeToolkitWrapper method) (openff.nagl.toolkits.rdkit.NAGLRDKitToolkitWrapper method)

T

Tanh (openff.nagl.nn.activation.ActivationFunction attribute) (openff.nagl.nn.ActivationFunction attribute) tensor_shape (openff.nagl.features.Feature property) test_step() (openff.nagl.training.training.TrainingGNNModel method) to() (openff.nagl.nn.DGLMoleculeDatasetEntry method) to_fragment() (openff.nagl.utils.resonance.ResonanceEnumerator method) to_openeye() (openff.nagl.toolkits.NAGLOpenEyeToolkitWrapper method) (openff.nagl.toolkits.openeye.NAGLOpenEyeToolkitWrapper method) to_pyarrow() (openff.nagl.nn.DGLMoleculeDataset method) to_rdkit() (openff.nagl.toolkits.NAGLRDKitToolkitWrapper method) (openff.nagl.toolkits.rdkit.NAGLRDKitToolkitWrapper method)

to_yaml() (openff.nagl.training.training.TrainingGNNModel method) toolkit_registry_function() (in module openff.nagl.toolkits.openff) training (openff.nagl.nn.gcn.GINConvStack attribute) (openff.nagl.nn.gcn.SAGEConvStack attribute) (openff.nagl.nn.postprocess.ComputePartialCharges attribute) (openff.nagl.nn.postprocess.RegularizedComputePartialCharges attribute) training_step() (openff.nagl.training.training.TrainingGNNModel method) TrainingGNNModel (class in openff.nagl.training.training) TYPE_CHECKING (in module openff.nagl.toolkits.openeye) (in module openff.nagl.toolkits.openff) (in module openff.nagl.toolkits.rdkit)

V

validate_smiles() (in module openff.nagl.toolkits.openff)

validation_step() (openff.nagl.training.training.TrainingGNNModel method)

W

with_layers() (openff.nagl.nn.gcn.BaseGCNStack class method) (openff.nagl.nn.SequentialLayers class method)