API Reference#
This section contains the complete API documentation for shepherd-score, automatically generated from the source code docstrings.
Core Modules#
- Container Module
- Conformer Generation
set_thread_limits()update_mol_coordinates()read_multi_xyz_file()embed_conformer()embed_conformer_from_smiles()conf_to_mol()generate_conformer_ensemble()cluster_conformers_butina()optimize_conformer_with_xtb()optimize_conformer_with_xtb_from_xyz_block()charges_from_single_point_conformer_with_xtb()single_point_xtb_from_xyz()optimize_conformer_ensemble_with_xtb()generate_opt_conformers_xtb()generate_opt_conformers()
- Profile Extraction
- extract_profiles
- generate_point_cloud
get_atom_coords()get_atomic_vdw_radii()sample_molecular_surface_with_radius()sample_molecular_surface_with_radius_fibonacci()get_point_cloud()get_molecular_surface_point_cloud()get_molecular_surface()get_molecular_surface_point_cloud_const_density()get_molecular_surface_const_density()get_electrostatics()get_electrostatics_given_point_charges()color_pcd_with_electrostatics()get_sample_atom_volume()get_molecular_volume()
Scoring#
Alignment#
- Alignment Functions
- Main Alignment Module
objective_ROCS_overlay()score_ROCS_overlay_with_avoid()objective_ROCS_overlay_with_avoid()objective_ROCS_esp_overlay()objective_esp_combo_score_overlay()objective_pharm_overlay()crippen_align()optimize_ROCS_overlay()optimize_ROCS_overlay_analytical()optimize_ROCS_esp_overlay()optimize_ROCS_esp_overlay_analytical()optimize_esp_combo_score_overlay()optimize_pharm_overlay()optimize_pharm_overlay_analytical()
- Analytical Gradients
rotation_matrix_jacobians_quat()project_grad_R_to_quaternion()build_lookup_tables_cached()build_lookup_tables()compute_overlap_and_grad_pharm()compute_self_overlaps_pharm()apply_tanimoto_chain_rule()apply_tversky_chain_rule()compute_overlap_and_grad_shape()compute_self_overlaps_shape()compute_self_overlaps_esp()compute_analytical_grad_se3_esp()compute_analytical_grad_se3_shape()compute_avoid_and_grad()compute_analytical_grad_se3_shape_with_avoid()compute_analytical_grad_se3()
- JAX Alignment
apply_SO3_transform_jax()vmap_apply_SO3_transform_jax()batched_obj_ROCS_overlay_helper()vmap_score_ROCS_overlay_with_avoid_jax()batched_obj_ROCS_overlay_with_avoid_helper()objective_ROCS_overlay_jax()objective_ROCS_overlay_with_avoid_jax()batched_obj_ROCS_overlay_precomputed()objective_ROCS_overlay_precomputed_jax()batched_obj_ROCS_overlay_precomputed_mask()objective_ROCS_overlay_precomputed_jax_mask()batched_obj_ROCS_esp_overlay_precomputed()objective_ROCS_esp_overlay_precomputed_jax()batched_obj_ROCS_esp_overlay_precomputed_mask()objective_ROCS_esp_overlay_precomputed_jax_mask()optimize_ROCS_esp_overlay_jax_mask()batched_obj_ROCS_overlay_with_avoid_precomputed()objective_ROCS_overlay_with_avoid_precomputed_jax()optimize_ROCS_overlay_jax()optimize_ROCS_overlay_jax_mask()batched_obj_ROCS_esp_overlay_helper()objective_ROCS_esp_overlay_jax()optimize_ROCS_esp_overlay_jax()batched_obj_esp_combo_score_helper()objective_esp_combo_score_overlay_jax()convert_to_jnp_array()optimize_esp_combo_score_overlay_jax()batched_obj_pharm_overlay_helper()objective_pharm_overlay_jax()optimize_pharm_overlay_jax()optimize_pharm_overlay_jax_vectorized()optimize_pharm_overlay_jax_vectorized_mask()
- JAX Parallel Alignment
- Alignment Utilities
- Main Alignment Module