Source code for openmicron.forcefield.functionterms.dihedral_terms
import pandas as pd
import openmm as mm
from openmm import unit
import numpy as np
[docs]
def native_dihd_term(nat_dihd_info,use_pbc=False,force_group=1):
"""
ordinary dihedral angle potential.
Parameters
----------
nat_dihd_info : pd.DataFrame
Information for all native dihedral.
use_pbc : bool, optional
Whether use periodic boundary conditions. If False (default),then pbc would not apply to force.
force_group : int
Force group.
"""
# create a custom Tortion force
nat_tortion_force = mm.CustomTorsionForce("k_dih1*(1 - cos(dth)) + k_dih3*(1 - cos(3*dth));dth=theta-theta0")
nat_tortion_force.addPerTorsionParameter("k_dih1")
nat_tortion_force.addPerTorsionParameter("theta0")
nat_tortion_force.addPerTorsionParameter("k_dih3")
for row in nat_dihd_info.itertuples():
nat_tortion_force.addTorsion(row.a1, row.a2, row.a3, row.a4, [row.k_dihd1,row.natdihd,row.k_dihd3])
nat_tortion_force.setUsesPeriodicBoundaryConditions(use_pbc)
nat_tortion_force.setForceGroup(force_group)
return nat_tortion_force
[docs]
def aicg_dihd_term(aicg_dihd_info,use_pbc=False,force_group=1):
"""
A structure-based local contact potential to describe the chirality of local interactions (dihedral angle of backbone) and reference from
"Li, W., Wang, W., & Takada, S. (2014). Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains.
Proceedings of the National Academy of Sciences, 111(29), 10550-10555".
Parameters
----------
aicg_dihd_info : pd.DataFrame
Information for all aicg dihedral angle
use_pbc : bool, optional
Whether use periodic boundary conditions. If False (default),then pbc would not apply to force.
force_group : int
Force group.
Return
------
aicg_dihd_force : Force
OpenMM Force object
"""
energy_function = f'''-epsilon*exp(gex);
gex=-dt_periodic^2/(2*width^2);
dt_periodic = dt-floor((dt+{np.pi})/(2*{np.pi}))*(2*{np.pi});
dt=theta - theta0
'''
aicg_dihd_force = mm.CustomTorsionForce(energy_function)
aicg_dihd_force.addPerTorsionParameter("epsilon")
aicg_dihd_force.addPerTorsionParameter("theta0")
aicg_dihd_force.addPerTorsionParameter("width")
for row in aicg_dihd_info.itertuples():
aicg_dihd_force.addTorsion(row.a1, row.a2, row.a3, row.a4, [row.epsilon, row.natdihd, row.width])
aicg_dihd_force.setUsesPeriodicBoundaryConditions(use_pbc)
aicg_dihd_force.setForceGroup(force_group)
return aicg_dihd_force
[docs]
def flex_dihd_term(flex_dihd_info,use_pbc=False,force_group=1):
"""a sequence dependence flexible local dihedral interaction
flex_dihd_info : pd.DataFrame
Information for all aicg dihedral angle
Parameters
----------
flex_dihd_info : pd.DataFrame
Information for all flexible local dihedral angle
use_pbc : bool, optional
Whether use periodic boundary conditions. If False (default),then pbc would not apply to force.
force_group : int
Force group.
Return
------
flex_dihd_force : Force
OpenMM Force object
"""
flex_dihd_force = mm.CustomTorsionForce("C+c1*cos(theta)+s1*sin(theta)+ \
c2*cos(2*theta)+s2*sin(2*theta)+\
c3*cos(3*theta)+s3*sin(3*theta)-fdih_ener_corr")
flex_dihd_force.addPerTorsionParameter("C")
flex_dihd_force.addPerTorsionParameter("c1")
flex_dihd_force.addPerTorsionParameter("s1")
flex_dihd_force.addPerTorsionParameter("c2")
flex_dihd_force.addPerTorsionParameter("s2")
flex_dihd_force.addPerTorsionParameter("c3")
flex_dihd_force.addPerTorsionParameter("s3")
flex_dihd_force.addPerTorsionParameter("fdih_ener_corr")
for _,row in flex_dihd_info.iterrows():
a1 = row['a1']
a2 = row['a2']
a3 = row['a3']
a4 = row['a4']
para = row[4:]
flex_dihd_force.addTorsion(a1,a2,a3,a4,para)
flex_dihd_force.setUsesPeriodicBoundaryConditions(use_pbc)
flex_dihd_force.setForceGroup(force_group)
return flex_dihd_force
