mofbuilder.io.XyzReader#

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

Bases: object

Reader for XYZ molecular coordinate files.

Handles loading of XYZ files with MPI-aware output and optional structure recentering.

Parameters:

  • comm (Any | None)

  • ostream (veloxchem.outputstream.OutputStream | None)

  • filepath (str | Path | None)

comm#

MPI communicator.

Type:

Any

rank#

MPI process rank.

Type:

int

nodes#

Number of MPI processes.

Type:

int

ostream#

Output stream for info/logging.

Type:

OutputStream

filepath#

Path to the input .xyz file.

Type:

Optional[str]

data#

Atom information as parsed and processed.

Type:

Optional[np.ndarray]

_debug#

Enables debug output if True.

Type:

bool

read_xyz()[source]#

Read, parse, and (optionally recenter) XYZ file into array format.

Parameters:

  • filepath (str | Path | None)

  • recenter (bool)

  • com_type (str | None)

  • residue_name (str)

  • residue_number (int)

Return type:

None

read_xyz(filepath=None, recenter=False, com_type=None, residue_name='MOL', residue_number=1)[source]#

Reads atom and coordinate information from an XYZ file, storing structure in a NumPy array.

Optionally recenters structure coordinates to a specified atom type or whole molecule center of mass.

Parameters:

  • filepath (Optional[str or Path]) – Path to the .xyz file. If not supplied, uses instance filepath.

  • recenter (bool) – If True, recenter coordinates to center-of-mass. Defaults to False.

  • com_type (Optional[str]) – If specified, use only atoms of this type for COM calculation.

  • residue_name (str) – Residue name assignment for all atoms. Defaults to ‘MOL’.

  • residue_number (int) – Residue number for all atoms. Defaults to 1.

Returns:

None

Raises:

FileNotFoundError – If the specified file path does not exist.

Return type:

None

Note

Assigns atom_type, atom_label (e.g., “C1”, “O2”), atom_number (1-based), residue_name, residue_number, x, y, z, spin (1.0), charge (from file or 0.0), and note (from file or empty) for each atom.

Array output shape is (num_atoms, 11).