def read(self, filename, format='auto'):
"""Load structure from a file, any original data become lost.
filename -- file to be loaded
format -- all structure formats are defined in Parsers submodule,
when format == 'auto' all Parsers are tried one by one
Return instance of data Parser used to process file. This
can be inspected for information related to particular format.
"""
import diffpy.Structure
import diffpy.Structure.Parsers
getParser = diffpy.Structure.Parsers.getParser
p = getParser(format)
new_structure = p.parseFile(filename)
# reinitialize data after successful parsing
# avoid calling __init__ from a derived class
Structure.__init__(self)
if new_structure is not None:
self.__dict__.update(new_structure.__dict__)
self[:] = new_structure
if not self.title:
import os.path
tailname = os.path.basename(filename)
tailbase = os.path.splitext(tailname)[0]
self.title = tailbase
return p
def read(self, filename, format='auto'):
"""Load structure from a file, any original data become lost.
filename -- file to be loaded
format -- all structure formats are defined in Parsers submodule,
when format == 'auto' all Parsers are tried one by one
Return instance of data Parser used to process file. This
can be inspected for information related to particular format.
"""
import diffpy.Structure
import diffpy.Structure.Parsers
getParser = diffpy.Structure.Parsers.getParser
p = getParser(format)
new_structure = p.parseFile(filename)
# reinitialize data after successful parsing
# avoid calling __init__ from a derived class
Structure.__init__(self)
if new_structure is not None:
self.__dict__.update(new_structure.__dict__)
self[:] = new_structure
if not self.title:
import os.path
tailname = os.path.basename(filename)
tailbase = os.path.splitext(tailname)[0]
self.title = tailbase
return p
def testWriter(self):
p = getParser()
from diffpy import Structure as matter
a = 1.5
lattice = matter.Lattice(2*a, 2*a, 2*a, 90,90,90)
atoms = [matter.Atom('Ni'), matter.Atom('Ni', (0.5,0.5,0.5))]
struct = Structure(lattice=lattice, atoms=atoms) #, sgid=229)
print('original unitcell, cartesian coords')
print('\n'.join(p.toLines(struct)))
print('original unitcell, fractional coords')
print('\n'.join(p.toLines(struct, use_fractional_coordinates=1, latticeAsDescription=1)))
# print 'primitive unitcell, cartesian coords'
# print '\n'.join(p.toLines(struct, use_primitive_unitcell=1))
# print 'primitive unitcell, fractional coords'
# print '\n'.join(p.toLines(struct, use_primitive_unitcell=1, use_fractional_coordinates=1))
return
def __copy__(self, target=None):
'''Create a deep copy of this instance.
target -- optional target instance for copying, useful for
copying a derived class. Defaults to new instance
of the same type as self.
Return a duplicate instance of this object.
'''
if target is None:
target = Structure()
elif target is self:
return target
# copy attributes as appropriate:
target.title = self.title
target.lattice = Lattice(self.lattice)
target.pdffit = copy.deepcopy(self.pdffit)
# copy all atoms to the target
target[:] = self
return target
def readStr(self, s, format='auto'):
"""Load structure from a string, any original data become lost.
s -- string with structure definition
format -- all structure formats are defined in Parsers submodule,
when format == 'auto' all Parsers are tried one by one
Return instance of data Parser used to process input string. This
can be inspected for information related to particular format.
"""
from diffpy.Structure.Parsers import getParser
p = getParser(format)
new_structure = p.parse(s)
# reinitialize data after successful parsing
# avoid calling __init__ from a derived class
Structure.__init__(self)
if new_structure is not None:
self.__dict__.update(new_structure.__dict__)
self[:] = new_structure
return p
def __copy__(self, target=None):
'''Create a deep copy of this instance.
target -- optional target instance for copying, useful for
copying a derived class. Defaults to new instance
of the same type as self.
Return a duplicate instance of this object.
'''
if target is None:
target = Structure()
elif target is self:
return target
# copy attributes as appropriate:
target.title = self.title
target.lattice = Lattice(self.lattice)
target.pdffit = copy.deepcopy(self.pdffit)
# copy all atoms to the target
target[:] = self
return target
def readStr(self, s, format='auto'):
"""Load structure from a string, any original data become lost.
s -- string with structure definition
format -- all structure formats are defined in Parsers submodule,
when format == 'auto' all Parsers are tried one by one
Return instance of data Parser used to process input string. This
can be inspected for information related to particular format.
"""
from diffpy.Structure.Parsers import getParser
p = getParser(format)
new_structure = p.parse(s)
# reinitialize data after successful parsing
# avoid calling __init__ from a derived class
Structure.__init__(self)
if new_structure is not None:
self.__dict__.update(new_structure.__dict__)
self[:] = new_structure
return p
def __emptySharedStructure(self):
'''Return empty Structure with standard attributes same as in self.
'''
rv = Structure()
rv.__dict__.update([(k, getattr(self, k)) for k in rv.__dict__])
return rv
