def __init__(self,
model=None,
xray_structure=None,
mask_atoms_atom_radius=None,
n_real=None,
map_manager=None):
'''
Create a mask (map object) with values of 1 near atoms in xray_structure
Parameters are:
model: required source of information about where atoms are
xray_structure: alternate source of information about where atoms are
mask_atoms_atom_radius: radius around atoms to mask
n_real: dimensions of map to create, e.g., existing map_data.all()
map_manager: alternate source of information for n_real. origin (0,0,0)
'''
assert (model is not None) or (xray_structure is not None)
assert mask_atoms_atom_radius is not None
assert (n_real is not None) or (map_manager is not None)
if not n_real:
assert map_manager.map_data().origin() == (0, 0, 0)
n_real = map_manager.map_data().all()
if model:
xray_structure = model.get_xray_structure()
self._crystal_symmetry = model.crystal_symmetry()
else:
self._crystal_symmetry = xray_structure.crystal_symmetry()
import boost.python
cctbx_maptbx_ext = boost.python.import_ext("cctbx_maptbx_ext")
radii = flex.double(xray_structure.sites_frac().size(),
mask_atoms_atom_radius)
self._mask = cctbx_maptbx_ext.mask(
sites_frac=xray_structure.sites_frac(),
unit_cell=xray_structure.unit_cell(),
n_real=n_real,
mask_value_inside_molecule=1,
mask_value_outside_molecule=0,
radii=radii)
# Set up map_manager with this mask
if map_manager:
self._map_manager = map_manager.customized_copy(
map_data=self._mask)
else:
from iotbx.map_manager import map_manager as map_man
self._map_manager = map_man(
map_data=self._mask,
unit_cell_crystal_symmetry=self.crystal_symmetry(),
unit_cell_grid=self._mask.all())
# Initialize soft mask
self._is_soft_mask = False
self._is_soft_mask_around_edges = False
def __init__(self,
model=None,
xray_structure=None,
mask_atoms_atom_radius=None,
n_real=None,
map_manager=None,
wrapping=None):
'''
Create a mask (map object) with values of 1 near atoms in xray_structure
Parameters are:
model: required source of information about where atoms are
xray_structure: alternate source of information about where atoms are
mask_atoms_atom_radius: radius around atoms to mask
n_real: dimensions of map to create, e.g., existing map_data.all()
map_manager: alternate source of information for n_real. origin (0, 0, 0)
and source of wrapping
wrapping: Whether map wraps around unit cell boundaries, where unit
cell is that defined by xray_structure or model
'''
assert (model is not None) or (xray_structure is not None)
assert mask_atoms_atom_radius is not None
assert (n_real is not None) or (map_manager is not None)
assert (map_manager is not None) or isinstance(wrapping, bool)
if not n_real:
assert map_manager.map_data().origin() == (0, 0, 0)
n_real = map_manager.map_data().all()
if model:
xray_structure = model.get_xray_structure()
self._crystal_symmetry = model.crystal_symmetry()
else:
self._crystal_symmetry = xray_structure.crystal_symmetry()
if map_manager and wrapping is None:
wrapping = map_manager.wrapping()
assert wrapping is not None
if (not wrapping) or (self._crystal_symmetry.space_group_number == 1):
# usual
sites_frac = xray_structure.sites_frac()
else: # wrapping and cs: need to expand
sites_frac = xray_structure.expand_to_p1().sites_frac()
import boost_adaptbx.boost.python as bp
cctbx_maptbx_ext = bp.import_ext("cctbx_maptbx_ext")
radii = flex.double(sites_frac.size(), mask_atoms_atom_radius)
self._mask = cctbx_maptbx_ext.mask(
sites_frac=sites_frac,
unit_cell=xray_structure.unit_cell(),
n_real=n_real,
mask_value_inside_molecule=1,
mask_value_outside_molecule=0,
radii=radii,
wrapping=wrapping)
# Set up map_manager with this mask
if map_manager:
self._map_manager = map_manager.customized_copy(
map_data=self._mask)
else:
from iotbx.map_manager import map_manager as map_man
self._map_manager = map_man(
map_data=self._mask,
unit_cell_crystal_symmetry=self.crystal_symmetry(),
unit_cell_grid=self._mask.all(),
wrapping=wrapping)
self._map_manager.set_is_mask(True)
# Initialize soft mask
self._is_soft_mask = False
self._is_soft_mask_around_edges = False