def expand_crystal(structure, n=1, name='XTAL'):
"""Expands the contents of a structure to a crystal of a given size. Returns
a `` StructureHolder`` entity instance.
Arguments:
- structure: ``Structure`` entity instance.
- n: number number of unit-cell layers.
- name: optional name.
Requires a PDB file with correct CRYST1 field and space group information.
"""
sh = structure.header
sn = structure.name
fmx = sh['uc_fmx']
omx = sh['uc_omx']
# get initial coorinates
atoms = einput(structure, 'A')
coords = array([atoms.getData('coords')]) # fake 3D
# expand the coordinates to crystal
all_coords = coords_to_crystal(coords, fmx, omx, n)
structures = StructureHolder(name)
rng = range(-n, n + 1) # a range like -2, -1, 0, 1, 2
vectors = [(x, y, z) for x in rng for y in rng for z in rng]
for i, (u, v, w) in enumerate(vectors):
new_structure = copy(structure)
new_atoms = einput(new_structure, 'A')
new_coords = all_coords[i, 0]
for (atom_id, new_coord) in izip(atoms.keys(), new_coords):
new_atoms[atom_id].coords = new_coord
new_structure.setName("%s_%s%s%s" % (sn, u, v, w))
structures.addChild(new_structure)
return structures
def expand_crystal(structure, n=1, name='XTAL'):
"""Expands the contents of a structure to a crystal of a given size. Returns
a `` StructureHolder`` entity instance.
Arguments:
- structure: ``Structure`` entity instance.
- n: number number of unit-cell layers.
- name: optional name.
Requires a PDB file with correct CRYST1 field and space group information.
"""
sh = structure.header
sn = structure.name
fmx = sh['uc_fmx']
omx = sh['uc_omx']
# get initial coorinates
atoms = einput(structure, 'A')
coords = array([atoms.getData('coords')]) # fake 3D
# expand the coordinates to crystal
all_coords = coords_to_crystal(coords, fmx, omx, n)
structures = StructureHolder(name)
rng = range(-n, n + 1) # a range like -2, -1, 0, 1, 2
vectors = [(x, y, z) for x in rng for y in rng for z in rng]
for i, (u, v, w) in enumerate(vectors):
new_structure = copy(structure)
new_atoms = einput(new_structure, 'A')
new_coords = all_coords[i, 0]
for (atom_id, new_coord) in izip(atoms.keys(), new_coords):
new_atoms[atom_id].coords = new_coord
new_structure.setName("%s_%s%s%s" % (sn, u, v, w))
structures.addChild(new_structure)
return structures
def expand_symmetry(model, mode='uc', name='UC', **kwargs):
"""Applies the symmetry operations defined by the header of the PDB files to
the given ``Model`` entity instance. Returns a ``ModelHolder`` entity.
Arguments:
- model: model entity to expand
- mode: 'uc', 'bio' or 'raw'
- name: optional name of the ``ModelHolder`` instance.
Requires a PDB file with a correct CRYST1 field and space group information.
"""
structure = model.getParent('S')
sh = structure.header
fmx = sh['uc_fmx']
omx = sh['uc_omx']
mxs = sh['uc_mxs']
# get initial coordinates
atoms = einput(model, 'A')
coords = array(atoms.getData('coords'))
# expand the coordinates to symmetry
all_coords = coords_to_symmetry(coords, fmx, omx, mxs, mode)
models = ModelHolder(name)
for i in xrange(0, len(mxs)):
# copy model
new_model = copy(model) # with additional models which
new_atoms = einput(new_model, 'A')
# patch with coordinates
new_coords = all_coords[i]
for (atom_id, new_coord) in izip(atoms.keys(), new_coords):
new_atoms[atom_id[1:]].coords = new_coord
# give it an id: the models are numbered by the symmetry operations with
# identity being the first model
new_model.setName(i)
models.addChild(new_model)
return models
def expand_symmetry(model, mode='uc', name='UC', **kwargs):
"""Applies the symmetry operations defined by the header of the PDB files to
the given ``Model`` entity instance. Returns a ``ModelHolder`` entity.
Arguments:
- model: model entity to expand
- mode: 'uc', 'bio' or 'raw'
- name: optional name of the ``ModelHolder`` instance.
Requires a PDB file with a correct CRYST1 field and space group information.
"""
structure = model.getParent('S')
sh = structure.header
fmx = sh['uc_fmx']
omx = sh['uc_omx']
mxs = sh['uc_mxs']
# get initial coordinates
atoms = einput(model, 'A')
coords = array(atoms.getData('coords'))
# expand the coordinates to symmetry
all_coords = coords_to_symmetry(coords, fmx, omx, mxs, mode)
models = ModelHolder(name)
for i in xrange(0, len(mxs)):
# copy model
new_model = copy(model) # with additional models which
new_atoms = einput(new_model, 'A')
# patch with coordinates
new_coords = all_coords[i]
for (atom_id, new_coord) in izip(atoms.keys(), new_coords):
new_atoms[atom_id[1:]].coords = new_coord
# give it an id: the models are numbered by the symmetry operations with
# identity being the first model
new_model.setName(i)
models.addChild(new_model)
return models