Index

A

add_angle() (mlcg.geometry.topology.Topology method) add_bond() (mlcg.geometry.topology.Topology method) add_chain_angles() (in module mlcg.geometry.topology) add_chain_bonds() (in module mlcg.geometry.topology) add_dihedral() (mlcg.geometry.topology.Topology method) AlanineDataset (class in mlcg.datasets.alanine_dipeptide), [1] angles (mlcg.geometry.topology.Topology attribute)

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

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) ChignolinDataset (class in mlcg.datasets.chignolin), [1] ChignolinDatasetWithDihedralPriors (class in mlcg.datasets.chignolin) compute_angles() (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) compute_torsions() (in module mlcg.geometry.internal_coordinates), [1] CosineCutoff (class in mlcg.nn.cutoff), [1] create_from_hdf5_group() (mlcg.datasets.h5_dataset.MetaSet static method)

D

DataModule (class in mlcg.pl) Dihedral (class in mlcg.nn.prior) dihedrals (mlcg.geometry.topology.Topology attribute)

dihedrals_from_edge_index() (mlcg.geometry.topology.Topology method) download() (mlcg.datasets.alanine_dipeptide.AlanineDataset method) (mlcg.datasets.chignolin.ChignolinDataset method) draw() (mlcg.geometry.topology.Topology method)

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) 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.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)

from_ase() (mlcg.data.atomic_data.AtomicData static method) (mlcg.geometry.topology.Topology static method) from_file() (mlcg.geometry.topology.Topology static method) from_mdtraj() (mlcg.geometry.topology.Topology static method) 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) get_dataloader() (mlcg.datasets.h5_dataset.H5SimpleDataset method)

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

H

H5Dataset (class in mlcg.datasets) (class in mlcg.datasets.h5_dataset) H5MetasetDataLoader (class in mlcg.datasets.h5_dataset) H5PartitionDataLoader (class in mlcg.datasets) (class in mlcg.datasets.h5_dataset)

H5SimpleDataset (class in mlcg.datasets.h5_dataset) 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)

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

K

kB (mlcg.datasets.alanine_dipeptide.AlanineDataset attribute) (mlcg.datasets.chignolin.ChignolinDataset attribute)

L

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

load_original_topology() (mlcg.datasets.alanine_dipeptide.AlanineDataset static method) Loss (class in mlcg.nn.losses)

M

make_baseline_models() (mlcg.datasets.alanine_dipeptide.AlanineDataset static method) make_cg_topology() (mlcg.datasets.alanine_dipeptide.AlanineDataset static method) make_data_slices_prior() (mlcg.datasets.alanine_dipeptide.AlanineDataset method) 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) masses (mlcg.data.atomic_data.AtomicData attribute), [1] message() (mlcg.nn.schnet.CFConv method) MetaSet (class in mlcg.datasets) (class in mlcg.datasets.h5_dataset) mlcg.cg.projection module mlcg.data.atomic_data module mlcg.datasets.alanine_dipeptide module mlcg.datasets.chignolin module mlcg.datasets.h5_dataset module 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.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 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.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) (class in mlcg.datasets.h5_dataset)

N

n_atoms (mlcg.geometry.topology.Topology property) name (mlcg.geometry.topology.Atom attribute) names (mlcg.geometry.topology.Topology attribute)

neighbor_list() (mlcg.geometry.topology.Topology method) (mlcg.nn.schnet.SchNet static method) neighborlist (mlcg.data.atomic_data.AtomicData attribute), [1]

O

OverdampedSimulation (class in mlcg.simulation)

P

Partition (class in mlcg.datasets) (class in mlcg.datasets.h5_dataset) pbc (mlcg.data.atomic_data.AtomicData attribute), [1] PLModel (class in mlcg.pl) plot() (mlcg.nn.radial_basis.radial_integral_gto.RIGTOBasis method)

pos (mlcg.data.atomic_data.AtomicData attribute), [1] process() (mlcg.datasets.alanine_dipeptide.AlanineDataset method) (mlcg.datasets.chignolin.ChignolinDataset method) processed_file_names (mlcg.datasets.alanine_dipeptide.AlanineDataset property) (mlcg.datasets.chignolin.ChignolinDataset property) PTSimulation (class in mlcg.simulation)

R

raw_file_names (mlcg.datasets.alanine_dipeptide.AlanineDataset property) (mlcg.datasets.chignolin.ChignolinDataset property) remove_angle() (mlcg.geometry.topology.Topology method) remove_bond() (mlcg.geometry.topology.Topology method) Repulsion (class in mlcg.nn.prior) repulsion_nls() (mlcg.datasets.alanine_dipeptide.AlanineDataset static method) reset_parameters() (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) resids (mlcg.geometry.topology.Topology attribute) resname (mlcg.geometry.topology.Atom attribute) resnames (mlcg.geometry.topology.Topology attribute) retrieve_hdf() (mlcg.datasets.h5_dataset.MetaSet static method) 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) sampling_setup() (mlcg.datasets.h5_dataset.Partition method) save_dataset() (mlcg.datasets.alanine_dipeptide.AlanineDataset method) SchNet (class in mlcg.nn.schnet), [1] ShiftedCosineCutoff (class in mlcg.nn.cutoff), [1] 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) StandardSchNet (class in mlcg.nn) (class in mlcg.nn.schnet) 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) (mlcg.datasets.chignolin.ChignolinDataset attribute) to_mdtraj() (mlcg.geometry.topology.Topology method) Topology (class in mlcg.geometry.topology) 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) training_validation_splitting() (mlcg.datasets.h5_dataset.H5Dataset method) trim_down_to() (mlcg.datasets.h5_dataset.MetaSet method) type (mlcg.geometry.topology.Atom attribute) types (mlcg.geometry.topology.Topology attribute)

V

validate_neighborlist() (in module mlcg.neighbor_list.neighbor_list), [1]

velocities (mlcg.data.atomic_data.AtomicData attribute), [1]

W

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