HappyDoc Generated Documentation ./CrystalContacts/crystal.py

. / CrystalContacts / crystal.py 

Functions   
  nearby_asymmetric_units 
nearby_asymmetric_units ( molecule,  distance )

Find nearby asymmetric units in a crystal by looking for overlapping bounding boxes. Contacts with each non-crystallographic symmetry (NCS) position are considered. Returns a list of triples, the first item being the NCS matrix, the second being a another matrix for symmetry placing an asymmetric unit nearby, and the third being identifiers for these two matrices positions (NCS1, NCS2, SMTRY2, unitcell2). The matrices are relative to the given molecule's local coordinates.

  create_unit_cell 
create_unit_cell (
        marker_set,
        axes,
        color,
        thickness,
        )

Create markers and links outlining unit cell.

  bounding_box 
bounding_box ( xyz )
  asymmetric_unit_contacts 
asymmetric_unit_contacts (
        molecule,
        distance,
        angle_tolerance,
        shift_tolerance,
        )

Angle and shift tolerance values are used to eliminate equivalent pairs of asymmetric units.

  translate_matrix 
translate_matrix ( t,  m )
  zoom_to_fit 
zoom_to_fit ( padding )
  pad_box 
pad_box ( box,  padding )
  unit_cell_translation 
unit_cell_translation ( ijk,  axes )

Translation vector for a unit cell with given indices.

  nearby_boxes 
nearby_boxes ( box,  crystal )

Apply crystal symmetry to given box and find all boxes that intersect any NCS symmetry of the given box.

  atom_coordinates 
atom_coordinates ( atoms )
  zero_translation 
zero_translation ( m )
  unique_asymmetric_unit_pairs 
unique_asymmetric_unit_pairs (
        plist,
        angle_tolerance,
        shift_tolerance,
        )

Group pairs of asymmetric units that have the same relative orientation together.

  transformed_bounding_box 
transformed_bounding_box ( box,  tf )
  crystal_contact_atoms 
crystal_contact_atoms (
        molecule,
        distance,
        angle_tolerance=None,
        shift_tolerance=None,
        )

Find the atoms of the asymmetric unit that make contacts with other asymmetric units anywhere in the crystal.

  contacting_asymmetric_units 
contacting_asymmetric_units (
        clist,
        crystal,
        include_000_unit_cell=None,
        )

From list of clashing pairs of asymmetric units determine list of asymmetric units to display.

  contact_marker_model 
contact_marker_model (
        molecule,
        crystal,
        clist,
        asu_list,
        )
  average_xyz 
average_xyz ( xyz )
  transform_as_numeric_array 
transform_as_numeric_array ( tf )
  make_asu_copies 
make_asu_copies (
        m,
        asu_list,
        crystal,
        )
  print_matrix 
print_matrix ( m,  format )
  contacting_asu 
contacting_asu ( clist )
  basis_coordinate_transform 
basis_coordinate_transform ( axes )

Transformation from xyz position to unit cell indices.

  distance 
distance ( xyz1,  xyz2 )
  check_orthogonality 
check_orthogonality (
        matrices,
        name,
        tolerance,
        )
  make_molecule_copies 
make_molecule_copies (
        m,
        xflist,
        names,
        )
  create_asymmetric_unit_markers 
create_asymmetric_unit_markers (
        marker_set,
        asu_list,
        asu_center,
        identity_smtry_index,
        rgba_ncs,
        rgba_uc,
        rgba_ouc,
        radius_ncs,
        radius_copies,
        )

Create a sphere representing each asymmetric unit. The sphere is created using the volume path tracer module.

  identity_matrix_index 
identity_matrix_index ( matrices )
  overlapping_translations 
overlapping_translations (
        box1,
        box2,
        axes,
        )

Boxes are in crystal axes coordinates.

  report_crystal_contacts 
report_crystal_contacts (
        molecule,
        distance,
        angle_tolerance=None,
        shift_tolerance=None,
        )

Determine clashing asymmetric units and print a text list of clashing pairs having unique relative orientations.

  box_center 
box_center ( box )
  show_crystal_contacts 
show_crystal_contacts (
        molecule,
        dist,
        make_copies=None,
        angle_tolerance=None,
        shift_tolerance=None,
        replace=None,
        )

Create a ball and stick model where balls represent asymmetric units of a crystal structure and sticks connect clashing asymmetric units. Or make copies of contacting asymmetric units.

  create_clash_links 
create_clash_links (
        clist,
        n,
        link_radius,
        link_rgba,
        markers,
        )

Create cylinders connecting spheres representing asymmetric unit that have close atomic contacts. The cylinders are volume path tracer links.

Classes   

Crystal

Symmetry matrices and crystal parameters from PDB header.

NCS_Asymmetric_Unit

Non-crystallographic symmetry (NCS) asymmetric unit.


This document was automatically generated Wed Jul 9 15:49:37 2008 by HappyDoc version 3.1