Pos

Provides functions for interacting with the positions of atoms in molecular structures.

This module offers utilities for analyzing and manipulating the spatial coordinates of atoms within an MDAnalysis Universe. Currently, it includes functionality to calculate the center of mass of a selected group of atoms.

get_com(atoms)

Compute the center of mass for a group of atoms.

The center of mass (COM) is the average position of all the parts of the system, weighted by their masses. For a collection of atoms, it is calculated as the weighted average of their coordinates, where the weights are the masses of the atoms. This function leverages the built-in center of mass calculation provided by MDAnalysis for an AtomGroup.

PARAMETER	DESCRIPTION
atoms	An MDAnalysis AtomGroup object representing the selection of atoms for which the center of mass needs to be computed. This object contains information about the atoms, including their positions and masses (if available in the topology). TYPE: AtomGroup

RETURNS	DESCRIPTION
NDArray[float64]	A NumPy array of shape (3,) containing the x, y, and z coordinates of
NDArray[float64]	the center of mass of the provided AtomGroup. The units of these
NDArray[float64]	coordinates will be the same as the units of the atomic coordinates
NDArray[float64]	within the MDAnalysis Universe (typically Angstroms).

Examples:

Calculating the center of mass of all atoms in a loaded structure:

import MDAnalysis as mda
from simlify.structure.io import load_mda
from simlify.structure.pos import get_com

# Load a molecular structure
try:
    universe = load_mda("protein.pdb")
    all_atoms = universe.atoms

    # Calculate the center of mass of all atoms
    center_of_mass = get_com(all_atoms)
    print(f"Center of mass of all atoms: {center_of_mass}")
except FileNotFoundError as e:
    print(f"Error: {e}")

Calculating the center of mass of a specific selection of atoms (e.g., protein):

import MDAnalysis as mda
from simlify.structure.io import load_mda
from simlify.structure.pos import get_com

# Load a molecular structure
try:
    universe = load_mda("complex.gro", "traj.xtc")
    protein = universe.select_atoms("protein")

    # Calculate the center of mass of the protein atoms
    protein_com = get_com(protein)
    print(f"Center of mass of the protein: {protein_com}")
except FileNotFoundError as e:
    print(f"Error: {e}")