Index

_

__call__() (agedi.models.translator.Translator method) __len__() (agedi.AtomsGraph method) (agedi.data.atoms_graph.AtomsGraph method) (agedi.data.AtomsGraph method) _beta_t() (agedi.diffusion.noisers.types.NoiseSchedule method) _big_phi() (agedi.utils.truncated_normal.TruncatedStandardNormal static method) _big_phi_a (agedi.utils.truncated_normal.TruncatedStandardNormal attribute) _big_phi_b (agedi.utils.truncated_normal.TruncatedStandardNormal attribute) _build_conditioning() (in module agedi.api._registry) _build_noisers() (in module agedi.api._registry) _build_regressor() (in module agedi.api._registry) _build_score_components() (in module agedi.api._registry) _build_type_map_from_data() (in module agedi.api._registry) (in module agedi.functional) _cell_list_to_graph() (agedi.AtomsGraph static method) (agedi.data.atoms_graph.AtomsGraph static method) (agedi.data.AtomsGraph static method) _check_confinement() (agedi.data.Dataset method) (agedi.data.dataset.Dataset method) _check_head_dimensions() (in module agedi.api._display) _compiled_reverse_step (agedi.Diffusion attribute) (agedi.diffusion.Diffusion attribute) (agedi.diffusion.diffusion.Diffusion attribute) _CONFINEMENT_CLAMP_EPS (in module agedi.diffusion.distributions.normal) _DEFAULT_NOISER (in module agedi.cli.train) _denoise() (agedi.diffusion.noisers.base.Noiser method) (agedi.diffusion.noisers.Noiser method) (agedi.diffusion.noisers.pos.PositionsNoiser method) (agedi.diffusion.noisers.PositionsNoiser method) (agedi.diffusion.noisers.sde.SDENoiser method) (agedi.diffusion.noisers.SDENoiser method) (agedi.diffusion.noisers.Types method) (agedi.diffusion.noisers.types.Types method) _dtype_max_lt_1 (agedi.utils.truncated_normal.TruncatedStandardNormal attribute) _dtype_min_gt_0 (agedi.utils.truncated_normal.TruncatedStandardNormal attribute) _entropy (agedi.utils.truncated_normal.TruncatedStandardNormal attribute) _extract_checkpoint_metrics() (in module agedi.cli.inspect) _extract_data_info() (in module agedi.api._display) _extract_diffusion_display_info() (in module agedi.api._display) _fit_start_time (agedi.data.callbacks.EpochProgressPrinter attribute) _flatten_for_tb() (agedi.data.callbacks.HParamsMetricLogger method) _flatten_hparams() (in module agedi.data.callbacks) _fmt_target() (in module agedi.api._display) _format_timing_line() (agedi.Diffusion static method) (agedi.diffusion.Diffusion static method) (agedi.diffusion.diffusion.Diffusion static method) _from_std_rv() (agedi.utils.truncated_normal.TruncatedNormal method) (agedi.utils.TruncatedNormal method) _get_device_info() (in module agedi.api._display) _get_representation() (agedi.models.schnetpack.SchNetPackTranslator method) (agedi.models.schnetpack.translator.SchNetPackTranslator method) (agedi.models.translator.Translator method) _get_scalar_attr() (agedi.AtomsGraph method) (agedi.data.atoms_graph.AtomsGraph method) (agedi.data.AtomsGraph method) _has_energy_forces() (agedi.data.Dataset method) (agedi.data.dataset.Dataset method) _hparams (agedi.data.callbacks.HParamsMetricLogger attribute) _initialize_graph() (agedi.Diffusion method) (agedi.diffusion.Diffusion method) (agedi.diffusion.diffusion.Diffusion method) _inv_big_phi() (agedi.utils.truncated_normal.TruncatedStandardNormal static method) _is_lower_triangular() (agedi.AtomsGraph static method) (agedi.data.atoms_graph.AtomsGraph static method) (agedi.data.AtomsGraph static method) _key (agedi.diffusion.noisers.base.Noiser attribute) (agedi.diffusion.noisers.Noiser attribute) (agedi.diffusion.noisers.pos.PositionsNoiser attribute) (agedi.diffusion.noisers.PositionsNoiser attribute) (agedi.diffusion.noisers.sde.SDENoiser attribute) (agedi.diffusion.noisers.SDENoiser attribute) (agedi.diffusion.noisers.Types attribute) (agedi.diffusion.noisers.types.Types attribute) (agedi.models.head.Head attribute) (agedi.models.schnetpack.heads.PositionsScore attribute) (agedi.models.schnetpack.heads.TypesScore attribute) (agedi.models.schnetpack.PositionsScore attribute) (agedi.models.schnetpack.regressor_heads.Energy attribute) (agedi.models.schnetpack.regressor_heads.Forces attribute) (agedi.models.schnetpack.TypesScore attribute) _little_phi() (agedi.utils.truncated_normal.TruncatedStandardNormal static method) _little_phi_a (agedi.utils.truncated_normal.TruncatedStandardNormal attribute) _little_phi_b (agedi.utils.truncated_normal.TruncatedStandardNormal attribute) _log_scale (agedi.utils.truncated_normal.TruncatedNormal attribute) (agedi.utils.TruncatedNormal attribute) _log_Z (agedi.utils.truncated_normal.TruncatedStandardNormal attribute) _loss() (agedi.diffusion.noisers.base.Noiser method) (agedi.diffusion.noisers.Noiser method) (agedi.diffusion.noisers.pos.PositionsNoiser method) (agedi.diffusion.noisers.PositionsNoiser method) (agedi.diffusion.noisers.sde.SDENoiser method) (agedi.diffusion.noisers.SDENoiser method) (agedi.diffusion.noisers.Types method) (agedi.diffusion.noisers.types.Types method) _lpbb_m_lpaa_d_Z (agedi.utils.truncated_normal.TruncatedStandardNormal attribute) _make_graph_matscipy() (agedi.AtomsGraph static method) (agedi.data.atoms_graph.AtomsGraph static method) (agedi.data.AtomsGraph static method)

_mean (agedi.utils.truncated_normal.TruncatedNormal attribute) (agedi.utils.truncated_normal.TruncatedStandardNormal attribute) (agedi.utils.TruncatedNormal attribute) _MODEL_REGISTRY (in module agedi.api._registry) _noise() (agedi.diffusion.noisers.base.Noiser method) (agedi.diffusion.noisers.Noiser method) (agedi.diffusion.noisers.pos.PositionsNoiser method) (agedi.diffusion.noisers.PositionsNoiser method) (agedi.diffusion.noisers.sde.SDENoiser method) (agedi.diffusion.noisers.SDENoiser method) (agedi.diffusion.noisers.Types method) (agedi.diffusion.noisers.types.Types method) _painn_factory() (in module agedi.api._registry) _parse_override_value() (in module agedi.cli.train) _prepare_epoch() (agedi.data.callbacks.TrainingPhase method) _print_loaded_model_info() (in module agedi.api._display) _print_log_path() (in module agedi.api._display) _print_sampling_config() (in module agedi.api._display) _print_sampling_timings() (agedi.Diffusion method) (agedi.diffusion.Diffusion method) (agedi.diffusion.diffusion.Diffusion method) _print_training_config() (in module agedi.api._display) _registry (agedi.diffusion.noisers.base.Noiser attribute) (agedi.diffusion.noisers.Noiser attribute) _regressor_training (agedi.Agedi attribute) (agedi.diffusion.Agedi attribute) (agedi.diffusion.agedi.Agedi attribute) _render_config_tree() (in module agedi.api._display) _resolve_hparams() (agedi.data.callbacks.HParamsMetricLogger method) _resolve_sde() (in module agedi.api._registry) _sample() (agedi.Diffusion method) (agedi.diffusion.Diffusion method) (agedi.diffusion.diffusion.Diffusion method) (agedi.diffusion.distributions.base.Distribution method) (agedi.diffusion.distributions.Categorical method) (agedi.diffusion.distributions.categorical.Categorical method) (agedi.diffusion.distributions.Constant method) (agedi.diffusion.distributions.constant.Constant method) (agedi.diffusion.distributions.Distribution method) (agedi.diffusion.distributions.Normal method) (agedi.diffusion.distributions.normal.Normal method) (agedi.diffusion.distributions.normal.StandardNormal method) (agedi.diffusion.distributions.normal.TruncatedNormal method) (agedi.diffusion.distributions.StandardNormal method) (agedi.diffusion.distributions.TruncatedNormal method) (agedi.diffusion.distributions.Uniform method) (agedi.diffusion.distributions.uniform.Uniform method) (agedi.diffusion.distributions.uniform.UniformCell method) (agedi.diffusion.distributions.UniformCell method) _sample_batch() (agedi.Diffusion method) (agedi.diffusion.Diffusion method) (agedi.diffusion.diffusion.Diffusion method) _scheduler_monitor() (agedi.Agedi method) (agedi.diffusion.Agedi method) (agedi.diffusion.agedi.Agedi method) _score() (agedi.models.head.Head method) (agedi.models.schnetpack.heads.PositionsScore method) (agedi.models.schnetpack.heads.TypesScore method) (agedi.models.schnetpack.PositionsScore method) (agedi.models.schnetpack.regressor_heads.Energy method) (agedi.models.schnetpack.regressor_heads.Forces method) (agedi.models.schnetpack.TypesScore method) _score_clip (agedi.models.head.Head attribute) _setup() (agedi.diffusion.distributions.base.Distribution method) (agedi.diffusion.distributions.Constant method) (agedi.diffusion.distributions.constant.Constant method) (agedi.diffusion.distributions.Distribution method) (agedi.diffusion.distributions.normal.StandardNormal method) (agedi.diffusion.distributions.normal.TruncatedNormal method) (agedi.diffusion.distributions.StandardNormal method) (agedi.diffusion.distributions.TruncatedNormal method) (agedi.diffusion.distributions.Uniform method) (agedi.diffusion.distributions.uniform.Uniform method) (agedi.diffusion.distributions.uniform.UniformCell method) (agedi.diffusion.distributions.uniform.UniformCellConfined method) (agedi.diffusion.distributions.UniformCell method) (agedi.diffusion.distributions.UniformCellConfined method) _sync_for_timing() (agedi.Diffusion static method) (agedi.diffusion.Diffusion static method) (agedi.diffusion.diffusion.Diffusion static method) _TB_EXCLUDE_KEYS (agedi.data.callbacks.HParamsMetricLogger attribute) _time_sampling_call() (agedi.Diffusion method) (agedi.diffusion.Diffusion method) (agedi.diffusion.diffusion.Diffusion method) _to_std_rv() (agedi.utils.truncated_normal.TruncatedNormal method) (agedi.utils.TruncatedNormal method) _TRAIN_FROM_ATOMS_KEYS (in module agedi.api.training) _TRAINER_KEYS (in module agedi.api.training) _translate() (agedi.models.schnetpack.SchNetPackTranslator method) (agedi.models.schnetpack.translator.SchNetPackTranslator method) (agedi.models.translator.Translator method) _translate_representation() (agedi.models.schnetpack.SchNetPackTranslator method) (agedi.models.schnetpack.translator.SchNetPackTranslator method) (agedi.models.translator.Translator method) _VALID_NOISERS (in module agedi.cli.train) _variance (agedi.utils.truncated_normal.TruncatedNormal attribute) (agedi.utils.truncated_normal.TruncatedStandardNormal attribute) (agedi.utils.TruncatedNormal attribute) _Z (agedi.utils.truncated_normal.TruncatedStandardNormal attribute)

A

add_atoms_data() (agedi.data.Dataset method) (agedi.data.dataset.Dataset method) add_batch_attr() (agedi.AtomsGraph method) (agedi.data.atoms_graph.AtomsGraph method) (agedi.data.AtomsGraph method) add_graph_data() (agedi.data.Dataset method) (agedi.data.dataset.Dataset method) add_prediction() (agedi.models.translator.Translator method) add_regressor_data() (agedi.data.Dataset method) (agedi.data.dataset.Dataset method) add_representation() (agedi.models.translator.Translator method) add_scores() (agedi.models.translator.Translator method) agedi module Agedi (class in agedi) (class in agedi.diffusion) (class in agedi.diffusion.agedi) agedi.api module agedi.api._display module agedi.api._registry module agedi.api.dataset module agedi.api.diffusion module agedi.api.prediction module agedi.api.sampling module agedi.api.training module agedi.cli module agedi.cli.inspect module agedi.cli.main module agedi.cli.predict module agedi.cli.sample module agedi.cli.train module agedi.cli.train_hydra module agedi.data module agedi.data.atoms_graph module agedi.data.callbacks module agedi.data.dataset module agedi.data.transforms module agedi.diffusion module agedi.diffusion.agedi module agedi.diffusion.diffusion module agedi.diffusion.distributions module agedi.diffusion.distributions.base module agedi.diffusion.distributions.categorical module agedi.diffusion.distributions.constant module

agedi.diffusion.distributions.normal module agedi.diffusion.distributions.uniform module agedi.diffusion.guidance module agedi.diffusion.noisers module agedi.diffusion.noisers.base module agedi.diffusion.noisers.pos module agedi.diffusion.noisers.sde module agedi.diffusion.noisers.types module agedi.diffusion.sdes module agedi.diffusion.sdes.base module agedi.diffusion.sdes.noise_schedules module agedi.diffusion.sdes.ve module agedi.diffusion.sdes.vp module agedi.functional module agedi.models module agedi.models.conditionings module agedi.models.conditionings.base module agedi.models.conditionings.integer module agedi.models.conditionings.scalar module agedi.models.conditionings.time module agedi.models.head module agedi.models.regressor module agedi.models.schnetpack module agedi.models.schnetpack.heads module agedi.models.schnetpack.regressor_heads module agedi.models.schnetpack.translator module agedi.models.score module agedi.models.translator module agedi.utils module agedi.utils.offsets module agedi.utils.truncated_normal module alpha() (agedi.diffusion.sdes.VP method) (agedi.diffusion.sdes.vp.VP method) apply_mask() (agedi.AtomsGraph method) (agedi.data.atoms_graph.AtomsGraph method) (agedi.data.AtomsGraph method) arg_constraints (agedi.utils.truncated_normal.TruncatedStandardNormal attribute) AtomsGraph (class in agedi) (class in agedi.data) (class in agedi.data.atoms_graph) auc (agedi.utils.truncated_normal.TruncatedStandardNormal property)

B

batch_setup (agedi.diffusion.diffusion.SamplingTimings attribute) batch_size (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute) batched() (in module agedi.data.atoms_graph) BatchedLBFGSStepSizer (class in agedi.diffusion.guidance) beta() (agedi.diffusion.sdes.VP method) (agedi.diffusion.sdes.vp.VP method)

beta_max (agedi.diffusion.noisers.types.NoiseSchedule attribute) (agedi.diffusion.sdes.VP attribute) (agedi.diffusion.sdes.vp.VP attribute) beta_min (agedi.diffusion.noisers.types.NoiseSchedule attribute) (agedi.diffusion.sdes.VP attribute) (agedi.diffusion.sdes.vp.VP attribute) build_gated_equivariant_mlp() (in module agedi.models.schnetpack.heads) (in module agedi.models.schnetpack.regressor_heads)

C

Categorical (class in agedi.diffusion.distributions) (class in agedi.diffusion.distributions.categorical) cdf() (agedi.utils.truncated_normal.TruncatedNormal method) (agedi.utils.truncated_normal.TruncatedStandardNormal method) (agedi.utils.TruncatedNormal method) cell (agedi.AtomsGraph property) (agedi.data.atoms_graph.AtomsGraph property) (agedi.data.AtomsGraph property) cell_to_vectors() (agedi.AtomsGraph static method) (agedi.data.atoms_graph.AtomsGraph static method) (agedi.data.AtomsGraph static method) cellpar (agedi.AtomsGraph property) (agedi.data.atoms_graph.AtomsGraph property) (agedi.data.AtomsGraph property) CellPositions (class in agedi.diffusion.noisers) (class in agedi.diffusion.noisers.pos) clear_graph() (agedi.AtomsGraph method) (agedi.data.atoms_graph.AtomsGraph method) (agedi.data.AtomsGraph method) cli() (in module agedi.cli.main) compiled_reverse_step (agedi.Diffusion property) (agedi.diffusion.Diffusion property) (agedi.diffusion.diffusion.Diffusion property) compute_step() (agedi.diffusion.guidance.BatchedLBFGSStepSizer method) (agedi.diffusion.guidance.LBFGSStepSizer method) concatenate() (agedi.models.Conditioning method) (agedi.models.conditionings.base.Conditioning method) (agedi.models.conditionings.Conditioning method) concatenation_type (agedi.models.Conditioning attribute) (agedi.models.conditionings.base.Conditioning attribute) (agedi.models.conditionings.Conditioning attribute) Conditioning (class in agedi.models) (class in agedi.models.conditionings) (class in agedi.models.conditionings.base) conditionings (agedi.models.score.ScoreModel attribute) (agedi.models.ScoreModel attribute)

configure_optimizers() (agedi.Agedi method) (agedi.diffusion.Agedi method) (agedi.diffusion.agedi.Agedi method) ConfinedCellPositions (class in agedi.diffusion.noisers) (class in agedi.diffusion.noisers.pos) confinement (agedi.AtomsGraph property) (agedi.data.atoms_graph.AtomsGraph property) (agedi.data.AtomsGraph property) CONST_INV_SQRT_2 (in module agedi.utils.truncated_normal) CONST_INV_SQRT_2PI (in module agedi.utils.truncated_normal) CONST_LOG_INV_SQRT_2PI (in module agedi.utils.truncated_normal) CONST_LOG_SQRT_2PI_E (in module agedi.utils.truncated_normal) CONST_SQRT_2 (in module agedi.utils.truncated_normal) Constant (class in agedi.diffusion.distributions) (class in agedi.diffusion.distributions.constant) corrector_step() (agedi.Diffusion method) (agedi.diffusion.Diffusion method) (agedi.diffusion.diffusion.Diffusion method) Cosine (class in agedi.diffusion.sdes.noise_schedules) create_dataset() (in module agedi) (in module agedi.api) (in module agedi.api.dataset) (in module agedi.functional) create_diffusion() (in module agedi) (in module agedi.api) (in module agedi.api.diffusion) (in module agedi.functional) create_trainer() (in module agedi) (in module agedi.api) (in module agedi.api.training) (in module agedi.functional) current_phase (agedi.data.callbacks.TrainingPhase attribute) cutoff (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute)

D

dataset (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute) Dataset (class in agedi.data) (class in agedi.data.dataset) denoise (agedi.diffusion.diffusion.SamplingTimings attribute) denoise() (agedi.diffusion.noisers.base.Noiser method) (agedi.diffusion.noisers.Noiser method) device (agedi.Diffusion property) (agedi.diffusion.Diffusion property) (agedi.diffusion.diffusion.Diffusion property) (agedi.diffusion.guidance.LBFGSStepSizer attribute) df2dt() (agedi.diffusion.sdes.noise_schedules.NoiseSchedule method) Diffusion (class in agedi) (class in agedi.diffusion) (class in agedi.diffusion.diffusion) diffusion() (agedi.diffusion.sdes.base.SDE method) (agedi.diffusion.sdes.SDE method) (agedi.diffusion.sdes.VE method) (agedi.diffusion.sdes.ve.VE method) (agedi.diffusion.sdes.VP method) (agedi.diffusion.sdes.vp.VP method)

diffusion_loss() (agedi.Agedi method) (agedi.diffusion.Agedi method) (agedi.diffusion.agedi.Agedi method) distribution (agedi.diffusion.noisers.base.Noiser attribute) (agedi.diffusion.noisers.Noiser attribute) Distribution (class in agedi.diffusion.distributions) (class in agedi.diffusion.distributions.base) drift() (agedi.diffusion.sdes.base.SDE method) (agedi.diffusion.sdes.SDE method) (agedi.diffusion.sdes.VE method) (agedi.diffusion.sdes.ve.VE method) (agedi.diffusion.sdes.VP method) (agedi.diffusion.sdes.vp.VP method) dtype (agedi.diffusion.distributions.Constant attribute) (agedi.diffusion.distributions.constant.Constant attribute)

E

embedder (agedi.models.conditionings.integer.IntegerConditioning attribute) (agedi.models.conditionings.IntegerConditioning attribute) (agedi.models.conditionings.scalar.ScalarConditioning attribute) (agedi.models.conditionings.ScalarConditioning attribute) empty() (agedi.AtomsGraph class method) (agedi.data.atoms_graph.AtomsGraph class method) (agedi.data.AtomsGraph class method) Energy (class in agedi.models.schnetpack.regressor_heads)

entropy (agedi.utils.truncated_normal.TruncatedStandardNormal property) epoch_counter (agedi.data.callbacks.TrainingPhase attribute) EpochProgressPrinter (class in agedi.data.callbacks) epochs_per_phase (agedi.data.callbacks.TrainingPhase attribute) eps (agedi.Diffusion attribute) (agedi.diffusion.Diffusion attribute) (agedi.diffusion.diffusion.Diffusion attribute) Exponential (class in agedi.diffusion.sdes.noise_schedules)

F

f() (agedi.diffusion.sdes.noise_schedules.Cosine method) (agedi.diffusion.sdes.noise_schedules.Exponential method) (agedi.diffusion.sdes.noise_schedules.Linear method) (agedi.diffusion.sdes.noise_schedules.NoiseSchedule method) fint() (agedi.diffusion.sdes.noise_schedules.Cosine method) (agedi.diffusion.sdes.noise_schedules.Exponential method) (agedi.diffusion.sdes.noise_schedules.Linear method) (agedi.diffusion.sdes.noise_schedules.NoiseSchedule method) force_field_guidance (agedi.diffusion.diffusion.SamplingTimings attribute) force_field_guidance_step() (agedi.Diffusion method) (agedi.diffusion.Diffusion method) (agedi.diffusion.diffusion.Diffusion method) (in module agedi.diffusion.guidance) force_threshold (agedi.diffusion.ForcefieldGuidanceConfig attribute) (agedi.diffusion.guidance.ForcefieldGuidanceConfig attribute) (agedi.ForcefieldGuidanceConfig attribute) ForcefieldGuidanceConfig (class in agedi) (class in agedi.diffusion) (class in agedi.diffusion.guidance) Forces (class in agedi.models.schnetpack.regressor_heads) forward() (agedi.Agedi method) (agedi.data.transforms.Repeat method) (agedi.diffusion.Agedi method) (agedi.diffusion.agedi.Agedi method) (agedi.models.Conditioning method) (agedi.models.conditionings.base.Conditioning method) (agedi.models.conditionings.Conditioning method) (agedi.models.conditionings.time.TimeConditioning method) (agedi.models.conditionings.TimeConditioning method) (agedi.models.head.Head method) (agedi.models.regressor.RegressorModel method) (agedi.models.score.ScoreModel method) (agedi.models.ScoreModel method) (agedi.models.TimeConditioning method)

forward_sample() (agedi.models.score.ScoreModel method) (agedi.models.ScoreModel method) forward_step() (agedi.Diffusion method) (agedi.diffusion.Diffusion method) (agedi.diffusion.diffusion.Diffusion method) forward_train() (agedi.models.score.ScoreModel method) (agedi.models.ScoreModel method) fprime() (agedi.diffusion.sdes.noise_schedules.Cosine method) (agedi.diffusion.sdes.noise_schedules.Exponential method) (agedi.diffusion.sdes.noise_schedules.Linear method) (agedi.diffusion.sdes.noise_schedules.NoiseSchedule method) frac (agedi.AtomsGraph property) (agedi.data.atoms_graph.AtomsGraph property) (agedi.data.AtomsGraph property) frac_to_pos() (agedi.AtomsGraph method) (agedi.data.atoms_graph.AtomsGraph method) (agedi.data.AtomsGraph method) from_atoms() (agedi.AtomsGraph class method) (agedi.data.atoms_graph.AtomsGraph class method) (agedi.data.AtomsGraph class method) from_tensor() (agedi.data.atoms_graph.Representation class method) (agedi.data.Representation class method)

G

gated_blocks (agedi.models.schnetpack.heads.PositionsScore attribute) (agedi.models.schnetpack.PositionsScore attribute) (agedi.models.schnetpack.regressor_heads.Forces attribute) get_callable() (agedi.diffusion.distributions.base.Distribution method) (agedi.diffusion.distributions.Distribution method) get_conditioning() (agedi.models.Conditioning method) (agedi.models.conditionings.base.Conditioning method) (agedi.models.conditionings.Conditioning method) (agedi.models.conditionings.integer.IntegerConditioning method) (agedi.models.conditionings.IntegerConditioning method) (agedi.models.conditionings.scalar.ScalarConditioning method) (agedi.models.conditionings.ScalarConditioning method) (agedi.models.conditionings.time.TimeConditioning method) (agedi.models.conditionings.TimeConditioning method) (agedi.models.TimeConditioning method) get_empty_conditioning() (agedi.models.Conditioning method) (agedi.models.conditionings.base.Conditioning method) (agedi.models.conditionings.Conditioning method) (agedi.models.conditionings.integer.IntegerConditioning method) (agedi.models.conditionings.IntegerConditioning method) (agedi.models.conditionings.scalar.ScalarConditioning method) (agedi.models.conditionings.ScalarConditioning method) (agedi.models.conditionings.time.TimeConditioning method) (agedi.models.conditionings.TimeConditioning method) (agedi.models.TimeConditioning method) get_hparams() (agedi.Agedi method) (agedi.diffusion.Agedi method) (agedi.diffusion.agedi.Agedi method) (agedi.diffusion.distributions.base.Distribution method) (agedi.diffusion.distributions.Constant method) (agedi.diffusion.distributions.constant.Constant method) (agedi.diffusion.distributions.Distribution method) (agedi.diffusion.distributions.normal.TruncatedNormal method) (agedi.diffusion.distributions.TruncatedNormal method) (agedi.diffusion.distributions.Uniform method) (agedi.diffusion.distributions.uniform.Uniform method) (agedi.diffusion.noisers.base.Noiser method) (agedi.diffusion.noisers.Noiser method) (agedi.diffusion.noisers.pos.Positions method) (agedi.diffusion.noisers.pos.PositionsNoiser method) (agedi.diffusion.noisers.Positions method) (agedi.diffusion.noisers.PositionsNoiser method) (agedi.diffusion.noisers.sde.SDENoiser method) (agedi.diffusion.noisers.SDENoiser method) (agedi.diffusion.noisers.Types method) (agedi.diffusion.noisers.types.NoiseSchedule method) (agedi.diffusion.noisers.types.Types method) (agedi.diffusion.sdes.base.SDE method) (agedi.diffusion.sdes.noise_schedules.NoiseSchedule method) (agedi.diffusion.sdes.SDE method) (agedi.diffusion.sdes.VE method) (agedi.diffusion.sdes.ve.VE method) (agedi.diffusion.sdes.VP method) (agedi.diffusion.sdes.vp.VP method) (agedi.models.Conditioning method) (agedi.models.conditionings.base.Conditioning method) (agedi.models.conditionings.Conditioning method) (agedi.models.conditionings.integer.IntegerConditioning method) (agedi.models.conditionings.IntegerConditioning method) (agedi.models.conditionings.time.TimeConditioning method) (agedi.models.conditionings.TimeConditioning method) (agedi.models.head.Head method) (agedi.models.regressor.RegressorModel method) (agedi.models.schnetpack.heads.PositionsScore method) (agedi.models.schnetpack.heads.TypesScore method) (agedi.models.schnetpack.PositionsScore method) (agedi.models.schnetpack.regressor_heads.Energy method) (agedi.models.schnetpack.regressor_heads.Forces method) (agedi.models.schnetpack.TypesScore method) (agedi.models.score.ScoreModel method) (agedi.models.ScoreModel method) (agedi.models.TimeConditioning method) (agedi.models.translator.Translator method)

get_representation_hparams() (agedi.models.schnetpack.SchNetPackTranslator method) (agedi.models.schnetpack.translator.SchNetPackTranslator method) (agedi.models.translator.Translator method) GradNormLogger (class in agedi.data.callbacks) guidance (agedi.diffusion.ForcefieldGuidanceConfig attribute) (agedi.diffusion.guidance.ForcefieldGuidanceConfig attribute) (agedi.ForcefieldGuidanceConfig attribute) (agedi.models.score.ScoreModel attribute) (agedi.models.ScoreModel attribute) guidance_neighbor_list (agedi.diffusion.diffusion.SamplingTimings attribute) guidance_neighbor_list_calls (agedi.diffusion.diffusion.SamplingTimings attribute) guidance_neighbor_list_rebuilds (agedi.diffusion.diffusion.SamplingTimings attribute) guidance_wrap_positions (agedi.diffusion.diffusion.SamplingTimings attribute)

H

H0_scaling (agedi.diffusion.guidance.LBFGSStepSizer attribute) has_rsample (agedi.utils.truncated_normal.TruncatedNormal attribute) (agedi.utils.truncated_normal.TruncatedStandardNormal attribute) (agedi.utils.TruncatedNormal attribute) Head (class in agedi.models.head) head_keys (agedi.models.regressor.RegressorModel attribute)

head_weights (agedi.models.regressor.RegressorModel attribute) heads (agedi.models.regressor.RegressorModel attribute) (agedi.models.score.ScoreModel attribute) (agedi.models.ScoreModel attribute) high (agedi.diffusion.distributions.Uniform attribute) (agedi.diffusion.distributions.uniform.Uniform attribute) HParamsMetricLogger (class in agedi.data.callbacks)

I

icdf() (agedi.utils.truncated_normal.TruncatedNormal method) (agedi.utils.truncated_normal.TruncatedStandardNormal method) (agedi.utils.TruncatedNormal method) index (agedi.diffusion.distributions.normal.TruncatedNormal attribute) (agedi.diffusion.distributions.TruncatedNormal attribute) initial_neighbor_list (agedi.diffusion.diffusion.SamplingTimings attribute) initial_step (agedi.diffusion.guidance.LBFGSStepSizer attribute) initialization (agedi.diffusion.diffusion.SamplingTimings attribute) initialize_graph() (agedi.diffusion.noisers.base.Noiser method) (agedi.diffusion.noisers.Noiser method) input_dim (agedi.models.Conditioning attribute) (agedi.models.conditionings.base.Conditioning attribute) (agedi.models.conditionings.Conditioning attribute) input_dim_scalar (agedi.models.schnetpack.heads.PositionsScore attribute) (agedi.models.schnetpack.heads.TypesScore attribute) (agedi.models.schnetpack.PositionsScore attribute) (agedi.models.schnetpack.regressor_heads.Energy attribute) (agedi.models.schnetpack.regressor_heads.Forces attribute) (agedi.models.schnetpack.TypesScore attribute)

input_dim_vector (agedi.models.schnetpack.heads.PositionsScore attribute) (agedi.models.schnetpack.heads.TypesScore attribute) (agedi.models.schnetpack.PositionsScore attribute) (agedi.models.schnetpack.regressor_heads.Forces attribute) (agedi.models.schnetpack.TypesScore attribute) input_modules (agedi.models.translator.Translator attribute) inspect() (in module agedi.cli.inspect) IntegerConditioning (class in agedi.models.conditionings) (class in agedi.models.conditionings.integer)

K

key (agedi.diffusion.distributions.base.Distribution attribute) (agedi.diffusion.distributions.Distribution attribute) (agedi.diffusion.noisers.base.Noiser property) (agedi.diffusion.noisers.Noiser property) (agedi.models.head.Head property)

L

langevin_step() (agedi.diffusion.noisers.base.Noiser method) (agedi.diffusion.noisers.Noiser method) lbfgs_step_sizer (agedi.Diffusion attribute) (agedi.diffusion.Diffusion attribute) (agedi.diffusion.diffusion.Diffusion attribute) LBFGSStepSizer (class in agedi.diffusion.guidance) Linear (class in agedi.diffusion.sdes.noise_schedules) load_diffusion() (in module agedi) (in module agedi.api) (in module agedi.api.diffusion) (in module agedi.functional) log_every_n_steps (agedi.data.callbacks.GradNormLogger attribute)

log_prob() (agedi.utils.truncated_normal.TruncatedNormal method) (agedi.utils.truncated_normal.TruncatedStandardNormal method) (agedi.utils.TruncatedNormal method) loss() (agedi.Agedi method) (agedi.diffusion.Agedi method) (agedi.diffusion.agedi.Agedi method) (agedi.diffusion.noisers.base.Noiser method) (agedi.diffusion.noisers.Noiser method) (agedi.models.regressor.RegressorModel method) loss_scaling (agedi.diffusion.noisers.base.Noiser attribute) (agedi.diffusion.noisers.Noiser attribute) low (agedi.diffusion.distributions.Uniform attribute) (agedi.diffusion.distributions.uniform.Uniform attribute)

M

m (agedi.data.transforms.Repeat attribute) make_graph() (agedi.AtomsGraph static method) (agedi.data.atoms_graph.AtomsGraph static method) (agedi.data.AtomsGraph static method) mask_forces (agedi.models.regressor.RegressorModel attribute) max (agedi.diffusion.sdes.noise_schedules.NoiseSchedule attribute) max_extra_steps (agedi.diffusion.ForcefieldGuidanceConfig attribute) (agedi.diffusion.guidance.ForcefieldGuidanceConfig attribute) (agedi.ForcefieldGuidanceConfig attribute) max_int (agedi.models.conditionings.integer.IntegerConditioning attribute) (agedi.models.conditionings.IntegerConditioning attribute) mean (agedi.utils.truncated_normal.TruncatedStandardNormal property) mean() (agedi.diffusion.sdes.base.SDE method) (agedi.diffusion.sdes.SDE method) (agedi.diffusion.sdes.VE method) (agedi.diffusion.sdes.ve.VE method) (agedi.diffusion.sdes.VP method) (agedi.diffusion.sdes.vp.VP method) memory_size (agedi.diffusion.guidance.LBFGSStepSizer attribute) min (agedi.diffusion.sdes.noise_schedules.NoiseSchedule attribute) module agedi agedi.api agedi.api._display agedi.api._registry agedi.api.dataset agedi.api.diffusion agedi.api.prediction agedi.api.sampling agedi.api.training agedi.cli agedi.cli.inspect agedi.cli.main agedi.cli.predict agedi.cli.sample agedi.cli.train agedi.cli.train_hydra agedi.data agedi.data.atoms_graph agedi.data.callbacks agedi.data.dataset agedi.data.transforms agedi.diffusion agedi.diffusion.agedi agedi.diffusion.diffusion agedi.diffusion.distributions agedi.diffusion.distributions.base agedi.diffusion.distributions.categorical agedi.diffusion.distributions.constant agedi.diffusion.distributions.normal agedi.diffusion.distributions.uniform agedi.diffusion.guidance agedi.diffusion.noisers agedi.diffusion.noisers.base agedi.diffusion.noisers.pos agedi.diffusion.noisers.sde agedi.diffusion.noisers.types agedi.diffusion.sdes agedi.diffusion.sdes.base agedi.diffusion.sdes.noise_schedules agedi.diffusion.sdes.ve agedi.diffusion.sdes.vp agedi.functional agedi.models agedi.models.conditionings agedi.models.conditionings.base agedi.models.conditionings.integer agedi.models.conditionings.scalar agedi.models.conditionings.time agedi.models.head agedi.models.regressor agedi.models.schnetpack agedi.models.schnetpack.heads agedi.models.schnetpack.regressor_heads agedi.models.schnetpack.translator agedi.models.score agedi.models.translator agedi.utils agedi.utils.offsets agedi.utils.truncated_normal

N

n_classes (agedi.diffusion.noisers.Types attribute) (agedi.diffusion.noisers.types.Types attribute) (agedi.models.schnetpack.heads.TypesScore attribute) (agedi.models.schnetpack.TypesScore attribute) n_phases (agedi.data.callbacks.TrainingPhase attribute) n_test (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute) n_train (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute) n_val (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute) NEIGHBOR_CACHE_KEYS (in module agedi.data.atoms_graph) neighbor_list (agedi.diffusion.diffusion.SamplingTimings attribute) neighbor_list_calls (agedi.diffusion.diffusion.SamplingTimings attribute) neighbor_list_rebuilds (agedi.diffusion.diffusion.SamplingTimings attribute) net (agedi.models.schnetpack.heads.PositionsScore attribute) (agedi.models.schnetpack.heads.TypesScore attribute) (agedi.models.schnetpack.PositionsScore attribute) (agedi.models.schnetpack.regressor_heads.Energy attribute) (agedi.models.schnetpack.regressor_heads.Forces attribute) (agedi.models.schnetpack.TypesScore attribute) noise() (agedi.diffusion.noisers.base.Noiser method) (agedi.diffusion.noisers.Noiser method) (agedi.diffusion.sdes.base.SDE method) (agedi.diffusion.sdes.SDE method)

noise_schedule (agedi.diffusion.noisers.Types attribute) (agedi.diffusion.noisers.types.Types attribute) (agedi.diffusion.sdes.VE attribute) (agedi.diffusion.sdes.ve.VE attribute) (agedi.diffusion.sdes.VP attribute) (agedi.diffusion.sdes.vp.VP attribute) noise_schedule_cls (agedi.diffusion.sdes.base.SDE attribute) (agedi.diffusion.sdes.SDE attribute) Noiser (class in agedi.diffusion.noisers) (class in agedi.diffusion.noisers.base) noiser_keys (agedi.Diffusion attribute) (agedi.diffusion.Diffusion attribute) (agedi.diffusion.diffusion.Diffusion attribute) noisers (agedi.Diffusion attribute) (agedi.diffusion.Diffusion attribute) (agedi.diffusion.diffusion.Diffusion attribute) NoiseSchedule (class in agedi.diffusion.noisers.types) (class in agedi.diffusion.sdes.noise_schedules) Normal (class in agedi.diffusion.distributions) (class in agedi.diffusion.distributions.normal) num_workers (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute) NVIDIA_CELL_LIST_IMPORT_ERROR (in module agedi.data.atoms_graph) NVIDIA_NEIGHBOR_IMPORT_ERROR (in module agedi.data.atoms_graph)

O

OFFSET_LIST (in module agedi.utils) (in module agedi.utils.offsets) omega (agedi.models.conditionings.time.TimeConditioning attribute) (agedi.models.conditionings.TimeConditioning attribute) (agedi.models.TimeConditioning attribute) on_before_optimizer_step() (agedi.data.callbacks.GradNormLogger method) on_fit_end() (agedi.data.callbacks.EpochProgressPrinter method) (agedi.data.callbacks.HParamsMetricLogger method) on_fit_start() (agedi.Agedi method) (agedi.data.callbacks.EpochProgressPrinter method) (agedi.diffusion.Agedi method) (agedi.diffusion.agedi.Agedi method)

on_train_start() (agedi.data.callbacks.HParamsMetricLogger method) on_validation_end() (agedi.data.callbacks.TrainingPhase method) on_validation_epoch_end() (agedi.data.callbacks.EpochProgressPrinter method) (agedi.data.callbacks.HParamsMetricLogger method) optim_config (agedi.Agedi attribute) (agedi.diffusion.Agedi attribute) (agedi.diffusion.agedi.Agedi attribute) output_dim (agedi.models.Conditioning attribute) (agedi.models.conditionings.base.Conditioning attribute) (agedi.models.conditionings.Conditioning attribute)

P

periodic_distance() (agedi.diffusion.noisers.pos.PositionsNoiser method) (agedi.diffusion.noisers.PositionsNoiser method) phase_transforms (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute) pos_to_frac() (agedi.AtomsGraph method) (agedi.data.atoms_graph.AtomsGraph method) (agedi.data.AtomsGraph method) Positions (class in agedi.diffusion.noisers) (class in agedi.diffusion.noisers.pos) positions_mask (agedi.AtomsGraph property) (agedi.data.atoms_graph.AtomsGraph property) (agedi.data.AtomsGraph property) PositionsNoiser (class in agedi.diffusion.noisers) (class in agedi.diffusion.noisers.pos) PositionsScore (class in agedi.models.schnetpack) (class in agedi.models.schnetpack.heads) post_diffusion_force_eval (agedi.diffusion.diffusion.SamplingTimings attribute) post_diffusion_neighbor_list (agedi.diffusion.diffusion.SamplingTimings attribute) post_diffusion_neighbor_list_calls (agedi.diffusion.diffusion.SamplingTimings attribute) post_diffusion_neighbor_list_rebuilds (agedi.diffusion.diffusion.SamplingTimings attribute) post_diffusion_relaxation (agedi.diffusion.diffusion.SamplingTimings attribute) post_diffusion_relaxation_force_eval (agedi.diffusion.diffusion.SamplingTimings attribute) post_diffusion_relaxation_step() (agedi.Diffusion method) (agedi.diffusion.Diffusion method) (agedi.diffusion.diffusion.Diffusion method) (in module agedi.diffusion.guidance) post_diffusion_relaxation_steps (agedi.diffusion.diffusion.SamplingTimings attribute) post_diffusion_wrap_positions (agedi.diffusion.diffusion.SamplingTimings attribute)

postprocess_noise() (agedi.diffusion.noisers.sde.SDENoiser method) (agedi.diffusion.noisers.SDENoiser method) postprocess_score() (agedi.diffusion.noisers.sde.SDENoiser method) (agedi.diffusion.noisers.SDENoiser method) predict() (agedi.models.schnetpack.regressor_heads.Energy method) (agedi.models.schnetpack.regressor_heads.Forces method) (in module agedi) (in module agedi.api) (in module agedi.api.prediction) (in module agedi.cli.predict) (in module agedi.functional) prepare_for_compile() (agedi.AtomsGraph method) (agedi.data.atoms_graph.AtomsGraph method) (agedi.data.AtomsGraph method) prev_forces (agedi.diffusion.guidance.LBFGSStepSizer attribute) prev_pos (agedi.diffusion.guidance.LBFGSStepSizer attribute) print_epoch_interval (agedi.data.callbacks.EpochProgressPrinter attribute) prior (agedi.diffusion.noisers.base.Noiser attribute) (agedi.diffusion.noisers.Noiser attribute) probability (agedi.models.Conditioning attribute) (agedi.models.conditionings.base.Conditioning attribute) (agedi.models.conditionings.Conditioning attribute) properties (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute) property (agedi.data.transforms.Repeat attribute) (agedi.models.Conditioning attribute) (agedi.models.conditionings.base.Conditioning attribute) (agedi.models.conditionings.Conditioning attribute)

R

rate_noise() (agedi.diffusion.noisers.types.NoiseSchedule method) register() (agedi.diffusion.noisers.base.Noiser class method) (agedi.diffusion.noisers.Noiser class method) register_model() (in module agedi) (in module agedi.api) (in module agedi.api._registry) (in module agedi.functional) regressor_dataset (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute) regressor_loss() (agedi.Agedi method) (agedi.diffusion.Agedi method) (agedi.diffusion.agedi.Agedi method) regressor_loss_weight (agedi.Agedi attribute) (agedi.diffusion.Agedi attribute) (agedi.diffusion.agedi.Agedi attribute) regressor_model (agedi.Diffusion attribute) (agedi.diffusion.Diffusion attribute) (agedi.diffusion.diffusion.Diffusion attribute) regressor_train_loader (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute) regressor_training (agedi.Agedi property) (agedi.diffusion.Agedi property) (agedi.diffusion.agedi.Agedi property)

RegressorModel (class in agedi.models.regressor) Repeat (class in agedi.data.transforms) representation (agedi.AtomsGraph property) (agedi.data.atoms_graph.AtomsGraph property) (agedi.data.AtomsGraph property) (agedi.models.regressor.RegressorModel attribute) (agedi.models.score.ScoreModel attribute) (agedi.models.ScoreModel attribute) Representation (class in agedi.data) (class in agedi.data.atoms_graph) reset() (agedi.diffusion.guidance.BatchedLBFGSStepSizer method) (agedi.diffusion.guidance.LBFGSStepSizer method) reverse_rate() (agedi.diffusion.noisers.Types method) (agedi.diffusion.noisers.types.Types method) reverse_step() (agedi.Diffusion method) (agedi.diffusion.Diffusion method) (agedi.diffusion.diffusion.Diffusion method) reverse_step_calls (agedi.diffusion.diffusion.SamplingTimings attribute) rho_list (agedi.diffusion.guidance.LBFGSStepSizer attribute) rsample() (agedi.utils.truncated_normal.TruncatedStandardNormal method)

S

s_list (agedi.diffusion.guidance.LBFGSStepSizer attribute) sample() (agedi.Diffusion method) (agedi.diffusion.Diffusion method) (agedi.diffusion.diffusion.Diffusion method) (in module agedi) (in module agedi.api) (in module agedi.api.sampling) (in module agedi.cli.sample) (in module agedi.functional) sample_mode() (agedi.models.Conditioning method) (agedi.models.conditionings.base.Conditioning method) (agedi.models.conditionings.Conditioning method) (agedi.models.score.ScoreModel method) (agedi.models.ScoreModel method) sample_rate() (agedi.diffusion.noisers.Types method) (agedi.diffusion.noisers.types.Types method) sample_time() (agedi.Diffusion method) (agedi.diffusion.Diffusion method) (agedi.diffusion.diffusion.Diffusion method) sample_transition() (agedi.diffusion.noisers.Types method) (agedi.diffusion.noisers.types.Types method) sampling_mask (agedi.diffusion.noisers.Types attribute) (agedi.diffusion.noisers.types.Types attribute) SamplingTimings (class in agedi.diffusion.diffusion) scalar (agedi.data.atoms_graph.Representation attribute) (agedi.data.Representation attribute) ScalarConditioning (class in agedi.models.conditionings) (class in agedi.models.conditionings.scalar) scheduler_config (agedi.Agedi attribute) (agedi.diffusion.Agedi attribute) (agedi.diffusion.agedi.Agedi attribute) SchNetPackTranslator (class in agedi.models.schnetpack) (class in agedi.models.schnetpack.translator)

score_entropy() (agedi.diffusion.noisers.Types method) (agedi.diffusion.noisers.types.Types method) score_keys (agedi.Diffusion attribute) (agedi.diffusion.Diffusion attribute) (agedi.diffusion.diffusion.Diffusion attribute) score_model (agedi.Diffusion attribute) (agedi.diffusion.Diffusion attribute) (agedi.diffusion.diffusion.Diffusion attribute) (agedi.diffusion.diffusion.SamplingTimings attribute) ScoreModel (class in agedi.models) (class in agedi.models.score) SDE (class in agedi.diffusion.sdes) (class in agedi.diffusion.sdes.base) SDENoiser (class in agedi.diffusion.noisers) (class in agedi.diffusion.noisers.sde) set_phase() (agedi.data.Dataset method) (agedi.data.dataset.Dataset method) setup() (agedi.Agedi method) (agedi.data.Dataset method) (agedi.data.dataset.Dataset method) (agedi.diffusion.Agedi method) (agedi.diffusion.agedi.Agedi method) sigma() (agedi.diffusion.sdes.VE method) (agedi.diffusion.sdes.ve.VE method) sigma_max (agedi.diffusion.sdes.VE attribute) (agedi.diffusion.sdes.ve.VE attribute) sigma_min (agedi.diffusion.sdes.VE attribute) (agedi.diffusion.sdes.ve.VE attribute) staggered_score() (agedi.diffusion.noisers.Types method) (agedi.diffusion.noisers.types.Types method) StandardNormal (class in agedi.diffusion.distributions) (class in agedi.diffusion.distributions.normal) step_sizers (agedi.diffusion.guidance.BatchedLBFGSStepSizer attribute) support() (agedi.utils.truncated_normal.TruncatedStandardNormal method)

T

test_dataloader() (agedi.data.Dataset method) (agedi.data.dataset.Dataset method) test_idx (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute) time (agedi.AtomsGraph property) (agedi.data.atoms_graph.AtomsGraph property) (agedi.data.AtomsGraph property) TimeConditioning (class in agedi.models) (class in agedi.models.conditionings) (class in agedi.models.conditionings.time) to_atoms() (agedi.AtomsGraph method) (agedi.data.atoms_graph.AtomsGraph method) (agedi.data.AtomsGraph method) to_tensor() (agedi.data.atoms_graph.Representation method) (agedi.data.Representation method) total_neighbor_list (agedi.diffusion.diffusion.SamplingTimings property) total_noise() (agedi.diffusion.noisers.types.NoiseSchedule method) total_wall (agedi.diffusion.diffusion.SamplingTimings attribute) train() (in module agedi) (in module agedi.api) (in module agedi.api.training) (in module agedi.cli.train) (in module agedi.functional) train_dataloader() (agedi.data.Dataset method) (agedi.data.dataset.Dataset method) train_from_atoms() (in module agedi) (in module agedi.api) (in module agedi.api.training) (in module agedi.functional) train_from_config() (in module agedi) (in module agedi.api) (in module agedi.api.training) (in module agedi.functional) train_hydra() (in module agedi.cli.train_hydra)

train_idx (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute) training_mode() (agedi.models.Conditioning method) (agedi.models.conditionings.base.Conditioning method) (agedi.models.conditionings.Conditioning method) (agedi.models.score.ScoreModel method) (agedi.models.ScoreModel method) training_step() (agedi.Agedi method) (agedi.diffusion.Agedi method) (agedi.diffusion.agedi.Agedi method) TrainingPhase (class in agedi.data.callbacks) Transition (class in agedi.diffusion.noisers.types) transition_kernel() (agedi.diffusion.sdes.base.SDE method) (agedi.diffusion.sdes.SDE method) translate_input() (agedi.models.translator.Translator method) translate_with_representation() (agedi.models.translator.Translator method) translator (agedi.models.regressor.RegressorModel attribute) (agedi.models.score.ScoreModel attribute) (agedi.models.ScoreModel attribute) Translator (class in agedi.models.translator) transp_rate() (agedi.diffusion.noisers.Types method) (agedi.diffusion.noisers.types.Types method) transp_transition() (agedi.diffusion.noisers.Types method) (agedi.diffusion.noisers.types.Types method) TruncatedNormal (class in agedi.diffusion.distributions) (class in agedi.diffusion.distributions.normal) (class in agedi.utils) (class in agedi.utils.truncated_normal) TruncatedStandardNormal (class in agedi.utils.truncated_normal) Types (class in agedi.diffusion.noisers) (class in agedi.diffusion.noisers.types) TypesNoiser (in module agedi.diffusion.noisers) (in module agedi.diffusion.noisers.types) TypesScore (class in agedi.models.schnetpack) (class in agedi.models.schnetpack.heads)

U

Uniform (class in agedi.diffusion.distributions) (class in agedi.diffusion.distributions.uniform) UniformCell (class in agedi.diffusion.distributions) (class in agedi.diffusion.distributions.uniform) UniformCellConfined (class in agedi.diffusion.distributions) (class in agedi.diffusion.distributions.uniform)

update_graph() (agedi.AtomsGraph method) (agedi.data.atoms_graph.AtomsGraph method) (agedi.data.AtomsGraph method) use_weighting (agedi.models.regressor.RegressorModel attribute)

V

val_dataloader() (agedi.data.Dataset method) (agedi.data.dataset.Dataset method) val_idx (agedi.data.Dataset attribute) (agedi.data.dataset.Dataset attribute) validation_step() (agedi.Agedi method) (agedi.diffusion.Agedi method) (agedi.diffusion.agedi.Agedi method) value (agedi.diffusion.distributions.Constant attribute) (agedi.diffusion.distributions.constant.Constant attribute) var() (agedi.diffusion.sdes.base.SDE method) (agedi.diffusion.sdes.SDE method) (agedi.diffusion.sdes.VE method) (agedi.diffusion.sdes.ve.VE method) (agedi.diffusion.sdes.VP method) (agedi.diffusion.sdes.vp.VP method)

variance (agedi.utils.truncated_normal.TruncatedStandardNormal property) VE (class in agedi.diffusion.sdes) (class in agedi.diffusion.sdes.ve) vector (agedi.data.atoms_graph.Representation attribute) (agedi.data.Representation attribute) vector_to_cell() (agedi.AtomsGraph static method) (agedi.data.atoms_graph.AtomsGraph static method) (agedi.data.AtomsGraph static method) VP (class in agedi.diffusion.sdes) (class in agedi.diffusion.sdes.vp)

W

w (agedi.models.score.ScoreModel attribute) (agedi.models.ScoreModel attribute) wrap_positions (agedi.diffusion.diffusion.SamplingTimings attribute)

wrap_positions() (agedi.AtomsGraph method) (agedi.data.atoms_graph.AtomsGraph method) (agedi.data.AtomsGraph method)

Y

y_list (agedi.diffusion.guidance.LBFGSStepSizer attribute)

Z

zeta (agedi.Diffusion attribute) (agedi.diffusion.Diffusion attribute) (agedi.diffusion.diffusion.Diffusion attribute) (agedi.diffusion.ForcefieldGuidanceConfig attribute) (agedi.diffusion.guidance.ForcefieldGuidanceConfig attribute) (agedi.ForcefieldGuidanceConfig attribute)