MDAnalysis

Create a pseudo box for PDB files and the shifting of coordinates within that box.

mda_psuedobox_from_atomgroup

mda_psuedobox_from_atomgroup(ag, cutoff=5.0)

Construct a pseudo box and shifts atomic coordinates to fit within this box.

This function takes an AtomGroup object and a cutoff distance as input, and it creates a pseudo box large enough to include all atoms plus the specified cutoff. It then shifts the coordinates of the atoms to fit within this box.

Parameters:

Name	Type	Description	Default
ag	AtomGroupType	An AtomGroup object representing the group of atoms for which the pseudo box is to be created.	required
cutoff	float	The minimum distance that should be allowed between the edges of the pseudo box and the atoms. Default is 5.0.	5.0

Returns:

Type	Description
tuple[NDArray[float32], NDArray[float32]]	tuple[NDArray[np.float32], NDArray[np.float32]]: The shifted coordinates of the atoms and the dimensions of the pseudo box.

Source code in lahuta/utils/mda.py

def mda_psuedobox_from_atomgroup(
    ag: AtomGroupType, cutoff: float = 5.0
) -> tuple[NDArray[np.float32], NDArray[np.float32]]:
    """Construct a pseudo box and shifts atomic coordinates to fit within this box.

    This function takes an AtomGroup object and a cutoff distance as input, and it creates
    a pseudo box large enough to include all atoms plus the specified cutoff. It then shifts
    the coordinates of the atoms to fit within this box.

    Args:
        ag (AtomGroupType): An AtomGroup object representing the group of atoms for which \
                             the pseudo box is to be created.
        cutoff (float, optional): The minimum distance that should be allowed between the \
                                  edges of the pseudo box and the atoms. Default is 5.0.

    Returns:
        tuple[NDArray[np.float32], NDArray[np.float32]]: The shifted coordinates of the atoms \
                                                        and the dimensions of the pseudo box.
    """
    lmax: float = ag.positions.max(axis=0)
    lmin: float = ag.positions.min(axis=0)
    pseudobox = np.zeros(6, dtype=np.float32)
    lengths = 1.1 * (lmax - lmin)
    lengths = np.maximum(lengths, 2 * cutoff)
    pseudobox = np.zeros(6, dtype=np.float32)
    pseudobox[:3] = lengths
    pseudobox[3:] = 90.0
    shift_coords: NDArray[np.float32] = ag.positions.copy()
    shift_coords -= lmin
    return shift_coords, pseudobox