HappyDoc Generated Documentation .\FitMap

. / FitMap 

Functions   
  average_map_value_at_atom_positions 
average_map_value_at_atom_positions ( atoms )
  shift_and_angle 
shift_and_angle ( tf,  center )
  apply_transform 
apply_transform ( tf,  xyz_array )
  atom_molecules 
atom_molecules ( atoms )
  step_to_maximum 
step_to_maximum (
        xyz_array,
        data_array,
        xyz_to_ijk_transform,
        steps,
        ijk_step_size,
        optimize_translation,
        optimize_rotation,
        rotation_center,
        )
  interpolated_gradients 
interpolated_gradients (
        data_array,
        xyz_to_ijk_transform,
        xyz_array,
        )
  rotation_step 
rotation_step (
        xyz_array,
        center,
        data_array,
        xyz_to_ijk_transform,
        ijk_step_size,
        )
  average_map_value 
average_map_value (
        xyz_array,
        xyz_to_ijk_transform,
        data_array,
        )
  translation_step 
translation_step (
        xyz_array,
        center,
        data_array,
        xyz_to_ijk_transform,
        ijk_step_size,
        )
  locate_maximum 
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 
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 
maximum_ijk_motion (
        xyz_array,
        xyz_to_ijk_transform,
        move_tf,
        )
  angle_step 
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 
cross_product_transform ( u )
  atom_coordinates 
atom_coordinates ( atoms )
  move_selected_atoms_to_maximum 
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 
norm ( u )
  data_region_xyz_to_ijk_transform 
data_region_xyz_to_ijk_transform ( data_region )
  remove_duplicates 
remove_duplicates ( seq )
  rotation_transform 
rotation_transform (
        axis,
        angle,
        center,
        )
  cross_products 
cross_products ( u,  v )
  maximum_norm 
maximum_norm ( v )
  cross_product 
cross_product ( u,  v )
  volume_data_region 
volume_data_region ()
Classes   
Python files   

ChimeraExtension.py

gui.py


This document was automatically generated Thu Feb 02 15:18:17 2006 by HappyDoc version 3.0.a1