#Init
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
import os
import random
import numpy as np
import matplotlib.pyplot as plt
import numpy as np
import time
from openeye import oechem
import openmm
from openff.toolkit.topology import Molecule, Topology
from openff.toolkit.typing.engines.smirnoff import ForceField
from openff.toolkit.utils import get_data_file_path
from openff.toolkit.utils.toolkits import RDKitToolkitWrapper, AmberToolsToolkitWrapper
from openff.units import unit
from pandas import read_csv
import espaloma_charge as espcharge
from espaloma_charge.openff_wrapper import EspalomaChargeToolkitWrapper
from openff.interchange import Interchange
from openff.interchange.components._packmol import UNIT_CUBE, pack_box, _max_dist_between_points
from functools import reduce
from statistics import mean
from rdkit.Chem.Descriptors import ExactMolWt
from openff.interchange import Interchange
#Build polymer - generic
[docs]
def build_polymer(sequence, monomer_list, reaction, terminal='hydroxyl', chain_num=1):
"""
Constructs a polymer from a given sequence of monomers.
Parameters
----------
sequence : str
A string representing the sequence of monomers (e.g., 'ABAB').
monomer_list : list
A list of SMILES strings representing the monomers.
reaction : rdkit.Chem.rdChemReactions.ChemicalReaction
An RDKit reaction object used to link monomers.
terminal : str, optional
The terminal group to be added to the polymer. Options are 'hydroxyl', 'carboxyl', or 'ester'.
Default is 'hydroxyl'.
chain_number : int, optional
The number of polymer chains to construct. Default is 1. Input used for ensemble build.
Returns
-------
rdkit.Chem.rdchem.Mol
The constructed polymer as an RDKit molecule object.
"""
from rdkit import RDLogger
RDLogger.DisableLog('rdApp.*')
monomers = {}
for x in sorted(list(set(sequence))):
ind = sorted(list(set(sequence))).index(x)
monomers[x] = monomer_list[ind]
hits = Chem.MolFromSmiles(monomers[sequence[0]]).GetSubstructMatches(Chem.MolFromSmarts('I'))
mw = Chem.RWMol(Chem.MolFromSmiles(monomers[sequence[0]]))
mw.ReplaceAtom(hits[0][0],Chem.Atom(17))
Chem.SanitizeMol(mw)
mw.CommitBatchEdit()
polymer = Chem.AddHs(mw)
info = Chem.AtomPDBResidueInfo()
info.SetResidueName(str(chain_num) + sequence[0] + str(1))
info.SetResidueNumber(1)
[atom.SetMonomerInfo(info) for atom in polymer.GetAtoms()]
Chem.SanitizeMol(polymer)
for i in range(len(sequence))[1:]:
if sequence[i] == 'A':
A = Chem.MolFromSmiles(monomers['A'])
A = Chem.AddHs(A)
info = Chem.AtomPDBResidueInfo()
info.SetResidueName(str(chain_num) + 'A' + str(i+1))
info.SetResidueNumber(i+1)
[atom.SetMonomerInfo(info) for atom in A.GetAtoms()]
polymer = reaction.RunReactants((polymer, A))[0][0]
Chem.SanitizeMol(polymer)
elif sequence[i] == 'B':
B = Chem.MolFromSmiles(monomers['B'])
B = Chem.AddHs(B)
info = Chem.AtomPDBResidueInfo()
info.SetResidueName(str(chain_num) + 'B' + str(i+1))
info.SetResidueNumber(i+1)
[atom.SetMonomerInfo(info) for atom in B.GetAtoms()]
polymer = reaction.RunReactants((polymer, B))[0][0]
Chem.SanitizeMol(polymer)
if terminal == 'hydroxyl':
hydrogen = Chem.MolFromSmiles('[H]')
info = Chem.AtomPDBResidueInfo()
info.SetResidueName(str(chain_num) + sequence[0] + str(1))
info.SetResidueNumber(1)
[atom.SetMonomerInfo(info) for atom in hydrogen.GetAtoms()]
polymer = Chem.ReplaceSubstructs(polymer, Chem.MolFromSmarts('Cl'), hydrogen)[0]
Chem.AddHs(polymer)
elif terminal == 'carboxyl':
carboxyl = Chem.MolFromSmiles('C(=O)[OH]')
info = Chem.AtomPDBResidueInfo()
info.SetResidueName(str(chain_num) + sequence[0] + str(1))
info.SetResidueNumber(1)
[atom.SetMonomerInfo(info) for atom in carboxyl.GetAtoms()]
polymer = Chem.ReplaceSubstructs(polymer, Chem.MolFromSmarts('Cl'), carboxyl)[0]
elif terminal == 'ester':
carbon = Chem.MolFromSmiles('C')
info = Chem.AtomPDBResidueInfo()
info.SetResidueName(str(chain_num) + sequence[0] + str(1))
info.SetResidueNumber(1)
[atom.SetMonomerInfo(info) for atom in carbon.GetAtoms()]
polymer = Chem.ReplaceSubstructs(polymer, Chem.MolFromSmarts('Cl'), carbon)[0]
Chem.AddHs(polymer)
polymer = Chem.ReplaceSubstructs(polymer, Chem.MolFromSmarts('Cl'), Chem.MolFromSmiles('C'))[0]
else:
hydrogen = Chem.MolFromSmiles('[H]')
info = Chem.AtomPDBResidueInfo()
info.SetResidueName(str(chain_num) + sequence[0] + str(1))
info.SetResidueNumber(1)
[atom.SetMonomerInfo(info) for atom in hydrogen.GetAtoms()]
polymer = Chem.ReplaceSubstructs(polymer, Chem.MolFromSmarts('Cl'), hydrogen)[0] #remove any excess iodine
hydrogen = Chem.MolFromSmiles('[H]')
info = Chem.AtomPDBResidueInfo()
info.SetResidueName(str(chain_num) + sequence[-1] + str(len(sequence)))
info.SetResidueNumber(len(sequence))
[atom.SetMonomerInfo(info) for atom in hydrogen.GetAtoms()]
polymer = Chem.ReplaceSubstructs(polymer, Chem.MolFromSmarts('I'), hydrogen)[0] #remove any excess iodine
Chem.SanitizeMol(polymer)
return polymer
[docs]
def build_linear_copolymer(sequence,
monomer_a_smiles,
monomer_b_smiles,
reaction=AllChem.ReactionFromSmarts('[C:1][HO:2].[HO:3][C:4]>>[C:1][O:2][C:4].[O:3]')):
"""
Constructs a linear co-polymer from the provided sequence of monomers.
This function takes a sequence of monomers represented as 'A' and 'B', and the SMILES strings of two monomers.
It constructs a co-polymer based on the sequence, using the provided reaction SMARTS for joining the monomers.
The function returns the sanitized polymer and the percentage composition of each monomer in the polymer.
Parameters
----------
sequence : str
A string representing the sequence of monomers. 'A' represents monomer_a and 'B' represents monomer_b.
monomer_a_smiles : str
The SMILES string of monomer A.
monomer_b_smiles : str
The SMILES string of monomer B.
reaction : rdkit.Chem.rdChemReactions.ChemicalReaction, optional
The reaction SMARTS used for joining the monomers. Defaults to '[C:1][HO:2].[HO:3][C:4]>>[C:1][O:2][C:4].[O:3]',
representing a condensation polymerisation.
Returns
-------
tuple
A tuple containing the following elements:
- sanitized_polymer (rdkit.Chem.rdchem.Mol): The constructed and sanitized polymer.
- percentage_monomer_a (float): The percentage composition of monomer A in the polymer.
- percentage_monomer_b (float): The percentage composition of monomer B in the polymer.
"""
# Initialize the polymer with an iodine blocker
polymer = Chem.MolFromSmiles('OC(=O)I')
A_count=0
B_count=0
A = Chem.MolFromSmiles(monomer_a_smiles)
B = Chem.MolFromSmiles(monomer_b_smiles)
# Build the polymer based on the sequence
for i in range(len(sequence)):
if sequence[i] == 'A':
polymer = reaction.RunReactants((polymer, A))[0][0]
Chem.SanitizeMol(polymer)
A_count+=1
elif sequence[i] == 'B':
polymer = reaction.RunReactants((polymer, B))[0][0]
Chem.SanitizeMol(polymer)
B_count+=1
# Calculate the percentage composition of each monomer
A_ratio = round((A_count/len(sequence))*100,2)
B_ratio = round((B_count/len(sequence))*100,2)
# Remove the iodine blocker
polymer = Chem.ReplaceSubstructs(polymer, Chem.MolFromSmarts('OC(=O)I'), Chem.MolFromSmarts('[O]'))[0]
Chem.SanitizeMol(polymer)
return polymer, A_ratio, B_ratio
[docs]
def PDI(chains):
"""
Calculates the Polydispersity Index (PDI), number-average molecular weight (Mn), and weight-average molecular weight (Mw) of a list of chains.
This function takes a list of molecular chains and calculates the PDI, which is the ratio of Mw to Mn. It also calculates Mn, which is the sum of the molecular weights of the chains divided by the number of chains, and Mw, which is the sum of the product of the weight fraction and molecular weight of each chain.
Parameters
----------
chains : list
A list of molecular chains. Each chain is represented as an RDKit molecule object.
Returns
-------
tuple
A tuple containing the following elements:
- PDI (float): The Polydispersity Index, which is the ratio of Mw to Mn.
- Mn (float): The number-average molecular weight.
- Mw (float): The weight-average molecular weight.
"""
# Calculate the molecular weights of the chains
mw_list = [ExactMolWt(chain) for chain in chains]
list = [round(mass) for mass in mw_list]
Mi = set(list)
NiMi = []
# Calculate the weight fraction of each chain
for i in Mi:
Ni = list.count(i)
NiMi.append(i*Ni)
sigNiMi = sum(NiMi)
Mn = sigNiMi/len(mw_list)
wf = [z/sigNiMi for z in NiMi]
# Calculate the weight-average molecular weight
WiMi = [wf[n]*NiMi[n] for n in range(len(wf))]
Mw = sum(WiMi)
# Calculate the polydispersity index
PDI = Mw/Mn
return PDI, Mn, Mw
[docs]
def blockiness_gen(sequence):
"""
Calculate the blockiness and average block length of a co-polymer sequence.
This function calculates the blockiness of a co-polymer sequence by counting the occurrences of 'BB' and 'BA' or 'AB' in the sequence.
It also calculates the average block length of 'A' and 'B' monomers in the sequence.
Parameters
----------
sequence : str
A string representing the co-polymer sequence. 'A' represents one type of monomer and 'B' represents another type.
Returns
-------
tuple
A tuple containing the following elements:
- blockiness (float): The blockiness of the co-polymer sequence. Calculated as the ratio of 'BB' to 'BA' or 'AB'.
- block_length_A (float): The average block length of 'A' in the sequence.
- block_length_B (float): The average block length of 'B' in the sequence.
Notes
-----
If the sequence does not contain both 'A' and 'B', the function returns a string indicating that the molecule is not a co-polymer.
"""
if 'A' in sequence and 'B' in sequence: #Check if sequence is a co-polymer
AB = sequence.count('AB')
BB = sequence.count('BB')
BA = sequence.count('BA')
AA = sequence.count('AA')
if 'BA' in sequence:
blockiness = BB/BA
else:
blockiness = BB/AB
#Calculate block length B
block_list_B = [x for x in sequence.split('A') if x!='']
block_length_B = mean([len(b) for b in block_list_B])
#Calculate block length A
block_list_A = [x for x in sequence.split('B') if x!='']
block_length_A = mean([len(b) for b in block_list_A])
return blockiness, block_length_B, block_length_A
else:
return 'Molecule is not a co-polymer, no blockiness calculation performed', 0, len(sequence)
[docs]
def calculate_box_components(chains, monomers, sequence, salt_concentration = 0.0 * unit.mole / unit.liter, residual_monomer = 0.00, solvated=True):
"""
Calculates the components required to construct a simulation box for a given set of molecular chains.
This function determines the quantity of each molecule type required, considering the salt concentration
and residual monomer concentration. It is adapted from the OpenFF Toolkit Packmol wrapper's solvate_topology function.
Parameters:
-----------
chains : list
A list of molecular chains to be included in the simulation box.
sequence : str
A string representing the sequence of the molecular chains. 'G' and 'L' represent different types of monomers.
salt_concentration : float, optional
The desired salt concentration in the simulation box. Defaults to 0 M.
residual_monomer : float, optional
The desired residual monomer concentration in the simulation box. Defaults to 0.00%.
solvated : bool, optional
Indicates whether the system contains water. Defaults to False.
Returns:
--------
tuple
A tuple containing the following elements:
- molecules (list): A list of molecules to be included in the simulation box.
- number_of_copies (list): A list indicating the quantity of each molecule to be included in the simulation box.
- topology (openff.toolkit.topology.Topology): The topology of the simulation box.
- box_vectors (numpy.ndarray): The vectors defining the dimensions of the simulation box.
Notes:
------
This function is adapted from the OpenFF Toolkit Packmol wrapper's solvate_topology function.
"""
from openff.toolkit.topology import Molecule, Topology
from openff.interchange.components._packmol import UNIT_CUBE, pack_box, RHOMBIC_DODECAHEDRON, solvate_topology
from openff.interchange.components._packmol import _max_dist_between_points, _compute_brick_from_box_vectors, _center_topology_at
import warnings
if not solvated and len(chains) < 15:
warnings.warn('Residual monomer calculation may not be accurate for small systems. Please check the output by querying the value of residual_monomer_actual')
#Create molecules for the purpose of mass calculation
#Water
water = Molecule.from_smiles('O')
water.generate_unique_atom_names()
water.generate_conformers()
water_mass = sum([atom.mass for atom in water.atoms])
#Sodium
na = Molecule.from_smiles('[Na+]')
na.generate_unique_atom_names()
na.generate_conformers()
#Chloride
cl = Molecule.from_smiles('[Cl-]')
cl.generate_unique_atom_names()
cl.generate_conformers()
nacl_mass = sum([atom.mass for atom in na.atoms]) + sum(
[atom.mass for atom in cl.atoms],)
# Create a topology from the chains
topology = Topology.from_molecules(chains)
nacl_conc=salt_concentration
padding= 0.1 * unit.nanometer
box_shape= UNIT_CUBE
target_density= 1.0 * unit.gram / unit.milliliter
# Compute box vectors from the solute length and requested padding
if chains[0].n_conformers == 0:
raise ValueError("The solvate_topology function requires that the solute has at least one conformer.")
solute_length = max(_max_dist_between_points(chains[i].to_topology().get_positions()) for i in range(len(chains)))
image_distance = solute_length + padding * 2
box_vectors = box_shape * image_distance
# Compute target masses of solvent
box_volume = np.linalg.det(box_vectors.m) * box_vectors.u**3
target_mass = box_volume * target_density
solvent_mass = target_mass - sum(sum([atom.mass for atom in molecule.atoms]) for molecule in topology.molecules)
# Compute the number of NaCl to add from the mass and concentration
nacl_mass_fraction = (nacl_conc * nacl_mass) / (55.5 * unit.mole / unit.liter * water_mass)
nacl_to_add = ((solvent_mass * nacl_mass_fraction) / nacl_mass).m_as(unit.dimensionless).round()
if solvated:
water_to_add = int(round((solvent_mass - nacl_mass) / water_mass).m_as(unit.dimensionless).round())
else:
water_to_add = 0
# Neutralise the system by adding and removing salt
solute_charge = sum([molecule.total_charge for molecule in topology.molecules])
na_to_add = int(round(np.ceil(nacl_to_add - solute_charge.m / 2.0)))
cl_to_add = int(round(np.floor(nacl_to_add + solute_charge.m / 2.0)))
rolling_mass=0
for m in topology.molecules:
rolling_mass += sum(atom.mass for atom in m.atoms)
rolling_mass += nacl_mass * nacl_to_add
if solvated:
rolling_mass += water_mass * water_to_add
# residual monomer to add
mass_to_add = (rolling_mass.magnitude/100-residual_monomer) * residual_monomer
if 'A' in sequence and 'B' in sequence:
A_rd = Chem.MolFromSmiles(monomers[0])
info = Chem.AtomPDBResidueInfo()
info.SetResidueName('A' + str(1))
info.SetResidueNumber(1)
[atom.SetMonomerInfo(info) for atom in A_rd.GetAtoms()]
A = Molecule.from_rdkit(A_rd)
A_mass = sum([atom.mass for atom in A.atoms])
B_rd = Chem.MolFromSmiles(monomers[0])
info = Chem.AtomPDBResidueInfo()
info.SetResidueName('B' + str(1))
info.SetResidueNumber(1)
[atom.SetMonomerInfo(info) for atom in B_rd.GetAtoms()]
B = Molecule.from_rdkit(B_rd)
B_mass = sum([atom.mass for atom in B.atoms])
for r in range(0,100):
if (r * A_mass.magnitude) + (r * B_mass.magnitude) <= mass_to_add:
A_to_add = r
B_to_add = r
else:
break
residual_monomer_actual = ((A_to_add * A_mass.magnitude + B_to_add * B_mass.magnitude) / rolling_mass.magnitude) *100
molecules = [water, na, cl, A, B]
number_of_copies=[water_to_add, na_to_add, cl_to_add, A_to_add, B_to_add]
elif 'A' in sequence and 'B' not in sequence:
A_rd = Chem.MolFromSmiles(monomers[0])
info = Chem.AtomPDBResidueInfo()
info.SetResidueName('A' + str(1))
info.SetResidueNumber(1)
[atom.SetMonomerInfo(info) for atom in A_rd.GetAtoms()]
A = Molecule.from_rdkit(A_rd)
A_mass = sum([atom.mass for atom in A.atoms])
B = Molecule.from_smiles('C')
for r in range(0,100):
if r * A_mass.magnitude <= mass_to_add:
A_to_add = r
else:
break
B_to_add = 0
residual_monomer_actual = ((A_to_add * A_mass.magnitude) / rolling_mass.magnitude) * 100
molecules = [water, na, cl, A, B]
number_of_copies=[water_to_add, na_to_add, cl_to_add, A_to_add, B_to_add]
return molecules, number_of_copies, topology, box_vectors, residual_monomer_actual
#Class object for generic polymer system
[docs]
class polymer_system:
from openeye import oechem
from openff.toolkit.utils.toolkits import RDKitToolkitWrapper, OpenEyeToolkitWrapper
from functools import reduce
from statistics import mean
from rdkit.Chem.Descriptors import ExactMolWt
from openff.interchange import Interchange
from openff.interchange.components._packmol import UNIT_CUBE, pack_box
from swiftpol.build import build_polymer, PDI, blockiness_gen, calculate_box_components
from openff.units import unit
from rdkit.Chem import AllChem
import numpy as np
[docs]
def __init__(self, monomer_list, reaction, length_target, num_chains, terminals='standard', perc_A_target=100, blockiness_target=1.0, copolymer=False, acceptance = 10):
"""
Initialize the polymer system and build the polymer chains.
**Parameters:**
------------
monomer_list (list): List of monomers to be used in the polymerization.
reaction (str): The type of reaction to be used for polymerization.
length_target (float): The target length of the polymer chains.
num_chains (int): The number of polymer chains to be generated.
terminals (str, optional): The type of terminal groups to be used. Default is 'standard'.
perc_A_target (float, optional): The target percentage of monomer A in the copolymer. Default is 100.
blockiness_target (float, optional): The target blockiness of the copolymer. Default is 1.0.
copolymer (bool, optional): Flag to indicate if the system is a copolymer. Default is False.
acceptance = % deviation of blockiness and A percentage from target values. Default is 10%
**Attributes:**
---------------
length_target (float): The target length of the polymer chains.
terminals (str): The type of terminal groups used.
blockiness_target (float): The target blockiness of the copolymer.
A_target (float): The target percentage of monomer A in the copolymer.
chains (list): List of polymer chains as OpenFF Molecule objects.
chain_rdkit (list): List of polymer chains as RDKit molecule objects.
lengths (list): List of lengths of the polymer chains.
perc_A_actual (list): List of actual percentages of monomer A in the polymer chains.
B_block_length (float): The average block length of monomer B in the copolymer.
A_block_length (float): The average block length of monomer A in the copolymer.
blockiness_list (list): List of blockiness values for the polymer chains.
mean_blockiness (float): The mean blockiness of the polymer chains.
mol_weight_average (float): The average molecular weight of the polymer chains.
PDI (float): The polydispersity index of the polymer chains.
Mn (float): The number-average molecular weight of the polymer chains.
Mw (float): The weight-average molecular weight of the polymer chains.
num_chains (int): The number of polymer chains generated.
length_average (float): The average length of the polymer chains.
min_length (float): The minimum length of the polymer chains.
max_length (float): The maximum length of the polymer chains.
"""
self.length_target = length_target
self.terminals = terminals
perc_A_actual = []
if copolymer==True:
self.blockiness_target = blockiness_target
self.A_target = perc_A_target
def spec(sequence, blockiness): #Define limits of A percentage and blockiness from input
acceptance_dec = acceptance/100
actual_A = (sequence.count('A')/len(sequence))*100
blockiness = blockiness_gen(sequence)[0]
return actual_A > perc_A_target*(1-acceptance_dec) and actual_A < perc_A_target*(1+acceptance_dec) and blockiness>blockiness_target*(1-acceptance_dec) and blockiness<blockiness_target*(1+acceptance_dec)
blockiness_list = []
out_of_spec = 0
BBL = []
ABL = []
chains = []
chains_rdkit = []
lengths = []
self.monomers = [mono.replace("[I]", "") for mono in monomer_list]
#First round of building - copolymer
if copolymer==True:
for n in range(num_chains):
length_actual = np.random.normal(length_target, 0.5)
sequence = reduce(lambda x, y: x + y, np.random.choice(['A', 'B'], size=(int(length_actual),), p=[perc_A_target/100,1-(perc_A_target/100)]))
blockiness = blockiness_gen(sequence)[0]
if spec(sequence, blockiness)==True:
pol = build_polymer(sequence=sequence, monomer_list = monomer_list, reaction = reaction, terminal=terminals, chain_num=n+1)
lengths.append(int(length_actual))
chains_rdkit.append(pol)
chain = Molecule.from_rdkit(pol)
chains.append(chain)
perc_A_actual.append((sequence.count('A')/len(sequence))*100)
blockiness_list.append(blockiness)
BBL.append(blockiness_gen(sequence)[1])
ABL.append(blockiness_gen(sequence)[2])
else:
out_of_spec +=1
#Second round of building
while out_of_spec >0:
length_actual = np.random.normal(length_target, 0.5)
sequence = reduce(lambda x, y: x + y, np.random.choice(['A', 'B'], size=(int(length_actual),), p=[perc_A_target/100,1-(perc_A_target/100)]))
blockiness = blockiness_gen(sequence)[0]
if spec(sequence, blockiness)==True:
pol = build_polymer(sequence=sequence, monomer_list = monomer_list, reaction = reaction, terminal=terminals, chain_num=n+1)
lengths.append(int(length_actual))
chains_rdkit.append(pol)
chain = Molecule.from_rdkit(pol)
chains.append(chain)
perc_A_actual.append((sequence.count('A')/len(sequence))*100)
blockiness_list.append(blockiness)
BBL.append(blockiness_gen(sequence)[1])
ABL.append(blockiness_gen(sequence)[2])
out_of_spec-=1
self.B_block_length = mean(BBL)
self.A_block_length = mean(ABL)
self.blockiness_list = blockiness_list
self.mean_blockiness = mean(blockiness_list)
self.perc_A_actual = perc_A_actual
self.A_actual = mean(perc_A_actual)
else:
for n in range(num_chains):
length_actual = np.random.normal(length_target, 0.5)
sequence = reduce(lambda x, y: x + y, np.random.choice(['A', 'B'], size=(int(length_actual),), p=[perc_A_target/100,1-(perc_A_target/100)]))
pol = build_polymer(sequence=sequence, monomer_list = monomer_list, reaction = reaction, terminal=terminals, chain_num=n+1)
lengths.append(int(length_actual))
chains_rdkit.append(pol)
chain = Molecule.from_rdkit(pol)
chains.append(chain)
perc_A_actual.append((sequence.count('A')/len(sequence))*100)
self.sequence = sequence
self.chains = chains
for i in range(len(self.chains)):
self.chains[i].name = 'chain' + str(i+1)
self.chain_rdkit = chains_rdkit
self.mol_weight_average = round(mean([ExactMolWt(c) for c in chains_rdkit]),2)
self.PDI, self.Mn, self.Mw = PDI(chains_rdkit)
self.num_chains = len(chains)
self.A_actual = mean(perc_A_actual)
self.perc_A_actual = perc_A_actual
self.length_average = mean(lengths)
self.lengths = lengths
self.min_length = min(lengths)
self.max_length = max(lengths)
print('System built!, size =', self.num_chains)
[docs]
def charge_system(self, charge_scheme):
"""
Assign partial charges to each polymer chain in the system.
This method uses one of AM1-BCC, Espaloma, or OpenFF NAGL to assign partial charges to each polymer chain in the system.
It iterates over each chain in the `self.chains` list and assigns partial charges to the chain.
Parameters
----------
charge_scheme : str
The charge assignment scheme to use. Options are 'AM1_BCC', 'espaloma', or 'NAGL'.
Raises
------
ImportError
If the selected toolkit is not available.
"""
from swiftpol.parameterize import charge_openff_polymer
for chain in self.chains:
chain.partial_charges = charge_openff_polymer(chain, charge_scheme)