average_map_value_at_atom_positions ( atoms )

shift_and_angle ( tf,  center )

apply_transform ( tf,  xyz_array )

atom_molecules ( atoms )

step_to_maximum (
        xyz_array,
        data_array,
        xyz_to_ijk_transform,
        steps,
        ijk_step_size,
        optimize_translation,
        optimize_rotation,
        rotation_center,
        )

interpolated_gradients (
        data_array,
        xyz_to_ijk_transform,
        xyz_array,
        )

rotation_step (
        xyz_array,
        center,
        data_array,
        xyz_to_ijk_transform,
        ijk_step_size,
        )

average_map_value (
        xyz_array,
        xyz_to_ijk_transform,
        data_array,
        )

translation_step (
        xyz_array,
        center,
        data_array,
        xyz_to_ijk_transform,
        ijk_step_size,
        )

locate_maximum (
        xyz_array,
        data_array,
        xyz_to_ijk_transform,
        max_steps,
        ijk_step_size_min,
        ijk_step_size_max,
        optimize_translation,
        optimize_rotation,
        request_stop_cb,
        )

Find transformation to move to local sum of densities maximum. Take gradient steps of fixed length and cut step length when several steps in a row produce little overall motion.

motion_to_maximum (
        atoms,
        data_region,
        max_steps,
        ijk_step_size_min,
        ijk_step_size_max,
        optimize_translation,
        optimize_rotation,
        request_stop_cb=None,
        )

maximum_ijk_motion (
        xyz_array,
        xyz_to_ijk_transform,
        move_tf,
        )

angle_step (
        axis,
        xyz_array,
        center,
        xyz_to_ijk_transform,
        ijk_step_size,
        )

Return angle such that rotating point about given axis and center causes the largest motion in ijk space to equal ijk_step_size.

cross_product_transform ( u )

atom_coordinates ( atoms )

move_selected_atoms_to_maximum (
        max_steps=100,
        ijk_step_size_min=0.01,
        ijk_step_size_max=0.5,
        optimize_translation=True,
        optimize_rotation=True,
        request_stop_cb=None,
        )

norm ( u )

data_region_xyz_to_ijk_transform ( data_region )

remove_duplicates ( seq )

rotation_transform (
        axis,
        angle,
        center,
        )

cross_products ( u,  v )

maximum_norm ( v )

cross_product ( u,  v )

volume_data_region ()

ChimeraExtension.py

gui.py