mofbuilder.io.CifWriter#

class mofbuilder.io.CifWriter(comm=None, ostream=None, filepath=None, debug=False)[source]#

Bases: object

Writer for crystallographic CIF files (Crystallographic Information File, .cif).

Handles CIF file creation in parallel MPI environments, with proper cell and atom formatting for MOF and other crystalline data.

Parameters:

  • comm (Any | None)

  • ostream (veloxchem.outputstream.OutputStream | None)

  • filepath (str | None)

  • debug (bool)

comm#

MPI communicator.

Type:

Any

rank#

MPI process rank.

Type:

int

nodes#

Number of MPI processes.

Type:

int

ostream#

Output stream for status messages or debugging.

Type:

OutputStream

filepath#

Default path to write CIF files.

Type:

Optional[Path]

_debug#

Enables debug-level status messages if True.

Type:

bool

cell_info#

Placeholder for unit cell parameters.

Type:

Optional[Any]

supercell_boundary#

Placeholder for supercell dimensions.

Type:

Optional[Any]

unit_cell#

Placeholder for unit cell dimensions.

Type:

Optional[Any]

file_dir#

Directory where the CIF will be written (set in write()).

Type:

Optional[Path]

write()[source]#

Writes a CIF file given cell, boundary, and atom data.

Parameters:

  • filepath (str | None)

  • header (str)

  • lines (List[List[Any]])

  • supercell_boundary (List[float] | None)

  • cell_info (List[float] | None)

Return type:

None

write(filepath=None, header='', lines=[], supercell_boundary=None, cell_info=None)[source]#

Write data to a CIF file.

This method writes atomic, cell, and symmetry data to a new or existing CIF file in the standard format. Used in the context of crystal structures generated by mofbuilder.

Parameters:

  • filepath (Optional[str]) – Output file path (.cif will be appended if missing).

  • header (str) – Optional string describing the creation method.

  • lines (List[List[Any]]) – Each sublist contains atom data in the form [atom_type, atom_label, atom_number, residue_name, residue_number, x, y, z, spin, charge, note].

  • supercell_boundary (Optional[List[float]]) – Max [x, y, z] of the supercell; used to normalize coordinates.

  • cell_info (Optional[List[float]]) – Cell parameters [a, b, c, alpha, beta, gamma].

Raises:

  • AssertionError – If no output filepath is specified.

  • ValueError – If required parameters (lines, boundary, cell_info) are missing or malformed.

Return type:

None

Example

>>> writer = CifWriter()
>>> writer.write(
...     filepath="my_structure.cif",
...     header="MOFbuilder v1.0",
...     lines=[["C", "C1", 1, "RES", 1, 1.0, 2.0, 3.0, 1.0, 0.0, ""]],
...     supercell_boundary=[10.0,10.0,10.0],
...     cell_info=[10.0,10.0,10.0,90.0,90.0,90.0]
... )