HappyDoc Generated Documentation ./FitMap

. / FitMap 

Functions   
  average_map_value_at_atom_positions 
average_map_value_at_atom_positions ( atoms,  volume=None )
  axis_center_angle_shift 
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 
map_overlap_and_correlation (
        map1,
        map2,
        above_threshold,
        )
  shift_and_angle 
shift_and_angle ( tf,  center )
  move_atoms_to_maxima 
move_atoms_to_maxima ()

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

  apply_transform 
apply_transform ( tf,  points )
  atom_molecules 
atom_molecules ( atoms )
  step_to_maximum 
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_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 
rotation_step (
        points,
        point_weights,
        center,
        data_array,
        xyz_to_ijk_transform,
        ijk_step_size,
        )
  average_map_value 
average_map_value (
        points,
        xyz_to_ijk_transform,
        data_array,
        )
  translation_step 
translation_step (
        points,
        point_weights,
        center,
        data_array,
        xyz_to_ijk_transform,
        ijk_step_size,
        )
  locate_maximum 
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 
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 
maximum_ijk_motion (
        points,
        xyz_to_ijk_transform,
        move_tf,
        )
  angle_step 
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 
float_array ( a )
  cross_product_transform 
cross_product_transform ( u )
  atom_coordinates 
atom_coordinates ( atoms )
  maximum_norm 
maximum_norm ( v )
  norm 
norm ( u )
  atoms_outside_contour 
atoms_outside_contour ( atoms,  volume=None )
  data_region_xyz_to_ijk_transform 
data_region_xyz_to_ijk_transform ( data_region )
  remove_duplicates 
remove_duplicates ( seq )
  points_outside_contour 
points_outside_contour (
        points,
        xf,
        dr,
        )
  rotation_transform 
rotation_transform (
        axis,
        angle,
        center,
        )
  cross_products 
cross_products ( u,  v )
  move_atoms_to_maximum 
move_atoms_to_maximum (
        atoms,
        volume,
        max_steps=None,
        ijk_step_size_min=None,
        ijk_step_size_max=None,
        optimize_translation=None,
        optimize_rotation=None,
        request_stop_cb=None,
        )
  overlap_and_correlation 
overlap_and_correlation ( v1,  v2 )
  move_selected_atoms_to_maximum 
move_selected_atoms_to_maximum (
        max_steps=None,
        ijk_step_size_min=None,
        ijk_step_size_max=None,
        optimize_translation=None,
        optimize_rotation=None,
        request_stop_cb=None,
        )
  cross_product 
cross_product ( u,  v )
  map_points_and_weights 
map_points_and_weights ( dr,  above_threshold )
  move_atom_to_maximum 
move_atom_to_maximum (
        a,
        max_steps=None,
        ijk_step_size_min=None,
        ijk_step_size_max=None,
        )
Classes   
Python files   

ChimeraExtension.py

gui.py


This document was automatically generated Wed Jul 9 15:49:15 2008 by HappyDoc version 3.1