Index

A

apply_mask() (DataCollatorForAtomModeling method) AtomformerConfig (class in atomgen.models.configuration_atomformer) AtomformerEncoder (class in atomgen.models.modeling_atomformer) AtomformerForCoordinateAM (class in atomgen.models.modeling_atomformer) AtomformerForMaskedAM (class in atomgen.models.modeling_atomformer) AtomFormerForSystemClassification (class in atomgen.models.modeling_atomformer) AtomformerModel (class in atomgen.models.modeling_atomformer) AtomformerPreTrainedModel (class in atomgen.models.modeling_atomformer) atomgen module atomgen.data module atomgen.data.data_collator module atomgen.data.tokenizer module

atomgen.data.utils module atomgen.models module atomgen.models.configuration_atomformer module atomgen.models.modeling_atomformer module atomgen.models.schnet module atomgen.models.tokengt module atomref (SchNetConfig attribute) AtomTokenizer (class in atomgen.data.tokenizer) autoregressive (DataCollatorForAtomModeling attribute), [1]

B

base_model_prefix (AtomformerPreTrainedModel attribute) (SchNetPreTrainedModel attribute) (TransformerPreTrainedModel attribute)

bos_token_id (SchNetConfig attribute) build_inputs_with_special_tokens() (AtomTokenizer method)

C

compute_metrics_lba() (in module atomgen.data.utils) compute_metrics_lep() (in module atomgen.data.utils) compute_metrics_msp() (in module atomgen.data.utils) compute_metrics_ppi() (in module atomgen.data.utils) compute_metrics_psr() (in module atomgen.data.utils) compute_metrics_res() (in module atomgen.data.utils) compute_metrics_rsr() (in module atomgen.data.utils)

compute_metrics_smp() (in module atomgen.data.utils) config_class (AtomformerPreTrainedModel attribute) (SchNetPreTrainedModel attribute) (TransformerPreTrainedModel attribute) convert_tokens_to_string() (AtomTokenizer method) coords_perturb (DataCollatorForAtomModeling attribute), [1] cutoff (SchNetConfig attribute)

D

DataCollatorForAtomModeling (class in atomgen.data.data_collator)

dipole (SchNetConfig attribute)

E

eos_token_id (SchNetConfig attribute)

F

flatten_batch() (DataCollatorForAtomModeling method) forward() (AtomformerEncoder method) (AtomformerForCoordinateAM method) (AtomformerForMaskedAM method) (AtomFormerForSystemClassification method) (AtomformerModel method) (GaussianLayer method) (InitialStructure2RelaxedEnergy method), [1] (InitialStructure2RelaxedStructure method), [1] (InitialStructure2RelaxedStructureAndEnergy method), [1] (ParallelBlock method), [1] (SchNetModel method) (Structure2Energy method) (Structure2EnergyAndForces method), [1] (Structure2Forces method) (Structure2TotalEnergyAndForces method) (TransformerEncoder method) (TransformerForCoordinateAM method) (TransformerForMaskedAM method) (TransformerModel method)

from_pretrained() (AtomTokenizer class method)

G

GaussianLayer (class in atomgen.models.modeling_atomformer)

get_vocab() (AtomTokenizer method) get_vocab_size() (AtomTokenizer method)

H

hidden_channels (SchNetConfig attribute)

I

InitialStructure2RelaxedEnergy (class in atomgen.models.modeling_atomformer) (class in atomgen.models.tokengt) InitialStructure2RelaxedStructure (class in atomgen.models.modeling_atomformer) (class in atomgen.models.tokengt)

InitialStructure2RelaxedStructureAndEnergy (class in atomgen.models.modeling_atomformer) (class in atomgen.models.tokengt) interaction_graph (SchNetConfig attribute)

K

k (DataCollatorForAtomModeling attribute), [1]

L

load_vocab() (AtomTokenizer static method)

M

mam (DataCollatorForAtomModeling attribute), [1] mask_token_id (SchNetConfig attribute) max_neighbors (DataCollatorForAtomModeling attribute), [1] max_num_neighbors (SchNetConfig attribute) max_radius (DataCollatorForAtomModeling attribute), [1] mean (SchNetConfig attribute) model_type (AtomformerConfig attribute) module atomgen atomgen.data atomgen.data.data_collator atomgen.data.tokenizer atomgen.data.utils atomgen.models atomgen.models.configuration_atomformer atomgen.models.modeling_atomformer atomgen.models.schnet atomgen.models.tokengt

N

num_filters (SchNetConfig attribute)

num_gaussians (SchNetConfig attribute) num_interactions (SchNetConfig attribute)

P

pad (DataCollatorForAtomModeling attribute), [1] pad() (AtomTokenizer method) pad_coords() (AtomTokenizer method) pad_fixed() (AtomTokenizer method)

pad_forces() (AtomTokenizer method) pad_to_multiple_of (DataCollatorForAtomModeling attribute), [1] pad_token_id (SchNetConfig attribute) ParallelBlock (class in atomgen.models.modeling_atomformer) (class in atomgen.models.tokengt)

R

readout (SchNetConfig attribute) return_edge_indices (DataCollatorForAtomModeling attribute), [1]

return_lap_pe (DataCollatorForAtomModeling attribute), [1] return_tensors (DataCollatorForAtomModeling attribute), [1]

S

save_vocabulary() (AtomTokenizer method) SchNetConfig (class in atomgen.models.schnet) SchNetModel (class in atomgen.models.schnet) SchNetPreTrainedModel (class in atomgen.models.schnet) std (SchNetConfig attribute) Structure2Energy (class in atomgen.models.modeling_atomformer)

Structure2EnergyAndForces (class in atomgen.models.modeling_atomformer) (class in atomgen.models.tokengt) Structure2Forces (class in atomgen.models.modeling_atomformer) Structure2TotalEnergyAndForces (class in atomgen.models.modeling_atomformer) supports_gradient_checkpointing (AtomformerPreTrainedModel attribute) (SchNetPreTrainedModel attribute) (TransformerPreTrainedModel attribute)

T

tokenizer (DataCollatorForAtomModeling attribute), [1] torch_call() (DataCollatorForAtomModeling method) torch_compute_edges() (DataCollatorForAtomModeling method) torch_compute_lap_pe() (DataCollatorForAtomModeling method) torch_mask_tokens() (DataCollatorForAtomModeling method) torch_perturb_coords() (DataCollatorForAtomModeling method)

TransformerConfig (class in atomgen.models.tokengt) TransformerEncoder (class in atomgen.models.tokengt) TransformerForCoordinateAM (class in atomgen.models.tokengt) TransformerForMaskedAM (class in atomgen.models.tokengt) TransformerModel (class in atomgen.models.tokengt) TransformerPreTrainedModel (class in atomgen.models.tokengt)

V

vocab_size (SchNetConfig attribute)