mofbuilder.io.GroWriter#

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

Bases: object

Write atomic structure data to GROMACS .gro coordinate files.

Handles formatting, unit conversion, residue management, and MPI-based output stream selection. Supports both orthorhombic and triclinic box specification.

Parameters:

  • comm (Any | None)

  • ostream (veloxchem.outputstream.OutputStream | None)

  • filepath (str | None)

  • debug (bool)

comm#

MPI communicator.

Type:

MPI.Comm

rank#

MPI process rank.

Type:

int

nodes#

Number of MPI processes.

Type:

int

ostream#

Output stream for printing/logging.

Type:

OutputStream

filepath#

Path to the target .gro file (default None, set by user).

Type:

Optional[str]

_debug#

Toggle debug printouts.

Type:

bool

file_dir#

Directory containing the output file (set during write).

Type:

Optional[Path]

write()[source]#

Write data to a .gro file. Handles formatting and box conversion.

Parameters:

  • filepath (str | None)

  • header (str)

  • lines (Sequence[Sequence[Any]])

  • box (Sequence[float] | None)

  • triclinic (bool)

Return type:

None

write(filepath=None, header='Generated by MofBuilder\n', lines=[], box=None, triclinic=False)[source]#

Write atomic coordinates and box information to a .gro coordinate file.

The input ‘lines’ should be a list of lists/arrays, one per atom, following this order: [atom_type, atom_label, atom_number, residue_name, residue_number, x, y, z, spin, charge, note]

Parameters:

  • filepath (Optional[str]) – Output .gro file path (overrides instance attribute, required if not set).

  • header (str) – Header string to write at the top of the .gro file. Defaults to “Generated by MofBuilder”.

  • lines (Sequence[Sequence[Any]]) – List of atom data lines.

  • box (Optional[Sequence[float]]) – Box vector or box+extra terms for triclinic (see Note). Units: angstroms.

  • triclinic (bool) – If True, expects box to have 6 elements.

Raises:

  • AssertionError – If filepath is not provided.

  • AssertionError – If triclinic=True and box does not have 6 elements.

Return type:

None

Note

Positions (x, y, z) are converted from angstroms to nanometers. Box lengths are also written in nanometers. Triclinic box format: [lx, ly, lz, xy, xz, yz].

Example

>>> writer = GroWriter()
>>> writer.write("output.gro", lines=atom_list, box=[30.0, 30.0, 30.0])