mlcg
Data Representation
Geometry
Neighbor Lists
Coarse Graining
Datasets
Priors
Models
Training
Simulations
Developer Documentation
Bibliography
mlcg
Index
Index
A
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B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
V
|
W
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]