Alignment Functions#
Functions for aligning molecules based on their interaction profiles.
- 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