def __init__(self,atom_id,atom_name,atomic_number,isotope=None, \
coords=[0.0,0.0,0.0],force=[0.0,0.0,0.0],velocity=[0.0,0.0,0.0]):
"""Initializes an atom.
atom_id: ID of the atom, should be unique.
atom_name: Name of the atom.
atomic_number: Atomic number.
isotope: Isotope selection. Default is the most abundant isotope.
coords: Coordinates of the atom, in a list.
force: The force acting on the atom, in a list. Default is [0.0,0.0,0.0].
velocity: The velocity of the atom, in a list. Default is [0.0,0.0,0.0].
"""
from BioNanoLEGO.Element import get_atomic_mass
self.atom_id = int(atom_id)
self.atom_name = atom_name
self.atomic_number = int(atomic_number)
self.atomic_mass = get_atomic_mass(atomic_number,isotope)
self.num_electrons = int(atomic_number)
# Effective charge
self.eff_charge = float(self.num_electrons)
self.coords = array(coords,'d')
self.force = array(force,'d')
self.velocity = array(velocity,'d')
return
def rotate(self,R):
"""Performs rotation operation by the rotation matrix R."""
from BioNanoLEGO.DenseMatrix import dot
# FIXME: this assignment is ugly in my opinion
new_coords = dot(R,self.coords)
self.coords = array([new_coords[0,0],new_coords[0,1],new_coords[0,2]])
return
def setForce(self,force):
"""Sets/updates the force acting on the atom."""
self.force = array(force,'d')
return
def setVelocity(self,velocity):
"""Sets/updates the velocity of the atom."""
self.velocity = array(velocity,'d')
return
def setCoords(self,coords):
"""Sets/updates the coordinates."""
self.coords = array(coords,'d')
return
