from molsysmt._private.exceptions import *
from molsysmt import pyunitwizard as puw
from copy import deepcopy
[docs]
class MolecularMechanics():
def __init__(self, forcefield=None, water_model=None, implicit_solvent=None,
non_bonded_method=None, cutoff_distance=None, switch_distance=None,
dispersion_correction=None, ewald_error_tolerance=None,
constraints=None, flexible_constraints=None,
rigid_water=None, hydrogen_mass=None,
salt_concentration=None, kappa=None,
solute_dielectric=None, solvent_dielectric=None,
formal_charge=None, partial_charge=None):
# default values:
# non_bonded_method='no_cutoff'
# use_dispersion_correction=False
# ewald_error_tolerance=0.0001
# flexible_constraints=False
# rigid_water=True
# ignore_external_bonds=False
# implicit_solvent_salt_conc=0.0 mol/L
# implicit_solvent_kappa=0.0 1/nm
# solute_dielectric=1.0
# solvent_dielectric=78.5
self.formal_charge = formal_charge
self.partial_charge = partial_charge
self.forcefield = forcefield
self.non_bonded_method = non_bonded_method
self.cutoff_distance = cutoff_distance
self.switch_distance = switch_distance
self.dispersion_correction = dispersion_correction
self.ewald_error_tolerance = ewald_error_tolerance
self.hydrogen_mass = hydrogen_mass
self.constraints = constraints
self.flexible_constraints = flexible_constraints
self.water_model = water_model
self.rigid_water = rigid_water
#self.residue_templates = residue_templates
#self.ignore_external_bonds = ignore_external_bonds
self.implicit_solvent = implicit_solvent
self.solute_dielectric = solute_dielectric
self.solvent_dielectric = solvent_dielectric
self.salt_concentration = salt_concentration
self.kappa = kappa
[docs]
def to_dict(self):
tmp_dict = {
'formal_charge': self.formal_charge,
'partial_charge': self.partial_charge,
'forcefield' : self.forcefield,
'non_bonded_method' : self.non_bonded_method,
'cutoff_distance' : self.cutoff_distance,
'switch_distance' : self.switch_distance,
'dispersion_correction' : self.dispersion_correction,
'ewald_error_tolerance' : self.ewald_error_tolerance,
'hydrogen_mass' : self.hydrogen_mass,
'constraints' : self.constraints,
'flexible_constraints' : self.flexible_constraints,
'water_model' : self.water_model,
'rigid_water' : self.rigid_water,
'implicit_solvent' : self.implicit_solvent,
'solute_dielectric' : self.solute_dielectric,
'solvent_dielectric' : self.solvent_dielectric,
'salt_concentration' : self.salt_concentration,
'kappa' : self.kappa,
}
[docs]
def copy(self):
tmp_molecular_mechanics = MolecularMechanics()
tmp_molecular_mechanics.formal_charge = deepcopy(self.formal_charge)
tmp_molecular_mechanics.partial_charge = deepcopy(self.partial_charge)
tmp_molecular_mechanics.forcefield = deepcopy(self.forcefield)
tmp_molecular_mechanics.non_bonded_method = deepcopy(self.non_bonded_method)
tmp_molecular_mechanics.cutoff_distance = deepcopy(self.cutoff_distance)
tmp_molecular_mechanics.switch_distance = deepcopy(self.switch_distance)
tmp_molecular_mechanics.dispersion_correction = deepcopy(self.dispersion_correction)
tmp_molecular_mechanics.ewald_error_tolerance = deepcopy(self.ewald_error_tolerance)
tmp_molecular_mechanics.hydrogen_mass = deepcopy(self.hydrogen_mass)
tmp_molecular_mechanics.constraints = deepcopy(self.constraints)
tmp_molecular_mechanics.flexible_constraints = deepcopy(self.flexible_constraints)
tmp_molecular_mechanics.water_model = deepcopy(self.water_model)
tmp_molecular_mechanics.rigid_water = deepcopy(self.rigid_water)
tmp_molecular_mechanics.implicit_solvent = deepcopy(self.implicit_solvent)
tmp_molecular_mechanics.solute_dielectric = deepcopy(self.solute_dielectric)
tmp_molecular_mechanics.solvent_dielectric = deepcopy(self.solvent_dielectric)
tmp_molecular_mechanics.salt_concentration = deepcopy(self.salt_concentration)
tmp_molecular_mechanics.kappa = deepcopy(self.kappa)
return tmp_molecular_mechanics
[docs]
def set_parameters(self, return_non_processed=False, **kwargs):
for argument, value in kwargs.items():
if argument.lower() in self.__dict__.keys():
self.__dict__[argument]=puw.standardize(value)
del(kwargs[argment.lower()])
if return_non_processed:
return kwargs
else:
pass
[docs]
def get_leap_parameters(self):
from molsysmt.molecular_mechanics.forcefields import get_forcefield_names
parameters = {}
parameters['forcefield'] = get_forcefield_names(self.forcefield, 'LEaP', water_model=self.water_model, implicit_solvent=self.implicit_solvent)
parameters['water_model'] = self.water_model
parameters['implicit_solvent'] = self.implicit_solvent
return parameters
[docs]
def get_openmm_forcefield_names(self):
from molsysmt.molecular_mechanics.forcefields import get_forcefield_names
return get_forcefield_names(self.forcefield, 'OpenMM', water_model=self.water_model, implicit_solvent=self.implicit_solvent)
[docs]
def to_openmm_ForceField(self):
from openmm.app import ForceField
forcefield_names = self.get_openmm_forcefield_names()
forcefield = ForceField(*forcefield_names)
return forcefield
[docs]
def get_openmm_System_parameters(self):
from openmm import app
parameters = {}
if self.non_bonded_method=='no_cutoff':
parameters['nonbondedMethod']=app.NoCutoff
elif self.non_bonded_method=='cutoff_non_periodic':
parameters['nonbondedMethod']=app.CutoffNonPeriodic
elif self.non_bonded_method=='cutoff_periodic':
parameters['nonbondedMethod']=app.CutoffPeriodic
elif self.non_bonded_method=='Ewald':
parameters['nonbondedMethod']=app.Ewald
elif self.non_bonded_method=='PME':
parameters['nonbondedMethod']=app.PME
elif self.non_bonded_method=='LJPME':
parameters['nonbondedMethod']=app.LJPME
else:
raise NotImplementedError()
if self.non_bonded_cutoff is not None:
parameters['nonbondedCutoff']=puw.convert(self.cutoff_distance, to_form='openmm.unit',
to_unit='nm')
if self.switch_distance is not None:
parameters['switchDistance']=puw.convert(self.switch_distance, to_form='openmm.unit',
to_unit='nm')
if self.constraints is not None:
if self.constraints == 'h_bonds':
parameters['constraints']=app.HBonds
elif self.constraints == 'all_bonds':
parameters['constraints']=app.HBonds
elif self.constraints == 'h_angles':
parameters['constraints']=app.HAngles
else:
raise NotImplementedError()
else:
parameters['constraints']=None
parameters['hydrogenMass']=self.hydrogen_mass
parameters['rigidWater']=self.rigid_water
#parameters['removeCMMotion']=self.remove_cm_motion
parameters['residueTemplates']=self.residue_templates
parameters['ignoreExternalBonds']=self.ignore_external_bonds
parameters['flexibleConstraints']=self.flexible_constraints
if self.implicit_solvent is not None:
if self.implicit_solvent == 'HCT':
parameters['implicitSolvent']=app.HCT
elif self.implicit_solvent == 'OBC1':
parameters['implicitSolvent']=app.OBC1
elif self.implicit_solvent == 'OBC2':
parameters['implicitSolvent']=app.OBC2
elif self.implicit_solvent == 'GBn':
parameters['implicitSolvent']=app.GBn
elif self.implicit_solvent == 'GBn2':
parameters['implicitSolvent']=app.GBn2
else:
raise NotImplementedError
parameters['implicitSolventSaltConc']=puw.convert(self.salt_concentration,
to_unit='mole/liter', to_form='openmm.unit')
parameters['implicitSolventKappa']=puw.convert(self.kappa,
to_unit='1/nm', to_form='openmm.unit')
parameters['soluteDielectric']=self.solute_dielectric
parameters['solventDielectric']=self.solvent_dielectric
else:
parameters['implicitSolvent']=None
return parameters
