pwtools.parse.CifFile

class pwtools.parse.CifFile(filename=None, block=None, *args, **kwds)[source]

Bases: StructureFileParser

Parse Cif file. Uses PyCifRW [1].

References

__init__(filename=None, block=None, *args, **kwds)[source]
Parameters:

  • filename (name of the input file)

  • block (data block name (i.e. 'data_foo' in the Cif file -> 'foo') – here). If None then the first data block in the file is used.

Methods

apply_units()

Like _apply_units_raw(), make sure that units are only applied once.

assert_attr(attr)

Raise AssertionError if self.<attr> is not set (is_set_attr() returns False.

assert_attr_lst(attr_lst)

assert_set_attr(attr)

Same as assert_attr(), but run try_set_attr() first.

assert_set_attr_lst(attr_lst)

check_set_attr(attr)

Run try_set_attr() and return the result of is_set_attr(), i.e. True or False.

check_set_attr_lst(attr_lst)

cif_clear_atom_symbol(st[, rex])

Remove digits and "+,-" from atom names.

cif_str2float(st)

'7.3782(7)' -> 7.3782

dump(dump_filename[, mkdir])

Write object to binary file using pickle.

get_cont([auto_calc])

Populate and return a Container object.

get_coords()

get_coords_frac()

get_cryst_const()

get_return_attr(attr_name)

Call try_set_attr() are return self.<attr_name> if set.

get_struct(**kwds)

get_symbols()

init_attr_lst([attr_lst])

Set each self.<attr> in attr_lst to None.

is_set_attr(attr)

Check if self has the attribute self.<attr> and if it is _not_ None.

is_set_attr_lst(attr_lst)

load(dump_filename)

Load pickled object.

parse()

raw_return(attr_name)

Call try_set_attr(_<attr_name>_raw) and return it if set, else None.

raw_slice_get(attr_name, sl, axis)

Shortcut method:

set_all([attr_lst])

Call getter for each attr name in attr_lst.

set_attr_lst(attr_lst)

Set self.attr_lst and init each attr to None.

try_set_attr(attr)

If self.<attr> does not exist or is None, then invoke an appropirately named getter as if this command would be executed.

try_set_attr_lst(attr_lst)

update_units(units)

Update self.units dict from units.

Attributes

default_units