def set_nmonomers(sefl,nmonomers):
"""Set the number of monomers to be in the chain and rebuild the monomer list."""
self.nmonomers = nmonomers
self.mono = []
for i in range(self.nmonomers):
self.mono.append(monomer(i+1))
def initialize_monomers(self):
self.monomers = []
for i in self.settings.monomers:
self.monomers.append(monomer(i, self.settings, inv_cnt=1, s_id=0))
self.probabilities = [i.probability for i in self.monomers]
if sum(self.probabilities) != 1:
raise ValueError("Sum of probabilities is not equal to 1")
def __init__(self,nmonomers=-1,poly_id=1):
"""Initialize empty lists which will need to be filled."""
# id number
self.poly_id = poly_id
# polymer type coefficients
self.coeff = {"atom":[],"bond":[],"angle":[],"pair":[],"dihedral":[],"improper":[]}
# polymer final arrays for writing
self.value = {"atom":[],"bond":[],"angle":[],"dihedral":[],"improper":[]}
# polymer pre-assignment prior to build
self.type_id = {"atom":[],"bond":[],"angle":[],"dihedral":[],"improper":[]}
self.unique_id = {"atom":[],"bond":[],"angle":[],"pair":[],"dihedral":[],"improper":[]}
self.connector_id = []
# monomer object
if nmonomers > 0:
self.nmonomers = nmonomers
self.mono = []
for i in range(self.nmonomers):
self.mono.append(monomer(i+1))