average_map_value_at_atom_positions ( atoms )

axis_center_angle_shift ( tf )

Determine the rotation axis, point on axis, rotation angle, and shift along the rotation axis that describes a transform.

map_overlap_and_correlation (
        map1,
        map2,
        above_threshold,
        )

shift_and_angle ( tf,  center )

move_atoms_to_maxima ()

Move selected atoms to local maxima of map shown by volume viewer. Each atom is moved independently.

apply_transform ( tf,  points )

atom_molecules ( atoms )

step_to_maximum (
        points,
        point_weights,
        data_array,
        xyz_to_ijk_transform,
        steps,
        ijk_step_size,
        optimize_translation,
        optimize_rotation,
        rotation_center,
        )

axis_point_adjust ( axis_point,  axis )

Return new axis point on axis with coordinate equal to zero for the largest magnitude component of the axis vector. This makes it easier for users to use the axis point as an offset to describe symmetry axis locations.

rotation_step (
        points,
        point_weights,
        center,
        data_array,
        xyz_to_ijk_transform,
        ijk_step_size,
        )

average_map_value (
        points,
        xyz_to_ijk_transform,
        data_array,
        )

translation_step (
        points,
        point_weights,
        center,
        data_array,
        xyz_to_ijk_transform,
        ijk_step_size,
        )

locate_maximum (
        points,
        point_weights,
        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 (
        points,
        point_weights,
        data_region,
        max_steps,
        ijk_step_size_min,
        ijk_step_size_max,
        optimize_translation,
        optimize_rotation,
        request_stop_cb=None,
        )

maximum_ijk_motion (
        points,
        xyz_to_ijk_transform,
        move_tf,
        )

angle_step (
        axis,
        points,
        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.

float_array ( a )

cross_product_transform ( u )

atom_coordinates ( atoms )

maximum_norm ( v )

volume_data_region ()

atoms_outside_contour ( atoms )

data_region_xyz_to_ijk_transform ( data_region )

remove_duplicates ( seq )

points_outside_contour (
        points,
        xf,
        dr,
        )

rotation_transform (
        axis,
        angle,
        center,
        )

cross_products ( u,  v )

overlap_and_correlation ( v1,  v2 )

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,
        )

cross_product ( u,  v )

norm ( u )

map_points_and_weights ( dr,  above_threshold )

move_atom_to_maximum (
        a,
        max_steps=100,
        ijk_step_size_min=0.001,
        ijk_step_size_max=0.5,
        )

ChimeraExtension.py

gui.py