Index

_

__init__() (espaloma.data.collection.qca method) (espaloma.data.dataset.Dataset method) (espaloma.data.dataset.GraphDataset method) (espaloma.data.md.MoleculeVacuumSimulation method) (espaloma.data.normalize.BaseNormalize method) (espaloma.data.normalize.DatasetLogNormalNormalize method) (espaloma.data.normalize.DatasetNormalNormalize method) (espaloma.data.normalize.ESOL100LogNormalNormalize method) (espaloma.data.normalize.ESOL100NormalNormalize method) (espaloma.data.normalize.NotNormalize method) (espaloma.data.normalize.PositiveNotNormalize method) (espaloma.data.qcarchive_utils.MolWithTargets method) (espaloma.graphs.graph.BaseGraph method) (espaloma.graphs.graph.Graph method) (espaloma.graphs.legacy_force_field.LegacyForceField method) (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

A

add_module() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) add_nonbonded_force() (in module espaloma.data.md) alkethoh() (in module espaloma.data.collection) angle() (in module espaloma.mm.geometry) angle_angle() (in module espaloma.mm.torsion) angle_angle_torsion() (in module espaloma.mm.torsion) angle_high() (in module espaloma.mm.angle) angle_indices() (in module espaloma.graphs.utils.offmol_indices) angle_torsion() (in module espaloma.mm.torsion) apply() (espaloma.data.dataset.Dataset method), [1] (espaloma.data.dataset.GraphDataset method) (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

apply_angle() (in module espaloma.mm.energy) (in module espaloma.mm.geometry) apply_angle_ii() (in module espaloma.mm.energy) apply_angle_linear_mixture() (in module espaloma.mm.energy) apply_bond() (in module espaloma.mm.energy) (in module espaloma.mm.geometry) apply_bond_gaussian() (in module espaloma.mm.energy) apply_bond_ii() (in module espaloma.mm.energy) apply_bond_linear_mixture() (in module espaloma.mm.energy) apply_coulomb() (in module espaloma.mm.energy) apply_improper_torsion() (in module espaloma.mm.energy) apply_nonbonded() (in module espaloma.mm.energy) apply_torsion() (in module espaloma.mm.energy) (in module espaloma.mm.geometry) apply_torsion_ii() (in module espaloma.mm.energy) arithmetic_mean() (in module espaloma.mm.nonbonded) atom_indices() (in module espaloma.graphs.utils.offmol_indices)

B

BaseGraph (class in espaloma.graphs.graph) BaseNormalize (class in espaloma.data.normalize) BaseReadout (class in espaloma.nn.readout.base_readout) batch() (in module espaloma.data.utils) bayer() (espaloma.data.collection.qca class method) benchmark() (espaloma.data.collection.qca class method) bfloat16() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

bond_angle() (in module espaloma.mm.angle) bond_bond() (in module espaloma.mm.angle) bond_high() (in module espaloma.mm.bond) bond_indices() (in module espaloma.graphs.utils.offmol_indices) bond_torsion() (in module espaloma.mm.torsion) breakdown_along_time_axis() (in module espaloma.data.qcarchive_utils) buffers() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

C

CarryII (class in espaloma.mm.energy) ChargeEquilibrium (class in espaloma.nn.readout.charge_equilibrium) children() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) collate_fn() (in module espaloma.data.utils) copy_src() (in module espaloma.mm.geometry) coulomb() (in module espaloma.mm.nonbonded) count() (espaloma.data.qcarchive_utils.MolWithTargets method) coverage() (espaloma.data.collection.qca class method) cpu() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

cuda() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

D

Dataset (class in espaloma.data.dataset) DatasetLogNormalNormalize (class in espaloma.data.normalize) DatasetNormalNormalize (class in espaloma.data.normalize) dihedral() (in module espaloma.mm.geometry) distance() (in module espaloma.mm.geometry) double() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

duplicate_index_ordering() (in module espaloma.graphs.utils.read_heterogeneous_graph)

E

emolecules() (espaloma.data.collection.qca class method) energies (espaloma.data.qcarchive_utils.MolWithTargets attribute) energy_in_graph() (in module espaloma.mm.energy) energy_in_graph_ii() (in module espaloma.mm.energy) EnergyInGraph (class in espaloma.mm.energy) EnergyInGraphII (class in espaloma.mm.energy) esol() (in module espaloma.data.collection) ESOL100LogNormalNormalize (class in espaloma.data.normalize) ESOL100NormalNormalize (class in espaloma.data.normalize) espaloma.data module espaloma.data.collection module espaloma.data.dataset module espaloma.data.md module espaloma.data.md17_utils module espaloma.data.normalize module espaloma.data.qcarchive_utils module espaloma.data.utils module espaloma.graphs module espaloma.graphs.deploy module espaloma.graphs.graph module espaloma.graphs.legacy_force_field module espaloma.graphs.utils module espaloma.graphs.utils.offmol_indices module espaloma.graphs.utils.read_heterogeneous_graph module espaloma.graphs.utils.read_homogeneous_graph module espaloma.graphs.utils.regenerate_impropers module espaloma.mm module espaloma.mm.angle module espaloma.mm.bond module espaloma.mm.energy module espaloma.mm.functional module espaloma.mm.geometry module espaloma.mm.nonbonded module espaloma.mm.torsion module

espaloma.nn module espaloma.nn.baselines module espaloma.nn.layers module espaloma.nn.layers.dgl_legacy module espaloma.nn.readout module espaloma.nn.readout.base_readout module espaloma.nn.readout.charge_equilibrium module espaloma.nn.readout.graph_level_readout module espaloma.nn.readout.janossy module espaloma.nn.readout.node_typing module espaloma.nn.sequential module eval() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) ExpCoefficients (class in espaloma.nn.readout.janossy) extra_repr() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

F

fda() (espaloma.data.collection.qca class method) fetch_td_record() (in module espaloma.data.qcarchive_utils) float() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) forward() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method), [1]

fp_oe() (in module espaloma.graphs.utils.read_homogeneous_graph) fp_rdkit() (in module espaloma.graphs.utils.read_homogeneous_graph) FreeParameterBaseline (class in espaloma.nn.baselines) FreeParameterBaselineInitMean (class in espaloma.nn.baselines) from_csv() (in module espaloma.data.utils) from_homogeneous_and_mol() (in module espaloma.graphs.utils.read_heterogeneous_graph) from_oemol() (in module espaloma.graphs.utils.read_homogeneous_graph) from_openff_toolkit_mol() (in module espaloma.graphs.utils.read_homogeneous_graph) from_rdkit_mol() (in module espaloma.graphs.utils.read_homogeneous_graph)

G

gaussian() (in module espaloma.mm.functional) gaussian_bond() (in module espaloma.mm.bond) geometric_mean() (in module espaloma.mm.nonbonded) geometry_in_graph() (in module espaloma.mm.geometry) GeometryInGraph (class in espaloma.mm.geometry) get_buffer() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) get_charges() (in module espaloma.nn.readout.charge_equilibrium) get_client() (in module espaloma.data.qcarchive_utils) get_collection() (in module espaloma.data.qcarchive_utils) get_coulomb_force() (in module espaloma.data.md) get_energy_and_gradient() (in module espaloma.data.qcarchive_utils) get_extra_state() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

get_graph() (in module espaloma.data.qcarchive_utils) get_molecule() (in module espaloma.data.md17_utils) get_parameter() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) get_submodule() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) GN (class in espaloma.nn.layers.dgl_legacy) gn() (in module espaloma.nn.layers.dgl_legacy) gradients (espaloma.data.qcarchive_utils.MolWithTargets attribute) Graph (class in espaloma.graphs.graph) GraphDataset (class in espaloma.data.dataset) GraphLevelReadout (class in espaloma.nn.readout.graph_level_readout)

H

h5_to_dataset() (in module espaloma.data.qcarchive_utils) half() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

harmonic() (in module espaloma.mm.functional) harmonic_angle() (in module espaloma.mm.angle) harmonic_bond() (in module espaloma.mm.bond) harmonic_harmonic_coupled() (in module espaloma.mm.functional) harmonic_harmonic_periodic_coupled() (in module espaloma.mm.functional) harmonic_periodic_coupled() (in module espaloma.mm.functional)

I

improper_torsion_indices() (in module espaloma.graphs.utils.offmol_indices)

index() (espaloma.data.qcarchive_utils.MolWithTargets method) infer_mol_from_coordinates() (in module espaloma.data.utils)

J

JanossyPooling (class in espaloma.nn.readout.janossy) JanossyPoolingImproper (class in espaloma.nn.readout.janossy)

JanossyPoolingNonbonded (class in espaloma.nn.readout.janossy) JanossyPoolingWithSmirnoffImproper (class in espaloma.nn.readout.janossy)

L

LegacyForceField (class in espaloma.graphs.legacy_force_field) linear_mixture() (in module espaloma.mm.functional) linear_mixture_angle() (in module espaloma.mm.angle) linear_mixture_bond() (in module espaloma.mm.bond) linear_mixture_to_original() (in module espaloma.mm.functional) LinearMixtureToOriginal (class in espaloma.nn.readout.janossy) lj() (in module espaloma.mm.functional) lj_12_6() (in module espaloma.mm.nonbonded) lj_9_6() (in module espaloma.mm.nonbonded) load() (espaloma.data.dataset.Dataset class method) (espaloma.data.dataset.Dataset method) (espaloma.data.dataset.GraphDataset class method) (espaloma.graphs.graph.Graph method) load_forcefield() (in module espaloma.graphs.deploy) load_state_dict() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

lorentz_berthelot() (in module espaloma.mm.nonbonded)

M

make_batch_size_consistent() (in module espaloma.data.qcarchive_utils) make_temp_directory() (in module espaloma.data.utils) md17_new() (in module espaloma.data.collection) md17_old() (in module espaloma.data.collection) module espaloma.data espaloma.data.collection espaloma.data.dataset espaloma.data.md espaloma.data.md17_utils espaloma.data.normalize espaloma.data.qcarchive_utils espaloma.data.utils espaloma.graphs espaloma.graphs.deploy espaloma.graphs.graph espaloma.graphs.legacy_force_field espaloma.graphs.utils espaloma.graphs.utils.offmol_indices espaloma.graphs.utils.read_heterogeneous_graph espaloma.graphs.utils.read_homogeneous_graph espaloma.graphs.utils.regenerate_impropers espaloma.mm espaloma.mm.angle espaloma.mm.bond espaloma.mm.energy espaloma.mm.functional espaloma.mm.geometry espaloma.mm.nonbonded espaloma.mm.torsion espaloma.nn espaloma.nn.baselines espaloma.nn.layers espaloma.nn.layers.dgl_legacy espaloma.nn.readout espaloma.nn.readout.base_readout espaloma.nn.readout.charge_equilibrium espaloma.nn.readout.graph_level_readout espaloma.nn.readout.janossy espaloma.nn.readout.node_typing espaloma.nn.sequential

modules() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) MoleculeVacuumSimulation (class in espaloma.data.md) MolWithTargets (class in espaloma.data.qcarchive_utils) multi_typing() (espaloma.graphs.legacy_force_field.LegacyForceField method) multiply_charges() (in module espaloma.mm.nonbonded)

N

named_buffers() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) named_children() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) named_modules() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

named_parameters() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) NodeTyping (class in espaloma.nn.readout.node_typing) normalize() (in module espaloma.data.utils) Note() (espaloma.data.dataset.GraphDataset method) NotNormalize (class in espaloma.data.normalize)

O

offmol (espaloma.data.qcarchive_utils.MolWithTargets attribute)

openmm_system_from_graph() (in module espaloma.graphs.deploy)

P

parameters() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

parametrize() (espaloma.graphs.legacy_force_field.LegacyForceField method), [1] periodic() (in module espaloma.mm.functional) periodic_fixed_phases() (in module espaloma.mm.functional) periodic_torsion() (in module espaloma.mm.torsion) pfizer() (espaloma.data.collection.qca class method) PositiveNotNormalize (class in espaloma.data.normalize) proper_torsion_indices() (in module espaloma.graphs.utils.offmol_indices)

Q

qca (class in espaloma.data.collection)

R

realize_molecule() (in module espaloma.data.md17_utils) reduce_stack() (in module espaloma.mm.geometry) regenerate_impropers() (espaloma.data.dataset.Dataset method) (espaloma.data.dataset.GraphDataset method) (in module espaloma.graphs.utils.regenerate_impropers) register_backward_hook() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) register_buffer() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) register_forward_hook() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) register_forward_pre_hook() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

register_full_backward_hook() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) register_module() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) register_parameter() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) relationship_indices_from_offmol() (in module espaloma.graphs.utils.read_heterogeneous_graph) requires_grad_() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) roche() (espaloma.data.collection.qca class method) run() (espaloma.data.md.MoleculeVacuumSimulation method)

S

save() (espaloma.data.dataset.Dataset method), [1] (espaloma.data.dataset.GraphDataset method) (espaloma.graphs.graph.Graph method) Sequential (class in espaloma.nn.sequential) set_extra_state() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) share_memory() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

shuffle() (espaloma.data.dataset.Dataset method) simulation_from_graph() (espaloma.data.md.MoleculeVacuumSimulation method) split() (espaloma.data.dataset.Dataset method), [1] (espaloma.data.dataset.GraphDataset method) (in module espaloma.data.utils) state_dict() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) subsample() (espaloma.data.dataset.Dataset method), [1] (espaloma.data.dataset.GraphDataset method) subtract_coulomb_force() (in module espaloma.data.md) subtract_nonbonded_force() (in module espaloma.data.md) subtract_nonbonded_force_except_14() (in module espaloma.data.md) sum_offsets() (in module espaloma.data.md17_utils) (in module espaloma.data.utils)

T

to() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) to_empty() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

train() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) type() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method) typing() (espaloma.graphs.legacy_force_field.LegacyForceField method), [1]

U

urey_bradley() (in module espaloma.mm.angle)

V

view() (espaloma.data.dataset.GraphDataset method), [1]

W

weight_by_snapshots() (in module espaloma.data.qcarchive_utils)

X

xpu() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

xyz (espaloma.data.qcarchive_utils.MolWithTargets attribute)

Z

zero_grad() (espaloma.mm.energy.CarryII method) (espaloma.mm.energy.EnergyInGraph method) (espaloma.mm.energy.EnergyInGraphII method) (espaloma.mm.geometry.GeometryInGraph method) (espaloma.nn.baselines.FreeParameterBaseline method) (espaloma.nn.baselines.FreeParameterBaselineInitMean method) (espaloma.nn.layers.dgl_legacy.GN method) (espaloma.nn.readout.base_readout.BaseReadout method) (espaloma.nn.readout.charge_equilibrium.ChargeEquilibrium method) (espaloma.nn.readout.graph_level_readout.GraphLevelReadout method) (espaloma.nn.readout.janossy.ExpCoefficients method) (espaloma.nn.readout.janossy.JanossyPooling method) (espaloma.nn.readout.janossy.JanossyPoolingImproper method) (espaloma.nn.readout.janossy.JanossyPoolingNonbonded method) (espaloma.nn.readout.janossy.JanossyPoolingWithSmirnoffImproper method) (espaloma.nn.readout.janossy.LinearMixtureToOriginal method) (espaloma.nn.readout.node_typing.NodeTyping method) (espaloma.nn.sequential.Sequential method)

zinc() (in module espaloma.data.collection)