Index

_

__call__() (EarlyStopping method)

A

append_contents() (in module fairmofsyncondition.read_write.filetyper) append_json() (in module fairmofsyncondition.read_write.filetyper) append_json_atom() (in module fairmofsyncondition.read_write.filetyper) append_pickle() (in module fairmofsyncondition.read_write.filetyper)

ase_coordinate() (in module fairmofsyncondition.read_write.coords_library) ase_database_to_lmdb() (in module fairmofsyncondition.read_write.coords_library) ase_to_pytorch_geometric() (in module fairmofsyncondition.read_write.coords_library) ase_to_xtb() (in module fairmofsyncondition.read_write.coords_library) AtomsEncoder (class in fairmofsyncondition.read_write.filetyper)

B

best_loss (EarlyStopping attribute)

C

calculate_distances() (in module fairmofsyncondition.read_write.coords_library) charge_and_ase_from_ams_gfn() (in module fairmofsyncondition.read_write.coords_library) check_periodicity() (in module fairmofsyncondition.read_write.coords_library) collect_coords() (in module fairmofsyncondition.read_write.coords_library)

combine_json_files() (in module fairmofsyncondition.read_write.filetyper) compute_esp() (in module fairmofsyncondition.read_write.coords_library) coordinate_definition() (in module fairmofsyncondition.read_write.coords_library) counter (EarlyStopping attribute) csv_read() (in module fairmofsyncondition.read_write.filetyper)

D

data_from_aseDb() (in module fairmofsyncondition.read_write.coords_library) default() (AtomsEncoder method) delta (EarlyStopping attribute)

display_model_helper() (in module fairmofsyncondition.model.thermodynamic_stability) dropout (EnergyGNN_GIN attribute) (GraphLatticeModel attribute)

E

early_stop (EarlyStopping attribute) EarlyStopping (class in fairmofsyncondition.model.thermodynamic_stability) EnergyGNN_GAT2Conv (class in fairmofsyncondition.model.thermodynamic_stability)

EnergyGNN_GIN (class in fairmofsyncondition.model.thermodynamic_stability) EnergyGNN_GIN_main_model() (in module fairmofsyncondition.model.thermodynamic_stability) entry_point() (in module fairmofsyncondition.model.thermodynamic_stability) evaluate() (in module fairmofsyncondition.model.thermodynamic_stability)

F

fairmofsyncondition.model.hyper_optimiser module fairmofsyncondition.model.thermodynamic_stability module fairmofsyncondition.read_write.cheminfo2iupac module fairmofsyncondition.read_write.coords_library module fairmofsyncondition.read_write.filetyper module

fairmofsyncondition.read_write.struct2iupac module file2smile() (in module fairmofsyncondition.read_write.struct2iupac) fine_opt_paramter() (in module fairmofsyncondition.model.hyper_optimiser) format_coords() (in module fairmofsyncondition.read_write.coords_library) forward() (EnergyGNN_GAT2Conv method) (EnergyGNN_GIN method), [1] (GraphLatticeModel method), [1]

G

GAT2Conv_main_model() (in module fairmofsyncondition.model.thermodynamic_stability) get_contents() (in module fairmofsyncondition.read_write.filetyper) get_pairwise_connections() (in module fairmofsyncondition.read_write.coords_library) get_section() (in module fairmofsyncondition.read_write.filetyper)

gjf_coordinate() (in module fairmofsyncondition.read_write.coords_library) gnn_hidden_dim (GraphLatticeModel attribute) GraphLatticeModel (class in fairmofsyncondition.model.thermodynamic_stability) GraphLatticeModel_main_model() (in module fairmofsyncondition.model.thermodynamic_stability)

H

hidden_dim (EnergyGNN_GIN attribute)

I

input_dim (EnergyGNN_GIN attribute) (GraphLatticeModel attribute)

inverse_normalize() (in module fairmofsyncondition.model.thermodynamic_stability)

J

json_to_aseatom() (in module fairmofsyncondition.read_write.filetyper)

json_to_numpy() (in module fairmofsyncondition.read_write.filetyper)

L

lattice_hidden_dim (GraphLatticeModel attribute) list_2_json() (in module fairmofsyncondition.read_write.filetyper) list_train_test_split() (in module fairmofsyncondition.read_write.coords_library) LMDBDataset (class in fairmofsyncondition.read_write.coords_library)

load_data() (in module fairmofsyncondition.read_write.filetyper) load_data_as_ase() (in module fairmofsyncondition.read_write.coords_library) load_dataset() (in module fairmofsyncondition.model.thermodynamic_stability) load_dict_msgpack() (in module fairmofsyncondition.read_write.filetyper) load_model() (in module fairmofsyncondition.model.thermodynamic_stability)

M

main() (in module fairmofsyncondition.model.hyper_optimiser) (in module fairmofsyncondition.read_write.cheminfo2iupac) (in module fairmofsyncondition.read_write.struct2iupac) module fairmofsyncondition.model.hyper_optimiser fairmofsyncondition.model.thermodynamic_stability fairmofsyncondition.read_write.cheminfo2iupac fairmofsyncondition.read_write.coords_library fairmofsyncondition.read_write.filetyper fairmofsyncondition.read_write.struct2iupac

N

normalize_data() (in module fairmofsyncondition.model.thermodynamic_stability)

num_layers (GraphLatticeModel attribute) numpy_to_json() (in module fairmofsyncondition.read_write.filetyper)

O

output_dim (EnergyGNN_GIN attribute) (GraphLatticeModel attribute)

P

parse_arguments() (in module fairmofsyncondition.model.thermodynamic_stability) path (EarlyStopping attribute) patience (EarlyStopping attribute) pickle_load() (in module fairmofsyncondition.read_write.filetyper) prepare_dataset() (in module fairmofsyncondition.read_write.coords_library)

print_helpful_information() (in module fairmofsyncondition.read_write.cheminfo2iupac) (in module fairmofsyncondition.read_write.struct2iupac) pubchem_to_inchikey() (in module fairmofsyncondition.read_write.cheminfo2iupac) (in module fairmofsyncondition.read_write.struct2iupac) put_contents() (in module fairmofsyncondition.read_write.filetyper) pytorch_geometric_to_ase() (in module fairmofsyncondition.read_write.coords_library)

Q

qchemcout() (in module fairmofsyncondition.read_write.coords_library)

qchemin() (in module fairmofsyncondition.read_write.coords_library) query_data() (in module fairmofsyncondition.read_write.filetyper)

R

read_and_return_ase_atoms() (in module fairmofsyncondition.read_write.coords_library) read_json() (in module fairmofsyncondition.read_write.filetyper)

read_zip() (in module fairmofsyncondition.read_write.filetyper) remove_trailing_commas() (in module fairmofsyncondition.read_write.filetyper)

S

save_checkpoint() (EarlyStopping method), [1] save_dict_msgpack() (in module fairmofsyncondition.read_write.filetyper) save_model() (in module fairmofsyncondition.model.thermodynamic_stability)

save_pickle() (in module fairmofsyncondition.read_write.filetyper) scm_out() (in module fairmofsyncondition.read_write.coords_library) split_data() (LMDBDataset method)

T

train() (in module fairmofsyncondition.model.thermodynamic_stability)

transform_target() (in module fairmofsyncondition.model.thermodynamic_stability)

W

write_ase_atoms() (in module fairmofsyncondition.read_write.coords_library)

write_json() (in module fairmofsyncondition.read_write.filetyper)

X

xtb_input() (in module fairmofsyncondition.read_write.coords_library)

xyz_coordinates() (in module fairmofsyncondition.read_write.coords_library)