"""
Functions for molecule analysis
"""
import numpy as np
from .measure import calculate_distance
from .atom_data import atomic_weights
[docs]def build_bond_list(coordinates, max_bond=1.5, min_bond=0):
"""
Build a list of bonds in a set of coordinates based on a distance criteria.
Parameters
----------
coordinates: np.ndarray
The coordinates of the atoms to analyze in an (natoms, ndim) array.
max_bond: float, optional
The maximum distance for two atoms to be considered bonded.
min_bond: float, optional
The minimum distance for two atoms to be considered bonded.
Returns
-------
bonds: dict
A dictionary containing bonded atoms with atom pairs as keys and the distance between the atoms as the value.
"""
if min_bond < 0:
raise ValueError("Invalid minimum bond distance entered! Minimum bond distance must be greater than zero!")
# Find the bonds in a molecule
bonds = {}
num_atoms = len(coordinates)
for atom1 in range(num_atoms):
for atom2 in range(atom1, num_atoms):
distance = calculate_distance(coordinates[atom1], coordinates[atom2])
if distance > min_bond and distance < max_bond:
bonds[(atom1, atom2)] = distance
return bonds
[docs]def calculate_molecular_mass(symbols):
"""Calculate the mass of a molecule.
Parameters
----------
symbols : list
A list of elements.
Returns
-------
mass : float
The mass of the molecule
"""
mass = 0
for atom in symbols:
mass += atomic_weights[atom]
return mass
[docs]def calculate_center_of_mass(symbols, coordinates):
"""Calculate the center of mass of a molecule.
The center of mass is weighted by each atom's weight.
Parameters
----------
symbols : list
A list of elements for the molecule
coordinates : np.ndarray
The coordinates of the molecule.
Returns
-------
center_of_mass: np.ndarray
The center of mass of the molecule.
Notes
-----
The center of mass is calculated with the formula
.. math:: \\vec{R}=\\frac{1}{M} \\sum_{i=1}^{n} m_{i}\\vec{r_{}i}
"""
total_mass = calculate_molecular_mass(symbols)
mass_array = np.zeros([len(symbols), 1])
for i in range(len(symbols)):
mass_array[i] = atomic_weights[symbols[i]]
center_of_mass = sum(coordinates * mass_array) / total_mass
return center_of_mass