Index

_

_ASE_prior_model() (in module mlcg.mol_utils)

_get_initial_data() (in module mlcg.mol_utils)

A

add_angle() (mlcg.geometry.topology.Topology method), [1] add_bond() (mlcg.geometry.topology.Topology method), [1] add_chain_angles() (in module mlcg.geometry.topology), [1] add_chain_bonds() (in module mlcg.geometry.topology), [1] add_dihedral() (mlcg.geometry.topology.Topology method), [1] aggregate() (mlcg.nn.painn.PaiNNInteraction method) AlanineDataset (class in mlcg.datasets.alanine_dipeptide), [1]

angles (mlcg.geometry.topology.Topology attribute), [1] angles_from_edge_index() (mlcg.geometry.topology.Topology method), [1] ase_neighbor_list() (in module mlcg.neighbor_list.ase_impl) Atom (class in mlcg.geometry.topology), [1] atom_types (mlcg.data.atomic_data.AtomicData attribute), [1] atomic_data2neighbor_list() (in module mlcg.neighbor_list.neighbor_list), [1] AtomicData (class in mlcg.data.atomic_data), [1] AttentiveSchNet (class in mlcg.nn.schnet)

B

batch (mlcg.data.atomic_data.AtomicData attribute), [1] bonds (mlcg.geometry.topology.Topology attribute), [1] bonds_from_edge_index() (mlcg.geometry.topology.Topology method), [1]

build_cg_matrix() (in module mlcg.cg.projection), [1] build_cg_topology() (in module mlcg.cg.projection), [1] build_opeps_connectivity_matrix() (in module mlcg.cg.projection)

C

cell (mlcg.data.atomic_data.AtomicData attribute), [1] CFConv (class in mlcg.nn.schnet), [1] charges (mlcg.geometry.topology.Topology attribute), [1] ChignolinDataset (class in mlcg.datasets.chignolin), [1] ChignolinDatasetWithDihedralPriors (class in mlcg.datasets.chignolin) compute_angles_cos() (in module mlcg.geometry.internal_coordinates), [1] compute_angles_raw() (in module mlcg.geometry.internal_coordinates), [1] compute_distance_vectors() (in module mlcg.geometry.internal_coordinates), [1]

compute_distances() (in module mlcg.geometry.internal_coordinates), [1] compute_images() (in module mlcg.neighbor_list.torch_impl), [1] compute_statistics() (in module mlcg.geometry.statistics), [1], [2] compute_torsions() (in module mlcg.geometry.internal_coordinates), [1] condense_all_priors_for_simulation() (in module mlcg.simulation.specialize_prior) CosineCutoff (class in mlcg.nn.cutoff), [1] create_from_hdf5_group() (mlcg.datasets.h5_dataset.MetaSet static method), [1] CustomRealAgnosticResidualInteractionBlock (class in mlcg.nn.mace)

D

DataModule (class in mlcg.pl) Dihedral (class in mlcg.nn.prior) dihedrals (mlcg.geometry.topology.Topology attribute), [1] dihedrals_from_edge_index() (mlcg.geometry.topology.Topology method), [1]

download() (mlcg.datasets.alanine_dipeptide.AlanineDataset method), [1] (mlcg.datasets.chignolin.ChignolinDataset method), [1] download_url() (in module mlcg.utils) draw() (mlcg.geometry.topology.Topology method), [1] dump_yaml() (in module mlcg.utils)

E

energy (mlcg.data.atomic_data.AtomicData attribute), [1] ExpNormalBasis (class in mlcg.nn.radial_basis) (class in mlcg.nn.radial_basis.exp_normal)

extended_initial_params() (mlcg.nn.radial_basis.exp_normal.ExtendedExpNormalBasis method) ExtendedExpNormalBasis (class in mlcg.nn.radial_basis.exp_normal)

F

fit_baseline_models() (in module mlcg.geometry.statistics), [1], [2] ForceMSE (class in mlcg.nn.losses) ForceRMSE (class in mlcg.nn.losses) forces (mlcg.data.atomic_data.AtomicData attribute), [1] forward() (mlcg.nn.angular_basis.spherical_harmonics.SphericalHarmonics method) (mlcg.nn.cutoff.CosineCutoff method) (mlcg.nn.cutoff.IdentityCutoff method) (mlcg.nn.cutoff.ShiftedCosineCutoff method) (mlcg.nn.mace.CustomRealAgnosticResidualInteractionBlock method) (mlcg.nn.mace.MACE method) (mlcg.nn.painn.PaiNN method) (mlcg.nn.painn.PaiNNInteraction method) (mlcg.nn.painn.PaiNNMixing method) (mlcg.nn.radial_basis.exp_normal.ExpNormalBasis method) (mlcg.nn.radial_basis.exp_normal.ExtendedExpNormalBasis method) (mlcg.nn.radial_basis.exp_spaced.SpacedExpBasis method) (mlcg.nn.radial_basis.gaussian.GaussianBasis method) (mlcg.nn.radial_basis.radial_integral_gto.RIGTOBasis method) (mlcg.nn.schnet.CFConv method) (mlcg.nn.schnet.InteractionBlock method) (mlcg.nn.schnet.SchNet method)

FourierSeries (class in mlcg.nn.prior) from_ase() (mlcg.data.atomic_data.AtomicData static method) (mlcg.geometry.topology.Topology static method), [1] from_file() (mlcg.geometry.topology.Topology static method), [1] from_mdtraj() (mlcg.geometry.topology.Topology static method), [1] from_points() (mlcg.data.atomic_data.AtomicData static method)

G

GaussianBasis (class in mlcg.nn.radial_basis) (class in mlcg.nn.radial_basis.gaussian) get_connectivity_matrix() (in module mlcg.geometry.topology), [1] get_dataloader() (mlcg.datasets.h5_dataset.H5SimpleDataset method), [1]

get_j_idx() (in module mlcg.neighbor_list.torch_impl) get_n_pairs() (in module mlcg.geometry.topology), [1] get_n_paths() (in module mlcg.geometry.topology), [1] grab_n_frames() (mlcg.datasets.h5_dataset.MetaSet static method), [1] GradientsOut (class in mlcg.nn.gradients)

H

H5Dataset (class in mlcg.datasets.h5_dataset), [1] H5MetasetDataLoader (class in mlcg.datasets.h5_dataset), [1] H5PartitionDataLoader (class in mlcg.datasets.h5_dataset), [1]

H5SimpleDataset (class in mlcg.datasets.h5_dataset), [1] Harmonic (class in mlcg.nn.prior) HarmonicAngles (class in mlcg.nn.prior) HarmonicBonds (class in mlcg.nn.prior)

I

IdentityCutoff (class in mlcg.nn.cutoff), [1] impropers (mlcg.geometry.topology.Topology attribute), [1]

impropers_from_edge_index() (mlcg.geometry.topology.Topology method), [1] InteractionBlock (class in mlcg.nn.schnet), [1] isolate_features() (in module mlcg.cg.projection)

K

kB (mlcg.datasets.alanine_dipeptide.AlanineDataset attribute), [1] (mlcg.datasets.chignolin.ChignolinDataset attribute), [1]

L

LangevinSimulation (class in mlcg.simulation) LightningCLI (class in mlcg.pl)

load_original_topology() (mlcg.datasets.alanine_dipeptide.AlanineDataset static method), [1] load_yaml() (in module mlcg.utils) Loss (class in mlcg.nn.losses)

M

MACE (class in mlcg.nn.mace), [1] make_baseline_models() (mlcg.datasets.alanine_dipeptide.AlanineDataset static method), [1] make_cg_topology() (mlcg.datasets.alanine_dipeptide.AlanineDataset static method), [1] make_data_slices_prior() (mlcg.datasets.alanine_dipeptide.AlanineDataset method), [1] make_neighbor_list() (in module mlcg.neighbor_list.neighbor_list), [1] make_non_bonded_set() (in module mlcg.cg.projection) make_opep_residue_indices() (in module mlcg.cg.projection) make_priors() (mlcg.datasets.alanine_dipeptide.AlanineDataset method), [1] make_splits() (in module mlcg.utils) masses (mlcg.data.atomic_data.AtomicData attribute), [1] message() (mlcg.nn.painn.PaiNNInteraction method) (mlcg.nn.schnet.CFConv method) MetaSet (class in mlcg.datasets.h5_dataset), [1] mlcg.cg.projection module mlcg.data.atomic_data module mlcg.datasets.alanine_dipeptide module mlcg.datasets.chignolin module mlcg.datasets.h5_dataset module, [1] mlcg.geometry.internal_coordinates module mlcg.neighbor_list.neighbor_list module mlcg.neighbor_list.torch_impl module mlcg.nn.angular_basis.spherical_harmonics module mlcg.nn.cutoff module mlcg.nn.mace module

mlcg.nn.painn module mlcg.nn.radial_basis.exp_normal module mlcg.nn.radial_basis.exp_spaced module mlcg.nn.radial_basis.gaussian module mlcg.nn.radial_basis.radial_integral_gto module mlcg.nn.schnet module mlcg.simulation.specialize_prior module module mlcg.cg.projection mlcg.data.atomic_data mlcg.datasets.alanine_dipeptide mlcg.datasets.chignolin mlcg.datasets.h5_dataset, [1] mlcg.geometry.internal_coordinates mlcg.neighbor_list.neighbor_list mlcg.neighbor_list.torch_impl mlcg.nn.angular_basis.spherical_harmonics mlcg.nn.cutoff mlcg.nn.mace mlcg.nn.painn mlcg.nn.radial_basis.exp_normal mlcg.nn.radial_basis.exp_spaced mlcg.nn.radial_basis.gaussian mlcg.nn.radial_basis.radial_integral_gto mlcg.nn.schnet mlcg.simulation.specialize_prior MolData (class in mlcg.datasets.h5_dataset), [1]

N

n_atoms (mlcg.geometry.topology.Topology property), [1] name (mlcg.geometry.topology.Atom attribute), [1] names (mlcg.geometry.topology.Topology attribute), [1] neighbor_list (mlcg.data.atomic_data.AtomicData attribute), [1]

neighbor_list() (mlcg.geometry.topology.Topology method), [1] (mlcg.nn.mace.MACE method) (mlcg.nn.painn.PaiNN method) (mlcg.nn.schnet.SchNet method)

O

on_train_epoch_end() (mlcg.pl.PLModel method) on_train_epoch_start() (mlcg.pl.PLModel method)

on_validation_epoch_end() (mlcg.pl.PLModel method) OverdampedSimulation (class in mlcg.simulation), [1]

P

PaiNN (class in mlcg.nn) (class in mlcg.nn.painn) PaiNNInteraction (class in mlcg.nn.painn) PaiNNMixing (class in mlcg.nn.painn) parse_arguments() (mlcg.pl.LightningCLI method) Partition (class in mlcg.datasets.h5_dataset), [1] pbc (mlcg.data.atomic_data.AtomicData attribute), [1] PLModel (class in mlcg.pl)

plot() (mlcg.nn.radial_basis.radial_integral_gto.RIGTOBasis method) Polynomial (class in mlcg.nn.prior) pos (mlcg.data.atomic_data.AtomicData attribute), [1] prepare_data() (mlcg.pl.DataModule method) process() (mlcg.datasets.alanine_dipeptide.AlanineDataset method), [1] (mlcg.datasets.chignolin.ChignolinDataset method), [1] processed_file_names (mlcg.datasets.alanine_dipeptide.AlanineDataset property), [1] (mlcg.datasets.chignolin.ChignolinDataset property), [1]

R

raw_file_names (mlcg.datasets.alanine_dipeptide.AlanineDataset property), [1] (mlcg.datasets.chignolin.ChignolinDataset property), [1] remove_angle() (mlcg.geometry.topology.Topology method), [1] remove_bond() (mlcg.geometry.topology.Topology method), [1] Repulsion (class in mlcg.nn.prior) repulsion_nls() (mlcg.datasets.alanine_dipeptide.AlanineDataset static method), [1] reset_parameters() (mlcg.nn.painn.PaiNN method) (mlcg.nn.painn.PaiNNInteraction method) (mlcg.nn.painn.PaiNNMixing method) (mlcg.nn.radial_basis.exp_normal.ExpNormalBasis method) (mlcg.nn.radial_basis.exp_spaced.SpacedExpBasis method) (mlcg.nn.radial_basis.gaussian.GaussianBasis method) (mlcg.nn.schnet.CFConv method) (mlcg.nn.schnet.SchNet method)

resid (mlcg.geometry.topology.Atom attribute), [1] resids (mlcg.geometry.topology.Topology attribute), [1] resname (mlcg.geometry.topology.Atom attribute), [1] resnames (mlcg.geometry.topology.Topology attribute), [1] retrieve_hdf() (mlcg.datasets.h5_dataset.MetaSet static method), [1] RIGTOBasis (class in mlcg.nn.radial_basis) (class in mlcg.nn.radial_basis.radial_integral_gto)

S

safe_norm() (in module mlcg.geometry.internal_coordinates) safe_normalization() (in module mlcg.geometry.internal_coordinates) safe_radius() (in module mlcg.neighbor_list.torch_impl) safe_radius_graph() (in module mlcg.neighbor_list.torch_impl) sampling_setup() (mlcg.datasets.h5_dataset.Partition method), [1] save_dataset() (mlcg.datasets.alanine_dipeptide.AlanineDataset method), [1] SchNet (class in mlcg.nn.schnet), [1] setup() (mlcg.pl.DataModule method) ShiftedCosineCutoff (class in mlcg.nn.cutoff), [1] So3krates (class in mlcg.nn) SpacedExpBasis (class in mlcg.nn.radial_basis) (class in mlcg.nn.radial_basis.exp_spaced)

SphericalHarmonics (class in mlcg.nn.angular_basis) (class in mlcg.nn.angular_basis.spherical_harmonics) StandardAllegro (class in mlcg.nn) StandardMACE (class in mlcg.nn) (class in mlcg.nn.mace) StandardPaiNN (class in mlcg.nn) (class in mlcg.nn.painn) StandardSchNet (class in mlcg.nn) (class in mlcg.nn.schnet) StandardSo3krates (class in mlcg.nn) strides_of() (in module mlcg.neighbor_list.torch_impl) SumOut (class in mlcg.nn.gradients) swap_mapping_rows() (in module mlcg.cg.projection)

T

tag (mlcg.data.atomic_data.AtomicData attribute), [1] temperature (mlcg.datasets.alanine_dipeptide.AlanineDataset attribute), [1] (mlcg.datasets.chignolin.ChignolinDataset attribute), [1] tensor2tuple() (in module mlcg.utils) test_dataloader() (mlcg.pl.DataModule method) test_step() (mlcg.pl.PLModel method) to_mdtraj() (mlcg.geometry.topology.Topology method), [1] to_reduce (in module mlcg.simulation.specialize_prior), [1] Topology (class in mlcg.geometry.topology), [1]

torch_neighbor_list() (in module mlcg.neighbor_list.torch_impl), [1] torch_neighbor_list_no_pbc() (in module mlcg.neighbor_list.torch_impl), [1] torch_neighbor_list_pbc() (in module mlcg.neighbor_list.torch_impl) train_dataloader() (mlcg.pl.DataModule method) training_step() (mlcg.pl.PLModel method) training_validation_splitting() (mlcg.datasets.h5_dataset.H5Dataset method), [1] trim_down_to() (mlcg.datasets.h5_dataset.MetaSet method), [1] type (mlcg.geometry.topology.Atom attribute), [1] types (mlcg.geometry.topology.Topology attribute), [1]

U

update() (mlcg.nn.painn.PaiNNInteraction method)

V

val_dataloader() (mlcg.pl.DataModule method) validate_neighborlist() (in module mlcg.neighbor_list.neighbor_list), [1]

validation_step() (mlcg.pl.PLModel method) velocities (mlcg.data.atomic_data.AtomicData attribute), [1]

W

wrap_positions() (in module mlcg.neighbor_list.torch_impl), [1]