mofbuilder.io.XyzWriter#

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

Bases: object

Writer for XYZ coordinate files.

Provides functionality to write molecular structure data to XYZ files, optionally with MPI parallel awareness and flexible stream/file handling.

Parameters:

  • comm (Any | None)

  • ostream (veloxchem.outputstream.OutputStream | None)

  • filepath (str | None)

  • debug (bool)

comm#

MPI communicator used for parallel operations.

Type:

Any

rank#

MPI rank of the current process.

Type:

int

nodes#

Total number of MPI nodes.

Type:

int

ostream#

Output stream for logging/info.

Type:

OutputStream

filepath#

Default path to write the XYZ file if not provided per call.

Type:

Optional[str]

_debug#

If True, debug information is printed.

Type:

bool

file_dir#

Directory of the current file to write (only set when writing).

Type:

Optional[Path]

write(filepath, header, lines)[source]#

Write the atom coordinates to an XYZ file.

Parameters:

  • filepath (str | None)

  • header (str)

  • lines (Sequence[Sequence[Any]])

Return type:

None

get_xyzlines(header, lines)[source]#

Return formatted XYZ lines as a list of strings.

Parameters:

  • header (str)

  • lines (Sequence[Sequence[Any]])

Return type:

List[str]

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

Write atom coordinate lines to an XYZ file.

Parameters:

  • filepath (Optional[str]) – Output XYZ file path. Uses instance default if not specified.

  • header (str) – Optional header/comment line (is line #2 in XYZ format).

  • lines (Sequence[Sequence[Any]]) –

    Each entry must have fields for atom_type, atom_label, atom_number, residue_name, residue_number, x, y, z, spin, charge, note.

    Only atom_label, x, y, z are directly written to the XYZ file.

Raises:

AssertionError – If filepath is not specified or invalid.

Return type:

None

Note

XYZ file will be written only by the master MPI rank. If the file extension is not ‘.xyz’, it is automatically added.

get_xyzlines(header='', lines=[])[source]#

Return formatted XYZ contents as a list of strings.

Args:

header (str): Optional header/comment line for XYZ content. lines (Sequence[Sequence[Any]]): List of per-atom info, each entry

having the fields: atom_type, atom_label, atom_number, residue_name, residue_number, x, y, z, spin, charge, note. Only atom_label, x, y, z are written.

Returns:

List[str]: Formatted XYZ contents as a list of strings.

Example:

xyz_lines = writer.get_xyzlines(header=”Example molecule”, lines=my_atomlist) # ‘

‘.join(xyz_lines) is a complete XYZ file or block.

Parameters:

  • header (str)

  • lines (Sequence[Sequence[Any]])

Return type:

List[str]