Index _ | A | B | C | D | E | F | G | J | L | M | N | O | P | Q | R | S | T | U | V | W _ __call__() (shepherd_score.evaluations.docking.docking.VinaSmiles method) __init__() (shepherd_score.container._core.Molecule method) (shepherd_score.container._core.MoleculePair method) (shepherd_score.evaluations.docking.docking.VinaBase method) (shepherd_score.evaluations.docking.docking.VinaSmiles method) (shepherd_score.evaluations.docking.pipelines.DockingEvalPipeline method) (shepherd_score.evaluations.evaluate.evals.ConditionalEval method) (shepherd_score.evaluations.evaluate.evals.ConfEval method) (shepherd_score.evaluations.evaluate.evals.ConsistencyEval method) (shepherd_score.evaluations.evaluate.pipelines.ConditionalEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.ConsistencyEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.UnconditionalEvalPipeline method) A align_with_esp() (shepherd_score.container._batch.MoleculePairBatch method) (shepherd_score.container._core.MoleculePair method) align_with_esp_combo() (shepherd_score.container._core.MoleculePair method) align_with_pharm() (shepherd_score.container._batch.MoleculePairBatch method) (shepherd_score.container._core.MoleculePair method) align_with_surf() (shepherd_score.container._batch.MoleculePairBatch method) (shepherd_score.container._core.MoleculePair method) align_with_vol() (shepherd_score.container._batch.MoleculePairBatch method) (shepherd_score.container._core.MoleculePair method) align_with_vol_esp() (shepherd_score.container._batch.MoleculePairBatch method) (shepherd_score.container._core.MoleculePair method) AlignmentResult (class in shepherd_score.container._core) angle_between_vecs() (in module shepherd_score.alignment.utils.pca) angle_between_vecs_jax() (in module shepherd_score.alignment.utils.pca_jax) angle_between_vecs_np() (in module shepherd_score.alignment.utils.pca_np) apply_SE3_transform() (in module shepherd_score.alignment.utils.se3) apply_SE3_transform_jax() (in module shepherd_score.alignment.utils.se3_jax) apply_SE3_transform_np() (in module shepherd_score.alignment.utils.se3_np) apply_SO3_transform() (in module shepherd_score.alignment.utils.se3) apply_SO3_transform_jax() (in module shepherd_score.alignment._jax) apply_SO3_transform_np() (in module shepherd_score.alignment.utils.se3_np) apply_tanimoto_chain_rule() (in module shepherd_score.score.analytical_gradients) apply_tversky_chain_rule() (in module shepherd_score.score.analytical_gradients) atom_ids (shepherd_score.pharm_utils.pharmacophore.Pharmacophore attribute) B batched_obj_esp_combo_score_helper() (in module shepherd_score.alignment._jax) batched_obj_pharm_overlay_helper() (in module shepherd_score.alignment._jax) batched_obj_ROCS_esp_overlay_helper() (in module shepherd_score.alignment._jax) batched_obj_ROCS_esp_overlay_precomputed() (in module shepherd_score.alignment._jax) batched_obj_ROCS_esp_overlay_precomputed_mask() (in module shepherd_score.alignment._jax) batched_obj_ROCS_overlay_helper() (in module shepherd_score.alignment._jax) batched_obj_ROCS_overlay_precomputed() (in module shepherd_score.alignment._jax) batched_obj_ROCS_overlay_precomputed_mask() (in module shepherd_score.alignment._jax) batched_obj_ROCS_overlay_with_avoid_helper() (in module shepherd_score.alignment._jax) batched_obj_ROCS_overlay_with_avoid_precomputed() (in module shepherd_score.alignment._jax) benchmark() (shepherd_score.evaluations.docking.pipelines.DockingEvalPipeline method) build_lookup_tables() (in module shepherd_score.score.analytical_gradients) build_lookup_tables_cached() (in module shepherd_score.score.analytical_gradients) C center_to() (shepherd_score.container._core.Molecule method) charges_from_single_point_conformer_with_xtb() (in module shepherd_score.conformer_generation) chimera_from_atom_sample() (in module shepherd_score.visualize) chimera_from_mol() (in module shepherd_score.visualize) chimera_from_molecule() (in module shepherd_score.visualize) chimera_from_sample() (in module shepherd_score.visualize) cluster_conformers_butina() (in module shepherd_score.conformer_generation) collate_npz_files() (in module shepherd_score.evaluations.utils.convert_data) color_pcd_with_electrostatics() (in module shepherd_score.generate_point_cloud) compute_analytical_grad_se3() (in module shepherd_score.score.analytical_gradients) compute_analytical_grad_se3_esp() (in module shepherd_score.score.analytical_gradients) compute_analytical_grad_se3_shape() (in module shepherd_score.score.analytical_gradients) compute_analytical_grad_se3_shape_with_avoid() (in module shepherd_score.score.analytical_gradients) compute_avoid_and_grad() (in module shepherd_score.score.analytical_gradients) compute_moment_of_inertia() (in module shepherd_score.alignment.utils.pca) compute_moment_of_inertia_jax() (in module shepherd_score.alignment.utils.pca_jax) compute_moment_of_inertia_np() (in module shepherd_score.alignment.utils.pca_np) compute_overlap_and_grad_pharm() (in module shepherd_score.score.analytical_gradients) compute_overlap_and_grad_shape() (in module shepherd_score.score.analytical_gradients) compute_principal_moments_of_interia() (in module shepherd_score.alignment.utils.pca) compute_principal_moments_of_interia_jax() (in module shepherd_score.alignment.utils.pca_jax) compute_principal_moments_of_interia_np() (in module shepherd_score.alignment.utils.pca_np) compute_self_overlaps_esp() (in module shepherd_score.score.analytical_gradients) compute_self_overlaps_pharm() (in module shepherd_score.score.analytical_gradients) compute_self_overlaps_shape() (in module shepherd_score.score.analytical_gradients) ConditionalEval (class in shepherd_score.evaluations.evaluate.evals) ConditionalEvalPipeline (class in shepherd_score.evaluations.evaluate.pipelines) conf_to_mol() (in module shepherd_score.conformer_generation) ConfEval (class in shepherd_score.evaluations.evaluate.evals) ConsistencyEval (class in shepherd_score.evaluations.evaluate.evals) ConsistencyEvalPipeline (class in shepherd_score.evaluations.evaluate.pipelines) convert_to_jnp_array() (in module shepherd_score.alignment._jax) crippen_align() (in module shepherd_score.alignment) D dock_ligand() (shepherd_score.evaluations.docking.docking.VinaBase method) DockingEvalPipeline (class in shepherd_score.evaluations.docking.pipelines) draw() (in module shepherd_score.visualize) draw_2d_highlight() (in module shepherd_score.visualize) draw_2d_valid() (in module shepherd_score.visualize) draw_atom_sample() (in module shepherd_score.visualize) draw_mol() (in module shepherd_score.visualize) draw_molecule() (in module shepherd_score.visualize) draw_pharm() (in module shepherd_score.visualize) draw_pharmacophores() (in module shepherd_score.visualize) draw_sample() (in module shepherd_score.visualize) draw_surface() (in module shepherd_score.visualize) E embed_conformer() (in module shepherd_score.conformer_generation) embed_conformer_from_smiles() (in module shepherd_score.conformer_generation) embed_conformer_from_smiles_fixed() (in module shepherd_score.evaluations.docking.docking) esp (shepherd_score.container.profiles.Surface attribute) esp_combo_score() (in module shepherd_score.score.electrostatic_scoring) esp_combo_score_jax() (in module shepherd_score.score.electrostatic_scoring_jax) esp_combo_score_np() (in module shepherd_score.score.electrostatic_scoring_np) evaluate() (shepherd_score.evaluations.docking.pipelines.DockingEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.ConditionalEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.ConsistencyEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.UnconditionalEvalPipeline method) evaluate_relax() (shepherd_score.evaluations.docking.pipelines.DockingEvalPipeline method) extract_mol_from_xyz_block() (in module shepherd_score.evaluations.utils.convert_data) F find_hydrophobes() (in module shepherd_score.pharm_utils.pharmacophore) force_neutralize() (in module shepherd_score.protonation.protonate) G generate_conformer_ensemble() (in module shepherd_score.conformer_generation) generate_opt_conformers() (in module shepherd_score.conformer_generation) generate_opt_conformers_xtb() (in module shepherd_score.conformer_generation) get_atom_coords() (in module shepherd_score.generate_point_cloud) get_atomic_vdw_radii() (in module shepherd_score.generate_point_cloud) get_attr() (shepherd_score.evaluations.evaluate.pipelines.ConditionalEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.UnconditionalEvalPipeline method) get_charges() (shepherd_score.container._core.Molecule method) get_diversity() (shepherd_score.evaluations.evaluate.pipelines.ConditionalEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.UnconditionalEvalPipeline method) get_electrostatic_potential() (in module shepherd_score.extract_profiles) (shepherd_score.container._core.Molecule method) get_electrostatics() (in module shepherd_score.generate_point_cloud) get_electrostatics_given_point_charges() (in module shepherd_score.generate_point_cloud) get_frac_consistent_graph() (shepherd_score.evaluations.evaluate.pipelines.ConditionalEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.UnconditionalEvalPipeline method) get_frac_unique() (shepherd_score.evaluations.evaluate.pipelines.ConditionalEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.UnconditionalEvalPipeline method) get_frac_unique_post_opt() (shepherd_score.evaluations.evaluate.pipelines.ConditionalEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.UnconditionalEvalPipeline method) get_frac_valid() (shepherd_score.evaluations.evaluate.pipelines.ConditionalEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.UnconditionalEvalPipeline method) get_frac_valid_post_opt() (shepherd_score.evaluations.evaluate.pipelines.ConditionalEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.UnconditionalEvalPipeline method) get_interaction_properties() (in module shepherd_score.score.pharmacophore_scoring_jax) get_linear_hard_sphere_overlap() (in module shepherd_score.score.gaussian_overlap) get_linear_hard_sphere_overlap_jax() (in module shepherd_score.score.gaussian_overlap_jax) get_linear_hard_sphere_overlap_np() (in module shepherd_score.score.gaussian_overlap_np) get_max_overlap() (in module shepherd_score.score.gaussian_overlap) get_max_overlap_jax() (in module shepherd_score.score.gaussian_overlap_jax) get_max_overlap_np() (in module shepherd_score.score.gaussian_overlap_np) get_mol_from_atom_pos() (in module shepherd_score.evaluations.utils.convert_data) get_molecular_surface() (in module shepherd_score.generate_point_cloud) get_molecular_surface_const_density() (in module shepherd_score.generate_point_cloud) get_molecular_surface_point_cloud() (in module shepherd_score.generate_point_cloud) get_molecular_surface_point_cloud_const_density() (in module shepherd_score.generate_point_cloud) get_molecular_volume() (in module shepherd_score.generate_point_cloud) get_overlap() (in module shepherd_score.score.gaussian_overlap) get_overlap_batch() (in module shepherd_score.score.gaussian_overlap) get_overlap_esp() (in module shepherd_score.score.electrostatic_scoring) get_overlap_esp_jax() (in module shepherd_score.score.electrostatic_scoring_jax) get_overlap_esp_jax_mask() (in module shepherd_score.score.electrostatic_scoring_jax) get_overlap_esp_np() (in module shepherd_score.score.electrostatic_scoring_np) get_overlap_full() (in module shepherd_score.score.gaussian_overlap) get_overlap_jax() (in module shepherd_score.score.gaussian_overlap_jax) get_overlap_jax_mask() (in module shepherd_score.score.gaussian_overlap_jax) get_overlap_np() (in module shepherd_score.score.gaussian_overlap_np) get_overlap_pharm() (in module shepherd_score.score.pharmacophore_scoring) get_overlap_pharm_jax() (in module shepherd_score.score.pharmacophore_scoring_jax) get_overlap_pharm_jax_vectorized() (in module shepherd_score.score.pharmacophore_scoring_jax) get_overlap_pharm_jax_vectorized_mask() (in module shepherd_score.score.pharmacophore_scoring_jax) get_overlap_pharm_np() (in module shepherd_score.score.pharmacophore_scoring_np) get_partial_charges() (shepherd_score.container._core.Molecule method) get_pc() (shepherd_score.container._core.Molecule method) get_pharm_combo_score() (in module shepherd_score.score.pharmacophore_scoring) (in module shepherd_score.score.pharmacophore_scoring_np) get_pharm_combo_score_jax() (in module shepherd_score.score.pharmacophore_scoring_jax) get_pharmacophore() (shepherd_score.container._core.Molecule method) get_pharmacophores() (in module shepherd_score.pharm_utils.pharmacophore) get_pharmacophores_dict() (in module shepherd_score.pharm_utils.pharmacophore) get_point_cloud() (in module shepherd_score.generate_point_cloud) get_positions() (shepherd_score.container._core.Molecule method) get_sample_atom_volume() (in module shepherd_score.generate_point_cloud) get_SE3_transform() (in module shepherd_score.alignment.utils.se3) get_SE3_transform_jax() (in module shepherd_score.alignment.utils.se3_jax) get_SE3_transform_np() (in module shepherd_score.alignment.utils.se3_np) get_smiles_from_atom_pos() (in module shepherd_score.evaluations.utils.convert_data) get_transformed_mol_and_feats() (shepherd_score.container._core.MoleculePair method) get_transformed_molecule() (shepherd_score.container._core.MoleculePair method) get_vector_volume_overlap_score() (in module shepherd_score.score.pharmacophore_scoring) get_vector_volume_overlap_score_batch() (in module shepherd_score.score.pharmacophore_scoring) get_vector_volume_overlap_score_jax() (in module shepherd_score.score.pharmacophore_scoring_jax) get_vector_volume_overlap_score_np() (in module shepherd_score.score.pharmacophore_scoring_np) get_volume_overlap_score() (in module shepherd_score.score.pharmacophore_scoring) get_volume_overlap_score_batch() (in module shepherd_score.score.pharmacophore_scoring) get_volume_overlap_score_extended_points() (in module shepherd_score.score.pharmacophore_scoring) get_volume_overlap_score_extended_points_jax() (in module shepherd_score.score.pharmacophore_scoring_jax) get_volume_overlap_score_extended_points_np() (in module shepherd_score.score.pharmacophore_scoring_np) get_volume_overlap_score_jax() (in module shepherd_score.score.pharmacophore_scoring_jax) get_volume_overlap_score_np() (in module shepherd_score.score.pharmacophore_scoring_np) get_xyz_content() (in module shepherd_score.evaluations.utils.convert_data) get_xyz_content_with_dummy() (in module shepherd_score.evaluations.utils.convert_data) GetAcceptor1FeatVects() (in module shepherd_score.pharm_utils.pharmvec) GetAcceptor1FeatVects_single() (in module shepherd_score.pharm_utils.pharmvec) GetAcceptor2FeatVects() (in module shepherd_score.pharm_utils.pharmvec) GetAcceptor2FeatVects_single() (in module shepherd_score.pharm_utils.pharmvec) GetAcceptor3FeatVects() (in module shepherd_score.pharm_utils.pharmvec) GetAcceptor3FeatVects_single() (in module shepherd_score.pharm_utils.pharmvec) GetAcceptorFeatVects() (in module shepherd_score.pharm_utils.pharmvec) GetAromaticFeatVects() (in module shepherd_score.pharm_utils.pharmvec) GetDonor1FeatVects_single() (in module shepherd_score.pharm_utils.pharmvec) GetDonor2FeatVects_single() (in module shepherd_score.pharm_utils.pharmvec) GetDonor3FeatVects_single() (in module shepherd_score.pharm_utils.pharmvec) GetDonorFeatVects() (in module shepherd_score.pharm_utils.pharmvec) GetHalogenFeatVects() (in module shepherd_score.pharm_utils.pharmvec) J jax_cdist() (in module shepherd_score.score.gaussian_overlap_jax) jax_sq_cdist() (in module shepherd_score.score.gaussian_overlap_jax) L labels (shepherd_score.pharm_utils.pharmacophore.Pharmacophore attribute) load_ligand_from_sdf() (shepherd_score.evaluations.docking.docking.VinaBase method) load_ligand_from_smiles() (shepherd_score.evaluations.docking.docking.VinaBase method) load_npz_to_df() (in module shepherd_score.evaluations.utils.convert_data) M module shepherd_score.alignment shepherd_score.alignment._jax shepherd_score.alignment._jax_parallel shepherd_score.alignment.utils.pca shepherd_score.alignment.utils.pca_jax shepherd_score.alignment.utils.pca_np shepherd_score.alignment.utils.se3 shepherd_score.alignment.utils.se3_jax shepherd_score.alignment.utils.se3_np shepherd_score.conformer_generation shepherd_score.evaluations.docking.docking shepherd_score.evaluations.docking.pipelines shepherd_score.evaluations.docking.targets shepherd_score.evaluations.evaluate.evals shepherd_score.evaluations.evaluate.pipelines shepherd_score.evaluations.utils.convert_data shepherd_score.extract_profiles shepherd_score.generate_point_cloud shepherd_score.pharm_utils.pharmacophore shepherd_score.pharm_utils.pharmvec shepherd_score.protonation.chemaxon_utils shepherd_score.protonation.molscrub_utils shepherd_score.protonation.protonate shepherd_score.score.analytical_gradients shepherd_score.score.constants shepherd_score.score.electrostatic_scoring shepherd_score.score.electrostatic_scoring_jax shepherd_score.score.electrostatic_scoring_np shepherd_score.score.gaussian_overlap shepherd_score.score.gaussian_overlap_jax shepherd_score.score.gaussian_overlap_np shepherd_score.score.pharmacophore_scoring shepherd_score.score.pharmacophore_scoring_jax shepherd_score.score.pharmacophore_scoring_np shepherd_score.visualize mol (shepherd_score.pharm_utils.pharmacophore.Pharmacophore attribute) mol_with_atom_index() (in module shepherd_score.visualize) Molecule (class in shepherd_score.container._core) MoleculePair (class in shepherd_score.container._core) MoleculePairBatch (class in shepherd_score.container._batch) N neutralize_atoms() (in module shepherd_score.protonation.protonate) O objective_esp_combo_score_overlay() (in module shepherd_score.alignment) objective_esp_combo_score_overlay_jax() (in module shepherd_score.alignment._jax) objective_pharm_overlay() (in module shepherd_score.alignment) objective_pharm_overlay_jax() (in module shepherd_score.alignment._jax) objective_ROCS_esp_overlay() (in module shepherd_score.alignment) objective_ROCS_esp_overlay_jax() (in module shepherd_score.alignment._jax) objective_ROCS_esp_overlay_precomputed_jax() (in module shepherd_score.alignment._jax) objective_ROCS_esp_overlay_precomputed_jax_mask() (in module shepherd_score.alignment._jax) objective_ROCS_overlay() (in module shepherd_score.alignment) objective_ROCS_overlay_jax() (in module shepherd_score.alignment._jax) objective_ROCS_overlay_precomputed_jax() (in module shepherd_score.alignment._jax) objective_ROCS_overlay_precomputed_jax_mask() (in module shepherd_score.alignment._jax) objective_ROCS_overlay_with_avoid() (in module shepherd_score.alignment) objective_ROCS_overlay_with_avoid_jax() (in module shepherd_score.alignment._jax) objective_ROCS_overlay_with_avoid_precomputed_jax() (in module shepherd_score.alignment._jax) optimize_conformer_ensemble_with_xtb() (in module shepherd_score.conformer_generation) optimize_conformer_with_xtb() (in module shepherd_score.conformer_generation) optimize_conformer_with_xtb_from_xyz_block() (in module shepherd_score.conformer_generation) optimize_esp_combo_score_overlay() (in module shepherd_score.alignment) optimize_esp_combo_score_overlay_jax() (in module shepherd_score.alignment._jax) optimize_ligand() (shepherd_score.evaluations.docking.docking.VinaBase method) optimize_pharm_overlay() (in module shepherd_score.alignment) optimize_pharm_overlay_analytical() (in module shepherd_score.alignment) optimize_pharm_overlay_jax() (in module shepherd_score.alignment._jax) optimize_pharm_overlay_jax_pharm_shmap() (in module shepherd_score.alignment._jax_parallel) optimize_pharm_overlay_jax_vectorized() (in module shepherd_score.alignment._jax) optimize_pharm_overlay_jax_vectorized_mask() (in module shepherd_score.alignment._jax) optimize_ROCS_esp_overlay() (in module shepherd_score.alignment) optimize_ROCS_esp_overlay_analytical() (in module shepherd_score.alignment) optimize_ROCS_esp_overlay_jax() (in module shepherd_score.alignment._jax) optimize_ROCS_esp_overlay_jax_mask() (in module shepherd_score.alignment._jax) optimize_ROCS_esp_overlay_jax_surf_esp_shmap() (in module shepherd_score.alignment._jax_parallel) optimize_ROCS_esp_overlay_jax_vol_esp_shmap() (in module shepherd_score.alignment._jax_parallel) optimize_ROCS_overlay() (in module shepherd_score.alignment) optimize_ROCS_overlay_analytical() (in module shepherd_score.alignment) optimize_ROCS_overlay_jax() (in module shepherd_score.alignment._jax) optimize_ROCS_overlay_jax_mask() (in module shepherd_score.alignment._jax) optimize_ROCS_overlay_jax_surf_shmap() (in module shepherd_score.alignment._jax_parallel) optimize_ROCS_overlay_jax_vol_shmap() (in module shepherd_score.alignment._jax_parallel) P pattern_of_smarts() (in module shepherd_score.pharm_utils.pharmacophore) pharm_ancs (shepherd_score.container._core.Molecule property) pharm_types (shepherd_score.container._core.Molecule property) pharm_vecs (shepherd_score.container._core.Molecule property) Pharmacophore (class in shepherd_score.pharm_utils.pharmacophore) pharmacophore (shepherd_score.container._core.Molecule property) positions (shepherd_score.container.profiles.Surface attribute) (shepherd_score.pharm_utils.pharmacophore.Pharmacophore attribute) precompute_geometry() (in module shepherd_score.score.pharmacophore_scoring_jax) priority_labels() (shepherd_score.pharm_utils.pharmacophore.Pharmacophore method) priority_pharm_labels() (in module shepherd_score.pharm_utils.pharmacophore) probe_radius (shepherd_score.container._core.Molecule property) (shepherd_score.container.profiles.Surface attribute) project_grad_R_to_quaternion() (in module shepherd_score.score.analytical_gradients) protonate_smiles() (in module shepherd_score.protonation.protonate) Q quaternion_from_axis_angle() (in module shepherd_score.alignment.utils.pca) quaternion_from_axis_angle_jax() (in module shepherd_score.alignment.utils.pca_jax) quaternion_from_axis_angle_np() (in module shepherd_score.alignment.utils.pca_np) quaternion_mult() (in module shepherd_score.alignment.utils.pca) quaternion_mult_jax() (in module shepherd_score.alignment.utils.pca_jax) quaternion_mult_np() (in module shepherd_score.alignment.utils.pca_np) quaternions_for_principal_component_alignment() (in module shepherd_score.alignment.utils.pca) quaternions_for_principal_component_alignment_jax() (in module shepherd_score.alignment.utils.pca_jax) quaternions_for_principal_component_alignment_np() (in module shepherd_score.alignment.utils.pca_np) quaternions_to_rotation_matrix() (in module shepherd_score.alignment.utils.se3) quaternions_to_rotation_matrix_jax() (in module shepherd_score.alignment.utils.se3_jax) quaternions_to_rotation_matrix_np() (in module shepherd_score.alignment.utils.se3_np) R read_multi_xyz_file() (in module shepherd_score.conformer_generation) remove_bad_protomers() (in module shepherd_score.protonation.protonate) resample_surf_scores() (in module shepherd_score.evaluations.evaluate.pipelines) resampling_surf_scores() (shepherd_score.evaluations.evaluate.pipelines.ConditionalEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.ConsistencyEvalPipeline method) resampling_upper_bounds() (shepherd_score.evaluations.evaluate.pipelines.ConsistencyEvalPipeline static method) rotation_axis() (in module shepherd_score.alignment.utils.pca) rotation_axis_jax() (in module shepherd_score.alignment.utils.pca_jax) rotation_axis_np() (in module shepherd_score.alignment.utils.pca_np) rotation_matrix_jacobians_quat() (in module shepherd_score.score.analytical_gradients) run_docking_benchmark() (in module shepherd_score.evaluations.docking.pipelines) run_docking_evaluation() (in module shepherd_score.evaluations.docking.pipelines) run_docking_evaluation_from_smiles() (in module shepherd_score.evaluations.docking.pipelines) S sample_molecular_surface_with_radius() (in module shepherd_score.generate_point_cloud) sample_molecular_surface_with_radius_fibonacci() (in module shepherd_score.generate_point_cloud) save_pose_to_file() (shepherd_score.evaluations.docking.docking.VinaBase method) score (shepherd_score.container._core.AlignmentResult attribute) score_ligand() (shepherd_score.evaluations.docking.docking.VinaBase method) score_ROCS_overlay_with_avoid() (in module shepherd_score.alignment) score_with_esp() (shepherd_score.container._core.MoleculePair method) score_with_pharm() (shepherd_score.container._core.MoleculePair method) score_with_surf() (shepherd_score.container._core.MoleculePair method) set_thread_limits() (in module shepherd_score.conformer_generation) shape_tanimoto() (in module shepherd_score.score.gaussian_overlap) shape_tanimoto_batched() (in module shepherd_score.score.gaussian_overlap) shape_tanimoto_esp() (in module shepherd_score.score.electrostatic_scoring) shape_tanimoto_esp_jax() (in module shepherd_score.score.electrostatic_scoring_jax) shape_tanimoto_esp_jax_mask() (in module shepherd_score.score.electrostatic_scoring_jax) shape_tanimoto_esp_np() (in module shepherd_score.score.electrostatic_scoring_np) shape_tanimoto_full() (in module shepherd_score.score.gaussian_overlap) shape_tanimoto_jax() (in module shepherd_score.score.gaussian_overlap_jax) shape_tanimoto_jax_mask() (in module shepherd_score.score.gaussian_overlap_jax) shape_tanimoto_np() (in module shepherd_score.score.gaussian_overlap_np) shepherd_score.alignment module shepherd_score.alignment._jax module shepherd_score.alignment._jax_parallel module shepherd_score.alignment.utils.pca module shepherd_score.alignment.utils.pca_jax module shepherd_score.alignment.utils.pca_np module shepherd_score.alignment.utils.se3 module shepherd_score.alignment.utils.se3_jax module shepherd_score.alignment.utils.se3_np module shepherd_score.conformer_generation module shepherd_score.evaluations.docking.docking module shepherd_score.evaluations.docking.pipelines module shepherd_score.evaluations.docking.targets module shepherd_score.evaluations.evaluate.evals module shepherd_score.evaluations.evaluate.pipelines module shepherd_score.evaluations.utils.convert_data module shepherd_score.extract_profiles module shepherd_score.generate_point_cloud module shepherd_score.pharm_utils.pharmacophore module shepherd_score.pharm_utils.pharmvec module shepherd_score.protonation.chemaxon_utils module shepherd_score.protonation.molscrub_utils module shepherd_score.protonation.protonate module shepherd_score.score.analytical_gradients module shepherd_score.score.constants module shepherd_score.score.electrostatic_scoring module shepherd_score.score.electrostatic_scoring_jax module shepherd_score.score.electrostatic_scoring_np module shepherd_score.score.gaussian_overlap module shepherd_score.score.gaussian_overlap_jax module shepherd_score.score.gaussian_overlap_np module shepherd_score.score.pharmacophore_scoring module shepherd_score.score.pharmacophore_scoring_jax module shepherd_score.score.pharmacophore_scoring_np module shepherd_score.visualize module sim_aligned_esp (shepherd_score.container._core.MoleculePair property) sim_aligned_esp_combo (shepherd_score.container._core.MoleculePair property) sim_aligned_pharm (shepherd_score.container._core.MoleculePair property) sim_aligned_surf (shepherd_score.container._core.MoleculePair property) sim_aligned_vol (shepherd_score.container._core.MoleculePair property) sim_aligned_vol_esp (shepherd_score.container._core.MoleculePair property) sim_aligned_vol_esp_noH (shepherd_score.container._core.MoleculePair property) sim_aligned_vol_noH (shepherd_score.container._core.MoleculePair property) single_point_xtb_from_xyz() (in module shepherd_score.conformer_generation) surf_esp (shepherd_score.container._core.Molecule property) surf_pos (shepherd_score.container._core.Molecule property) Surface (class in shepherd_score.container.profiles) surface (shepherd_score.container._core.Molecule property) T tanimoto_func() (in module shepherd_score.score.pharmacophore_scoring) tanimoto_func_jax() (in module shepherd_score.score.pharmacophore_scoring_jax) tanimoto_func_np() (in module shepherd_score.score.pharmacophore_scoring_np) tautomerize_chemaxon() (in module shepherd_score.protonation.chemaxon_utils) tautomerize_molscrub() (in module shepherd_score.protonation.molscrub_utils) to_pandas() (shepherd_score.evaluations.docking.pipelines.DockingEvalPipeline method) (shepherd_score.evaluations.evaluate.evals.ConfEval method) (shepherd_score.evaluations.evaluate.pipelines.ConditionalEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.ConsistencyEvalPipeline method) (shepherd_score.evaluations.evaluate.pipelines.UnconditionalEvalPipeline method) to_pandas_relaxed() (shepherd_score.evaluations.docking.pipelines.DockingEvalPipeline method) transform (shepherd_score.container._core.AlignmentResult attribute) transform_esp (shepherd_score.container._core.MoleculePair property) transform_esp_combo (shepherd_score.container._core.MoleculePair property) transform_pharm (shepherd_score.container._core.MoleculePair property) transform_surf (shepherd_score.container._core.MoleculePair property) transform_vol (shepherd_score.container._core.MoleculePair property) transform_vol_esp (shepherd_score.container._core.MoleculePair property) transform_vol_esp_noH (shepherd_score.container._core.MoleculePair property) transform_vol_noH (shepherd_score.container._core.MoleculePair property) tversky_func() (in module shepherd_score.score.pharmacophore_scoring) tversky_func_jax() (in module shepherd_score.score.pharmacophore_scoring_jax) tversky_func_np() (in module shepherd_score.score.pharmacophore_scoring_np) types (shepherd_score.pharm_utils.pharmacophore.Pharmacophore attribute) U UnconditionalEvalPipeline (class in shepherd_score.evaluations.evaluate.pipelines) update_mol_coordinates() (in module shepherd_score.conformer_generation) (in module shepherd_score.container._core) V VAB_2nd_order() (in module shepherd_score.score.gaussian_overlap) VAB_2nd_order_batched() (in module shepherd_score.score.gaussian_overlap) VAB_2nd_order_cosine() (in module shepherd_score.score.gaussian_overlap) VAB_2nd_order_cosine_jax() (in module shepherd_score.score.gaussian_overlap_jax) VAB_2nd_order_cosine_jax_mask() (in module shepherd_score.score.gaussian_overlap_jax) VAB_2nd_order_cosine_mask() (in module shepherd_score.score.gaussian_overlap) VAB_2nd_order_cosine_mask_batch() (in module shepherd_score.score.gaussian_overlap) VAB_2nd_order_cosine_np() (in module shepherd_score.score.gaussian_overlap_np) VAB_2nd_order_esp() (in module shepherd_score.score.electrostatic_scoring) VAB_2nd_order_esp_jax() (in module shepherd_score.score.electrostatic_scoring_jax) VAB_2nd_order_esp_jax_mask() (in module shepherd_score.score.electrostatic_scoring_jax) VAB_2nd_order_esp_np() (in module shepherd_score.score.electrostatic_scoring_np) VAB_2nd_order_full() (in module shepherd_score.score.gaussian_overlap) VAB_2nd_order_jax() (in module shepherd_score.score.gaussian_overlap_jax) VAB_2nd_order_jax_mask() (in module shepherd_score.score.gaussian_overlap_jax) VAB_2nd_order_mask() (in module shepherd_score.score.gaussian_overlap) VAB_2nd_order_mask_batch() (in module shepherd_score.score.gaussian_overlap) VAB_2nd_order_np() (in module shepherd_score.score.gaussian_overlap_np) vectors (shepherd_score.pharm_utils.pharmacophore.Pharmacophore attribute) view_sample_trajectory() (in module shepherd_score.visualize) VinaBase (class in shepherd_score.evaluations.docking.docking) VinaSmiles (class in shepherd_score.evaluations.docking.docking) vmap_angle_between_vecs_jax() (in module shepherd_score.alignment.utils.pca_jax) vmap_apply_SO3_transform_jax() (in module shepherd_score.alignment._jax) vmap_quaternion_from_axis_angle_jax() (in module shepherd_score.alignment.utils.pca_jax) vmap_quaternion_mult_jax() (in module shepherd_score.alignment.utils.pca_jax) vmap_score_ROCS_overlay_with_avoid_jax() (in module shepherd_score.alignment._jax) W write_xyz_file() (in module shepherd_score.evaluations.utils.convert_data) write_xyz_file_with_dummy() (in module shepherd_score.evaluations.utils.convert_data)
