/ . / 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.
|
|
|