Index

_

__init__() (mxtaltools.models.modules.components.Scalarizer method) (mxtaltools.models.task_models.crystal_models.MolecularCrystalModel method) (mxtaltools.models.task_models.regression_models.MoleculeScalarRegressor method)

A

Activation (class in mxtaltools.models.modules.components) adaptive_batched_analysis() (in module mxtaltools.common.adaptive_batching) ae_reconstruction_loss() (in module mxtaltools.models.autoencoder_utils) align_mol_batch_to_standard_axes() (in module mxtaltools.crystal_building.utils) angle2components() (in module mxtaltools.common.geometry_utils) append_init_node_features() (mxtaltools.models.graph_models.molecule_graph_model.MolecularCrystalGraphModel method) (mxtaltools.models.graph_models.molecule_graph_model.MoleculeClusterModel method) (mxtaltools.models.graph_models.molecule_graph_model.ScalarMoleculeGraphModel method) (mxtaltools.models.graph_models.molecule_graph_model.VectorMoleculeGraphModel method) apply_rotation_to_batch() (in module mxtaltools.common.geometry_utils)

argwhere_minimum_image_convention_edges() (in module mxtaltools.models.functions.minimum_image_neighbors) ase_mol_from_crystaldata() (in module mxtaltools.common.ase_interface) ase_write_cif() (in module mxtaltools.common.ase_interface) assign_regression_targets() (mxtaltools.dataset_utils.dataset_manager.DataManager method) asymmetric_radius_graph() (in module mxtaltools.models.functions.radial_graph) ATOM_WEIGHTS (in module mxtaltools.constants.atom_properties) AugSoftmaxAggregation (class in mxtaltools.models.modules.augmented_softmax_aggregator) aunit2ucell() (in module mxtaltools.crystal_building.utils) AunitTransform (class in mxtaltools.crystal_building.crystal_latent_transforms) azimuth_to_std_normal() (mxtaltools.crystal_building.crystal_latent_transforms.RotationTransform method) azimuth_to_uniform() (mxtaltools.crystal_building.crystal_latent_transforms.RotationTransform method)

B

BaseGraphModel (class in mxtaltools.models.graph_models.base_graph_model) basic_stats() (in module mxtaltools.dataset_utils.utils) batch_cell_vol_torch() (in module mxtaltools.common.geometry_utils) batch_compute_dipole() (in module mxtaltools.common.utils) batch_compute_fractional_transform() (in module mxtaltools.common.geometry_utils) batch_compute_mol_mass() (in module mxtaltools.common.geometry_utils) batch_compute_mol_radius() (in module mxtaltools.common.geometry_utils)

batch_compute_molecule_volume() (in module mxtaltools.common.geometry_utils) batch_get_furthest_node_vector() (in module mxtaltools.common.geometry_utils) batch_molecule_principal_axes_torch() (in module mxtaltools.common.geometry_utils) batch_rmsd() (in module mxtaltools.models.autoencoder_utils) BesselBasisLayer (class in mxtaltools.models.modules.basis_functions) block_repeat_interleave() (in module mxtaltools.common.utils) BoundedTransform (class in mxtaltools.crystal_building.crystal_latent_transforms) build_radial_graph() (in module mxtaltools.models.functions.radial_graph)

C

canonicalize_aunit_order() (in module mxtaltools.crystal_building.utils) canonicalize_rotvec() (in module mxtaltools.crystal_building.utils) cart2sph_rotvec() (in module mxtaltools.common.geometry_utils) cell_parameters_to_box_vectors() (in module mxtaltools.common.geometry_utils) cell_vol_angle_factor() (in module mxtaltools.common.geometry_utils) cell_vol_np() (in module mxtaltools.common.geometry_utils) cell_vol_torch() (in module mxtaltools.common.geometry_utils) center_batch() (in module mxtaltools.common.geometry_utils) check_convergence() (in module mxtaltools.common.training_utils) (in module mxtaltools.crystal_search.crystal_opt_utils) check_embedding_quality() (mxtaltools.models.task_models.autoencoder_models.Mo3ENet method) chunkify() (in module mxtaltools.common.utils) classifier_reporting() (in module mxtaltools.common.mol_classifier_utils) clean_cell_params() (in module mxtaltools.models.utils) clean_generator_output() (in module mxtaltools.models.utils) cleanup_invalid_rotvecs() (in module mxtaltools.crystal_building.utils) collate_data_list() (in module mxtaltools.dataset_utils.utils) collect_extra_outputs() (mxtaltools.models.graph_models.molecule_graph_model.MolecularCrystalGraphModel static method) (mxtaltools.models.graph_models.molecule_graph_model.MoleculeClusterModel static method) (mxtaltools.models.graph_models.molecule_graph_model.ScalarMoleculeGraphModel static method) (mxtaltools.models.graph_models.molecule_graph_model.VectorMoleculeGraphModel static method) compile_self() (mxtaltools.models.graph_models.base_graph_model.BaseGraphModel method) (mxtaltools.models.task_models.autoencoder_models.Mo3ENet method) components2angle() (in module mxtaltools.common.geometry_utils) CompositeTransform (class in mxtaltools.crystal_building.crystal_latent_transforms) compute_auxiliary_loss() (in module mxtaltools.crystal_search.crystal_opt_utils)

compute_coord_evaluation_overlap() (in module mxtaltools.models.autoencoder_utils) compute_cosine_similarity_matrix() (in module mxtaltools.common.ellipsoid_ops) (in module mxtaltools.common.geometry_utils) compute_edges() (mxtaltools.dataset_utils.dataset_manager.DataManager method) compute_ellipsoid_overlap() (in module mxtaltools.common.ellipsoid_ops) compute_ellipsoid_volume() (in module mxtaltools.common.geometry_utils) compute_filter() (mxtaltools.dataset_utils.dataset_manager.DataManager method) compute_full_evaluation_overlap() (in module mxtaltools.models.autoencoder_utils) compute_gaussian_overlap() (in module mxtaltools.models.autoencoder_utils) compute_inertial_tensor_torch() (in module mxtaltools.common.geometry_utils) compute_Ip_handedness() (in module mxtaltools.common.geometry_utils) compute_latent_distance() (in module mxtaltools.common.geometry_utils) compute_loss() (in module mxtaltools.crystal_search.crystal_opt_utils) compute_mol_mass() (in module mxtaltools.common.geometry_utils) compute_mol_radii() (in module mxtaltools.common.mol_classifier_utils) compute_mol_radius() (in module mxtaltools.common.geometry_utils) compute_niggli_overlap() (in module mxtaltools.crystal_building.crystal_latent_transforms) compute_principal_axes_np() (in module mxtaltools.common.geometry_utils) compute_prior_loss() (in module mxtaltools.models.utils) compute_reduced_volume_fraction() (in module mxtaltools.models.utils) compute_type_evaluation_overlap() (in module mxtaltools.models.autoencoder_utils) convert_box_to_cell_params() (in module mxtaltools.common.mol_classifier_utils) convert_box_to_cell_vectors() (in module mxtaltools.common.mol_classifier_utils) coor_trans_matrix_np() (in module mxtaltools.common.geometry_utils) correct_Ip_directions() (in module mxtaltools.common.geometry_utils) crystal_parameter_distmat() (in module mxtaltools.common.geometry_utils) CrystalParams (class in mxtaltools.crystal_search.crystal_opt_utils)

D

data_batch_to_ase_mols_list() (in module mxtaltools.common.ase_interface) DataManager (class in mxtaltools.dataset_utils.dataset_manager) dataset_filtration() (mxtaltools.dataset_utils.dataset_manager.DataManager method) decode() (mxtaltools.models.task_models.autoencoder_models.Mo3ENet method) decode_to_sph_rotvec() (in module mxtaltools.models.utils) decode_to_sph_rotvec2() (in module mxtaltools.models.utils)

decoding2mol_batch() (in module mxtaltools.models.autoencoder_utils) delete_pandas_dataframe_rows() (in module mxtaltools.common.mol_classifier_utils) denormalize_generated_cell_params() (in module mxtaltools.models.utils) descale_asymmetric_unit() (in module mxtaltools.crystal_building.utils) dict2namespace() (in module mxtaltools.common.config_processing) (in module mxtaltools.crystal_search.crystal_opt_utils) dict_of_tensors_to_cpu_numpy() (in module mxtaltools.models.utils)

E

ema_trajectory() (in module mxtaltools.crystal_search.crystal_opt_utils) embed_crystal_list() (in module mxtaltools.models.utils) embed_vector_to_rank3() (in module mxtaltools.common.geometry_utils) EmbeddingBlock (class in mxtaltools.models.modules.components) enable_dropout() (in module mxtaltools.common.training_utils) encode() (mxtaltools.models.task_models.autoencoder_models.Mo3ENet method) enforce_1d_bound() (in module mxtaltools.models.utils) enforce_crystal_system() (in module mxtaltools.common.geometry_utils)

enforce_crystal_system2() (in module mxtaltools.common.geometry_utils) enforce_niggli_plane() (in module mxtaltools.crystal_building.crystal_latent_transforms) Envelope (class in mxtaltools.models.modules.basis_functions) EquivariantEmbeddingRegressor (class in mxtaltools.models.task_models.embedding_regression_models) extract_aunit_orientation() (in module mxtaltools.crystal_building.utils) extract_batching_info() (in module mxtaltools.common.geometry_utils) extract_misc_stats_and_indices() (mxtaltools.dataset_utils.dataset_manager.DataManager method) extract_rotmat() (in module mxtaltools.common.geometry_utils)

F

featurize_input_graph() (mxtaltools.models.graph_models.base_graph_model.BaseGraphModel method) filter_duplicate_molecules() (mxtaltools.dataset_utils.dataset_manager.DataManager method) filter_graph_nodewise() (in module mxtaltools.dataset_utils.utils) filter_polymorphs() (mxtaltools.dataset_utils.dataset_manager.DataManager method) filter_protons() (mxtaltools.dataset_utils.dataset_manager.DataManager method) find_coord_in_box_torch() (in module mxtaltools.crystal_building.utils) flatten_dict() (in module mxtaltools.common.utils) flatten_wandb_params() (in module mxtaltools.common.training_utils) force_molecules_into_box() (in module mxtaltools.common.mol_classifier_utils) forward() (mxtaltools.crystal_building.crystal_latent_transforms.AunitTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.BoundedTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.CompositeTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.IdentityTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.LogNormalTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.NiggliTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.PhiTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.ProbitTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.RotationTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.RTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.SquashingTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.ThetaTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.UnitToPMUnit method) (mxtaltools.crystal_building.crystal_latent_transforms.UnitTransform method) (mxtaltools.models.graph_models.base_graph_model.BaseGraphModel method) (mxtaltools.models.graph_models.graph_neural_network.MolCrystalScalarGNN method) (mxtaltools.models.graph_models.graph_neural_network.ScalarGNN method) (mxtaltools.models.graph_models.graph_neural_network.VectorGNN method) (mxtaltools.models.graph_models.molecule_graph_model.MolecularCrystalGraphModel method) (mxtaltools.models.graph_models.molecule_graph_model.MoleculeClusterModel method) (mxtaltools.models.graph_models.molecule_graph_model.ScalarMoleculeGraphModel method) (mxtaltools.models.graph_models.molecule_graph_model.VectorMoleculeGraphModel method) (mxtaltools.models.modules.augmented_softmax_aggregator.AugSoftmaxAggregation method) (mxtaltools.models.modules.augmented_softmax_aggregator.VectorAugSoftmaxAggregation method) (mxtaltools.models.modules.basis_functions.BesselBasisLayer method) (mxtaltools.models.modules.basis_functions.Envelope method) (mxtaltools.models.modules.basis_functions.GaussianEmbedding method) (mxtaltools.models.modules.components.Activation method) (mxtaltools.models.modules.components.EmbeddingBlock method) (mxtaltools.models.modules.components.KernelActivation method) (mxtaltools.models.modules.components.Normalization method) (mxtaltools.models.modules.components.ResidualMLP method) (mxtaltools.models.modules.components.Scalarizer method) (mxtaltools.models.modules.components.scalarMLP method) (mxtaltools.models.modules.components.VectorActivation method) (mxtaltools.models.modules.components.vectorMLP method) (mxtaltools.models.modules.graph_convolution.MConv method) (mxtaltools.models.modules.graph_convolution.v_MConv method) (mxtaltools.models.modules.vector_LayerNorm.VectorLayerNorm method) (mxtaltools.models.task_models.autoencoder_models.Mo3ENet method) (mxtaltools.models.task_models.autoencoder_models.Mo3ENetDecoder method) (mxtaltools.models.task_models.autoencoder_models.Mo3ENetEncoder method) (mxtaltools.models.task_models.autoencoder_models.Mo3ENetGraphDecoder method) (mxtaltools.models.task_models.crystal_models.MolecularCrystalModel method) (mxtaltools.models.task_models.embedding_regression_models.EquivariantEmbeddingRegressor method) (mxtaltools.models.task_models.embedding_regression_models.InvariantEmbeddingRegressor method) (mxtaltools.models.task_models.mol_classifier.MoleculeClusterClassifier method)

fractional_transform() (in module mxtaltools.common.geometry_utils) fractional_transform_np() (in module mxtaltools.common.geometry_utils) fractional_transform_torch() (in module mxtaltools.common.geometry_utils)

G

GaussianEmbedding (class in mxtaltools.models.modules.basis_functions) generate_mol2crystal_mapping() (mxtaltools.dataset_utils.dataset_manager.DataManager method) generate_random_eigenvalues() (in module mxtaltools.common.ellipsoid_ops) generate_random_rotations() (in module mxtaltools.common.ellipsoid_ops) generate_sorted_fractional_translations() (in module mxtaltools.crystal_building.utils) get_annealing_factor() (in module mxtaltools.crystal_search.crystal_opt_utils) get_aunit_positions() (in module mxtaltools.crystal_building.utils) get_batch_centroids() (in module mxtaltools.common.geometry_utils) get_cart_translations() (in module mxtaltools.crystal_building.utils) get_condition_values() (mxtaltools.dataset_utils.dataset_manager.DataManager method) get_data_dimensions() (mxtaltools.dataset_utils.dataset_manager.DataManager method) get_data_stats() (mxtaltools.models.graph_models.base_graph_model.BaseGraphModel method) get_dataloaders() (in module mxtaltools.dataset_utils.utils) get_dataset_filter_inds() (mxtaltools.dataset_utils.dataset_manager.DataManager method) get_identifier_duplicates() (mxtaltools.dataset_utils.dataset_manager.DataManager method) get_loss() (in module mxtaltools.common.mol_classifier_utils) get_main_config() (in module mxtaltools.common.config_processing) get_max_cos() (in module mxtaltools.crystal_building.crystal_latent_transforms) get_mc_noised_samples() (in module mxtaltools.crystal_search.crystal_opt_utils)

get_model_nans() (in module mxtaltools.common.training_utils) get_model_sizes() (in module mxtaltools.models.utils) get_mol_embedding_for_proxy() (in module mxtaltools.models.utils) get_n_config() (in module mxtaltools.common.training_utils) get_niggli_cell() (in module mxtaltools.common.ase_interface) get_node_weights() (in module mxtaltools.models.autoencoder_utils) get_overlaps() (in module mxtaltools.common.geometry_utils) get_plotly_fig_size_mb() (in module mxtaltools.common.utils) get_point_density() (in module mxtaltools.common.utils) get_point_density_knn() (in module mxtaltools.common.utils) get_reduced_volume_fraction() (mxtaltools.dataset_utils.dataset_manager.DataManager method) get_regression_loss() (in module mxtaltools.models.utils) get_residues() (mxtaltools.models.modules.components.vectorMLP method) get_target() (mxtaltools.dataset_utils.dataset_manager.DataManager method) get_user_config() (in module mxtaltools.common.config_processing) gradient_descent_optimization() (in module mxtaltools.crystal_search.crystal_opt_utils) greedy_bottom_up_anchors() (in module mxtaltools.common.clustering) grid_compute_molecule_volume() (in module mxtaltools.common.geometry_utils) grid_compute_molecule_volume_pointwise() (in module mxtaltools.common.geometry_utils)

H

histogram_overlap_np() (in module mxtaltools.common.utils)

I

identify_canonical_asymmetric_unit() (in module mxtaltools.crystal_building.utils) identify_surface_molecules() (in module mxtaltools.common.mol_classifier_utils) identify_unique_molecules_in_crystals() (mxtaltools.dataset_utils.dataset_manager.DataManager method) IdentityTransform (class in mxtaltools.crystal_building.crystal_latent_transforms) increment_value() (in module mxtaltools.models.utils) init_atom_properties() (mxtaltools.dataset_utils.dataset_manager.DataManager method) init_decoded_data() (in module mxtaltools.models.autoencoder_utils) init_mc_state() (in module mxtaltools.crystal_search.crystal_opt_utils) init_opt() (in module mxtaltools.crystal_search.crystal_opt_utils) init_optimizer() (in module mxtaltools.common.training_utils) init_scalar_filters() (mxtaltools.models.modules.components.scalarMLP method) init_scalar_transforms() (mxtaltools.models.modules.components.scalarMLP method) init_scheduler() (in module mxtaltools.common.training_utils) init_sym_info() (in module mxtaltools.common.sym_utils) init_vector_filters() (mxtaltools.models.modules.components.vectorMLP method) init_vector_transforms() (mxtaltools.models.modules.components.vectorMLP method) instantiate_cluster() (in module mxtaltools.crystal_building.utils)

inter_overlap_loss() (in module mxtaltools.crystal_search.crystal_opt_utils) InvariantEmbeddingRegressor (class in mxtaltools.models.task_models.embedding_regression_models) inverse() (mxtaltools.crystal_building.crystal_latent_transforms.AunitTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.BoundedTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.CompositeTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.IdentityTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.LogNormalTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.NiggliTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.PhiTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.ProbitTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.RotationTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.RTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.SquashingTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.ThetaTransform method) (mxtaltools.crystal_building.crystal_latent_transforms.UnitToPMUnit method) (mxtaltools.crystal_building.crystal_latent_transforms.UnitTransform method) invert_softplus_shift() (in module mxtaltools.common.utils) is_cuda_oom() (in module mxtaltools.common.utils)

K

kernel() (mxtaltools.models.modules.components.KernelActivation method)

KernelActivation (class in mxtaltools.models.modules.components)

L

lat2sph_rotvec() (in module mxtaltools.common.geometry_utils) lattice_energy_calculation() (mxtaltools.mlip_interfaces.mace_utils.SPMaceCalculator method) list_molecule_principal_axes_torch() (in module mxtaltools.common.geometry_utils) llipsoid_volume() (in module mxtaltools.common.ellipsoid_ops) load_chunks() (mxtaltools.dataset_utils.dataset_manager.DataManager method) load_crystal_score_model() (in module mxtaltools.common.training_utils) load_dataset_for_modelling() (mxtaltools.dataset_utils.dataset_manager.DataManager method)

load_encoder() (in module mxtaltools.models.utils) load_molecule_autoencoder() (in module mxtaltools.common.training_utils) load_molecule_scalar_regressor() (in module mxtaltools.common.training_utils) load_training_dataset() (mxtaltools.dataset_utils.dataset_manager.DataManager method) load_yaml() (in module mxtaltools.common.config_processing) log_rescale_positive() (in module mxtaltools.common.utils) LogNormalTransform (class in mxtaltools.crystal_building.crystal_latent_transforms) loss_and_backprop() (in module mxtaltools.crystal_search.crystal_opt_utils)

M

make_sequential_directory() (in module mxtaltools.common.training_utils) MConv (class in mxtaltools.models.modules.graph_convolution) message() (mxtaltools.models.modules.graph_convolution.MConv method) (mxtaltools.models.modules.graph_convolution.v_MConv method) message_dim (mxtaltools.models.modules.graph_convolution.MConv attribute) (mxtaltools.models.modules.graph_convolution.v_MConv attribute) Mo3ENet (class in mxtaltools.models.task_models.autoencoder_models) Mo3ENetDecoder (class in mxtaltools.models.task_models.autoencoder_models) Mo3ENetEncoder (class in mxtaltools.models.task_models.autoencoder_models) Mo3ENetGraphDecoder (class in mxtaltools.models.task_models.autoencoder_models) module mxtaltools.common.adaptive_batching mxtaltools.common.ase_interface mxtaltools.common.clustering mxtaltools.common.config_processing mxtaltools.common.ellipsoid_ops mxtaltools.common.geometry_utils mxtaltools.common.mol_classifier_utils mxtaltools.common.sym_utils mxtaltools.common.training_utils mxtaltools.common.utils mxtaltools.constants.asymmetric_units mxtaltools.constants.atom_properties mxtaltools.constants.classifier_constants mxtaltools.constants.csd_stats mxtaltools.constants.mol_classifier_constants mxtaltools.constants.space_group_info mxtaltools.constants.space_group_reference mxtaltools.crystal_building.crystal_latent_transforms mxtaltools.crystal_building.utils mxtaltools.crystal_search.crystal_opt_utils mxtaltools.dataset_utils.dataset_manager mxtaltools.dataset_utils.utils mxtaltools.mlip_interfaces.mace_utils mxtaltools.models.autoencoder_utils mxtaltools.models.functions.minimum_image_neighbors mxtaltools.models.functions.radial_graph mxtaltools.models.graph_models.base_graph_model mxtaltools.models.graph_models.graph_neural_network mxtaltools.models.graph_models.molecule_graph_model mxtaltools.models.modules.augmented_softmax_aggregator mxtaltools.models.modules.basis_functions mxtaltools.models.modules.components mxtaltools.models.modules.graph_convolution mxtaltools.models.modules.vector_LayerNorm mxtaltools.models.task_models.autoencoder_models mxtaltools.models.task_models.crystal_models mxtaltools.models.task_models.embedding_regression_models mxtaltools.models.task_models.mol_classifier mxtaltools.models.task_models.regression_models mxtaltools.models.utils mol_batch_vdW_volume() (in module mxtaltools.common.geometry_utils) mol_fc (mxtaltools.models.graph_models.molecule_graph_model.MolecularCrystalGraphModel attribute) (mxtaltools.models.graph_models.molecule_graph_model.MoleculeClusterModel attribute) (mxtaltools.models.graph_models.molecule_graph_model.ScalarMoleculeGraphModel attribute) (mxtaltools.models.graph_models.molecule_graph_model.VectorMoleculeGraphModel attribute) MolCrystalScalarGNN (class in mxtaltools.models.graph_models.graph_neural_network) MolecularCrystalGraphModel (class in mxtaltools.models.graph_models.molecule_graph_model) MolecularCrystalModel (class in mxtaltools.models.task_models.crystal_models) molecule_cluster_dataset_processing() (mxtaltools.dataset_utils.dataset_manager.DataManager method) molecule_cluster_edge_indexing() (mxtaltools.dataset_utils.dataset_manager.DataManager method) MoleculeClusterClassifier (class in mxtaltools.models.task_models.mol_classifier) MoleculeClusterModel (class in mxtaltools.models.graph_models.molecule_graph_model) MoleculeScalarRegressor (class in mxtaltools.models.task_models.regression_models) mxtaltools.common.adaptive_batching module mxtaltools.common.ase_interface module mxtaltools.common.clustering module mxtaltools.common.config_processing module

mxtaltools.common.ellipsoid_ops module mxtaltools.common.geometry_utils module mxtaltools.common.mol_classifier_utils module mxtaltools.common.sym_utils module mxtaltools.common.training_utils module mxtaltools.common.utils module mxtaltools.constants.asymmetric_units module mxtaltools.constants.atom_properties module mxtaltools.constants.classifier_constants module mxtaltools.constants.csd_stats module mxtaltools.constants.mol_classifier_constants module mxtaltools.constants.space_group_info module mxtaltools.constants.space_group_reference module mxtaltools.crystal_building.crystal_latent_transforms module mxtaltools.crystal_building.utils module mxtaltools.crystal_search.crystal_opt_utils module mxtaltools.dataset_utils.dataset_manager module mxtaltools.dataset_utils.utils module mxtaltools.mlip_interfaces.mace_utils module mxtaltools.models.autoencoder_utils module mxtaltools.models.functions.minimum_image_neighbors module mxtaltools.models.functions.radial_graph module mxtaltools.models.graph_models.base_graph_model module mxtaltools.models.graph_models.graph_neural_network module mxtaltools.models.graph_models.molecule_graph_model module mxtaltools.models.modules.augmented_softmax_aggregator module mxtaltools.models.modules.basis_functions module mxtaltools.models.modules.components module mxtaltools.models.modules.graph_convolution module mxtaltools.models.modules.vector_LayerNorm module mxtaltools.models.task_models.autoencoder_models module mxtaltools.models.task_models.crystal_models module mxtaltools.models.task_models.embedding_regression_models module mxtaltools.models.task_models.mol_classifier module mxtaltools.models.task_models.regression_models module mxtaltools.models.utils module

N

namespace2dict() (in module mxtaltools.common.utils) nan_hook() (in module mxtaltools.common.geometry_utils) NiggliTransform (class in mxtaltools.crystal_building.crystal_latent_transforms)

norm_circular_components() (in module mxtaltools.common.geometry_utils) norm_scores() (in module mxtaltools.models.utils) Normalization (class in mxtaltools.models.modules.components) normalize_np() (in module mxtaltools.common.utils)

O

OOMRetry (class in mxtaltools.common.training_utils)

P

parameterize_crystal_batch() (in module mxtaltools.crystal_building.utils) pare_cluster_radius() (in module mxtaltools.common.mol_classifier_utils) pare_fragmented_molecules() (in module mxtaltools.common.mol_classifier_utils) parse_mc_step() (in module mxtaltools.crystal_search.crystal_opt_utils) parse_to_torch() (in module mxtaltools.common.utils) periodize_molecular_crystal() (mxtaltools.models.graph_models.graph_neural_network.MolCrystalScalarGNN method) PhiTransform (class in mxtaltools.crystal_building.crystal_latent_transforms)

polar_to_std_normal() (mxtaltools.crystal_building.crystal_latent_transforms.RotationTransform method) print_dict() (in module mxtaltools.common.config_processing) probe_compute_molecule_volume() (in module mxtaltools.common.geometry_utils) ProbitTransform (class in mxtaltools.crystal_building.crystal_latent_transforms) process_main_config() (in module mxtaltools.common.config_processing) process_new_dataset() (mxtaltools.dataset_utils.dataset_manager.DataManager method) process_trajectory_results_dict() (in module mxtaltools.common.mol_classifier_utils) protonate_mol() (in module mxtaltools.crystal_building.utils)

Q

quick_combine_crystal_embedding_dataloaders() (in module mxtaltools.dataset_utils.utils)

quick_combine_dataloaders() (in module mxtaltools.dataset_utils.utils)

R

radial_embedding() (mxtaltools.models.graph_models.graph_neural_network.MolCrystalScalarGNN method) (mxtaltools.models.graph_models.graph_neural_network.ScalarGNN method) (mxtaltools.models.graph_models.graph_neural_network.VectorGNN method) RAW_ASYM_UNITS (in module mxtaltools.constants.asymmetric_units) rebuild_crystal_indices() (mxtaltools.dataset_utils.dataset_manager.DataManager method) record_step_results() (in module mxtaltools.common.mol_classifier_utils) reindex_molecules() (in module mxtaltools.common.mol_classifier_utils) reindex_mols() (in module mxtaltools.common.mol_classifier_utils) reload_model() (in module mxtaltools.common.mol_classifier_utils) (in module mxtaltools.common.training_utils) remove_zpg1_info() (mxtaltools.dataset_utils.dataset_manager.DataManager method) renormalize_generated_cell_params() (in module mxtaltools.models.utils)

repeat_interleave() (in module mxtaltools.common.utils) rescale_asymmetric_unit() (in module mxtaltools.crystal_building.utils) reset_parameters() (mxtaltools.models.modules.augmented_softmax_aggregator.AugSoftmaxAggregation method) (mxtaltools.models.modules.augmented_softmax_aggregator.VectorAugSoftmaxAggregation method) (mxtaltools.models.modules.basis_functions.BesselBasisLayer method) (mxtaltools.models.modules.vector_LayerNorm.VectorLayerNorm method) ResidualMLP (class in mxtaltools.models.modules.components) rotation_to_std_normal() (mxtaltools.crystal_building.crystal_latent_transforms.RotationTransform method) RotationTransform (class in mxtaltools.crystal_building.crystal_latent_transforms) rotmat2rotvec() (in module mxtaltools.common.geometry_utils) rotvec2rotmat() (in module mxtaltools.common.geometry_utils) RTransform (class in mxtaltools.crystal_building.crystal_latent_transforms)

S

safe_batched_eigh() (in module mxtaltools.common.geometry_utils) sample_random_valid_rotvecs() (in module mxtaltools.common.geometry_utils) sample_triangular_right() (in module mxtaltools.common.ellipsoid_ops) (in module mxtaltools.common.utils) sample_uniform() (in module mxtaltools.common.utils) save_checkpoint() (in module mxtaltools.common.training_utils) ScalarGNN (class in mxtaltools.models.graph_models.graph_neural_network) Scalarizer (class in mxtaltools.models.modules.components) scalarMLP (class in mxtaltools.models.modules.components) ScalarMoleculeGraphModel (class in mxtaltools.models.graph_models.molecule_graph_model) scale_bh_energy() (in module mxtaltools.common.utils) scatter_compute_Ip() (in module mxtaltools.common.geometry_utils) set_lr() (in module mxtaltools.common.training_utils) siginv() (in module mxtaltools.common.utils) signed_log() (in module mxtaltools.common.utils) simple_latent_distance() (in module mxtaltools.common.geometry_utils) SimpleDataset (class in mxtaltools.dataset_utils.utils) single_molecule_principal_axes_torch() (in module mxtaltools.common.geometry_utils)

slash_batch() (in module mxtaltools.common.training_utils) smooth_constraint() (in module mxtaltools.common.utils) softmax_and_score() (in module mxtaltools.models.utils) softmax_np() (in module mxtaltools.common.utils) softplus_shift() (in module mxtaltools.common.utils) sph2cart_rotvec() (in module mxtaltools.common.geometry_utils) sph_rotvec2lat() (in module mxtaltools.common.geometry_utils) SPMaceCalculator (class in mxtaltools.mlip_interfaces.mace_utils) spoof_gpu_compute() (in module mxtaltools.common.training_utils) spoof_gpu_memory() (in module mxtaltools.common.training_utils) spoof_usage() (in module mxtaltools.common.training_utils) SquashingTransform (class in mxtaltools.crystal_building.crystal_latent_transforms) stacked() (mxtaltools.crystal_search.crystal_opt_utils.CrystalParams method) standardize() (mxtaltools.models.graph_models.base_graph_model.BaseGraphModel method) standardize_np() (in module mxtaltools.common.utils) std_normal_to_azimuth() (mxtaltools.crystal_building.crystal_latent_transforms.RotationTransform method) std_normal_to_polar() (mxtaltools.crystal_building.crystal_latent_transforms.RotationTransform method) std_normal_to_rotation() (mxtaltools.crystal_building.crystal_latent_transforms.RotationTransform method) std_normal_to_uniform() (in module mxtaltools.common.utils)

T

test_decoder_equivariance() (in module mxtaltools.models.autoencoder_utils) test_encoder_equivariance() (in module mxtaltools.models.autoencoder_utils) test_gradient_flow() (in module mxtaltools.models.utils) ThetaTransform (class in mxtaltools.crystal_building.crystal_latent_transforms)

torch_ptp() (in module mxtaltools.common.utils) trailing_relative_diffs() (in module mxtaltools.common.ellipsoid_ops) traj_fig() (in module mxtaltools.crystal_search.crystal_opt_utils) truncate_and_shuffle_dataset() (mxtaltools.dataset_utils.dataset_manager.DataManager method)

U

ucell2cluster() (in module mxtaltools.crystal_building.utils) undo_1d_bound() (in module mxtaltools.models.utils) uniform_to_azimuth() (mxtaltools.crystal_building.crystal_latent_transforms.RotationTransform method) uniform_to_std_normal() (in module mxtaltools.common.utils) UnitToPMUnit (class in mxtaltools.crystal_building.crystal_latent_transforms)

UnitTransform (class in mxtaltools.crystal_building.crystal_latent_transforms) update_dataloader_batch_size() (in module mxtaltools.dataset_utils.utils) update_params() (mxtaltools.crystal_search.crystal_opt_utils.CrystalParams method) update_record() (in module mxtaltools.crystal_search.crystal_opt_utils) update_stats_dict() (in module mxtaltools.common.training_utils)

V

v_MConv (class in mxtaltools.models.modules.graph_convolution) VectorActivation (class in mxtaltools.models.modules.components) VectorAugSoftmaxAggregation (class in mxtaltools.models.modules.augmented_softmax_aggregator)

VectorGNN (class in mxtaltools.models.graph_models.graph_neural_network) VectorLayerNorm (class in mxtaltools.models.modules.vector_LayerNorm) vectorMLP (class in mxtaltools.models.modules.components) VectorMoleculeGraphModel (class in mxtaltools.models.graph_models.molecule_graph_model)

W

weight_reset() (in module mxtaltools.common.training_utils)

wrap_to_pi() (mxtaltools.crystal_building.crystal_latent_transforms.RotationTransform method) write_non_overlapping_configs() (in module mxtaltools.common.config_processing)