# -*- coding: utf-8 -*-
## Test with `python -m arbdmodel.hps_polymer_model`
import numpy as np
## Local imports
from .logger import logger
from . import ParticleType, PointParticle
from .polymer import PolymerBeads, PolymerModel
from .interactions import AbstractPotential, HarmonicBond
"""Define particle types"""
_types = dict(
A = ParticleType("ALA",
mass = 71.08,
charge = 0,
sigma = 5.04,
lambda_ = 0.72973,
),
R = ParticleType("ARG",
mass = 156.2,
charge = 1,
sigma = 6.56,
lambda_ = 0.0,
),
N = ParticleType("ASN",
mass = 114.1,
charge = 0,
sigma = 5.68,
lambda_ = 0.432432,
),
D = ParticleType("ASP",
mass = 115.1,
charge = -1,
sigma = 5.58,
lambda_ = 0.378378,
),
C = ParticleType("CYS",
mass = 103.1,
charge = 0,
sigma = 5.48,
lambda_ = 0.594595,
),
Q = ParticleType("GLN",
mass = 128.1,
charge = 0,
sigma = 6.02,
lambda_ = 0.513514,
),
E = ParticleType("GLU",
mass = 129.1,
charge = -1,
sigma = 5.92,
lambda_ = 0.459459,
),
G = ParticleType("GLY",
mass = 57.05,
charge = 0,
sigma = 4.5,
lambda_ = 0.648649,
),
H = ParticleType("HIS",
mass = 137.1,
charge = 0.5,
sigma = 6.08,
lambda_ = 0.513514,
),
I = ParticleType("ILE",
mass = 113.2,
charge = 0,
sigma = 6.18,
lambda_ = 0.972973,
),
L = ParticleType("LEU",
mass = 113.2,
charge = 0,
sigma = 6.18,
lambda_ = 0.972973,
),
K = ParticleType("LYS",
mass = 128.2,
charge = 1,
sigma = 6.36,
lambda_ = 0.513514,
),
M = ParticleType("MET",
mass = 131.2,
charge = 0,
sigma = 6.18,
lambda_ = 0.837838,
),
F = ParticleType("PHE",
mass = 147.2,
charge = 0,
sigma = 6.36,
lambda_ = 1.0,
),
P = ParticleType("PRO",
mass = 97.12,
charge = 0,
sigma = 5.56,
lambda_ = 1.0,
),
S = ParticleType("SER",
mass = 87.08,
charge = 0,
sigma = 5.18,
lambda_ = 0.594595,
),
T = ParticleType("THR",
mass = 101.1,
charge = 0,
sigma = 5.62,
lambda_ = 0.675676,
),
W = ParticleType("TRP",
mass = 186.2,
charge = 0,
sigma = 6.78,
lambda_ = 0.945946,
),
Y = ParticleType("TYR",
mass = 163.2,
charge = 0,
sigma = 6.46,
lambda_ = 0.864865,
),
V = ParticleType("VAL",
mass = 99.07,
charge = 0,
sigma = 5.86,
lambda_ = 0.891892,
)
)
for k,t in _types.items():
t.resname = t.name
[docs]
class HpsNonbonded(AbstractPotential):
def __init__(self, debye_length=10, resolution=0.1, range_=(0,None)):
AbstractPotential.__init__(self, resolution=resolution, range_=range_)
self.debye_length = debye_length
self.max_force = 50
[docs]
def potential(self, r, types):
""" Electrostatics """
typeA,typeB = types
ld = self.debye_length
q1 = typeA.charge
q2 = typeB.charge
D = 80 # dielectric of water
## units "e**2 / (4 * pi * epsilon0 AA)" kcal_mol
A = 332.06371
u_elec = (A*q1*q2/D)*np.exp(-r/ld) / r
""" Hydrophobicity scale model """
lambda_ = 0.5 * (typeA.lambda_ + typeB.lambda_)
sigma = 0.5 * (typeA.sigma + typeB.sigma)
epsilon = 0.2
r6 = (sigma/r)**6
r12 = r6**2
u_lj = 4 * epsilon * (r12-r6)
u_hps = lambda_ * np.array(u_lj)
s = r<=sigma*2**(1/6)
u_hps[s] = u_lj[s] + (1-lambda_) * epsilon
u = u_elec + u_hps
return u
[docs]
class HpsBeads(PolymerBeads):
def __init__(self, polymer, sequence=None,
spring_constant = 2.3900574,
rest_length = 3.8, **kwargs):
if sequence is None:
raise NotImplementedError
# ... set random sequence
self.spring_constant = spring_constant
PolymerBeads.__init__(self, polymer, sequence, rest_length=rest_length, **kwargs)
assert(self.monomers_per_bead_group == 1)
if len(sequence) != polymer.num_monomers:
raise ValueError("Length of sequence does not match length of polymer")
def _generate_ith_bead_group(self, i, r, o):
s = self.sequence[i]
return PointParticle(_types[s], r,
name = s,
resid = i+1)
def _join_adjacent_bead_groups(self, ids):
## Two consecutive nts
if len(ids) == 2:
b1,b2 = [self.children[i] for i in ids]
""" units "10 kJ/N_A" kcal_mol """
bond = HarmonicBond(k = self.spring_constant,
r0 = self.rest_length,
range_ = (0,500),
resolution = 0.01,
max_force = 10)
self.add_bond( i=b1, j=b2, bond = bond, exclude=True )
elif len(ids) == 3:
...
else:
pass
[docs]
class HpsModel(PolymerModel):
def __init__(self, polymers,
sequences = None,
rest_length = 3.8,
spring_constant = 2.3900574,
debye_length = 10,
damping_coefficient = 10,
DEBUG=False,
**kwargs):
"""
[debye_length]: angstroms
[damping_coefficient]: 1/ns
"""
if 'timestep' not in kwargs: kwargs['timestep'] = 10e-6
if 'cutoff' not in kwargs: kwargs['cutoff'] = max(4*debye_length,20)
if 'decomp_period' not in kwargs:
kwargs['decomp_period'] = 1000
self.rest_length = rest_length
self.spring_constant = spring_constant
""" Assign sequences """
if sequences is None:
raise NotImplementedError("HpsModel must be provided a sequences argument")
PolymerModel.__init__(self, polymers, sequences, monomers_per_bead_group=1, **kwargs)
""" Update type diffusion coefficients """
self.types = all_types = [t for key,t in _types.items()]
self.set_damping_coefficient( damping_coefficient )
""" Set up nonbonded interactions """
nonbonded = HpsNonbonded(debye_length)
self.types
for i in range(len(all_types)):
t1 = all_types[i]
for j in range(i,len(all_types)):
t2 = all_types[j]
self.add_nonbonded_interaction( nonbonded, typeA=t1, typeB=t2 )
def _generate_polymer_beads(self, polymer, sequence, polymer_index=None):
return HpsBeads(polymer, sequence,
rest_length = self.rest_length,
spring_constant = self.spring_constant,
monomers_per_bead_group = self.monomers_per_bead_group,
polymer_index = polymer_index
)
[docs]
def set_damping_coefficient(self, damping_coefficient):
for t in self.types:
t.damping_coefficient = damping_coefficient
# t.diffusivity = 831447.2 * temperature / (t.mass * damping_coefficient)
if __name__ == "__main__":
print("TYPES")
for n,t in _types.items():
print("{}\t{}\t{}\t{}\t{}".format(t.name, t.mass, t.charge, t.sigma, t.lambda_))