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Commit 74f6ea57 authored by tic20's avatar tic20
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Numpyfication of custom GB forces

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wrappers/python/simtk/openmm/app/internal/customgbforces.py
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......@@ -34,6 +34,7 @@ from __future__ import division, absolute_import
from collections import defaultdict
import copy
import numpy
from simtk.openmm.app import element as E
from simtk.openmm import CustomGBForce, Discrete2DFunction
import simtk.unit as u
......@@ -48,7 +49,8 @@ def strip_unit(value, unit):
# GBn and GBn2 lookup tables
d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
d0= numpy.array(
[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196,
3.18854,3.24498,3.30132,3.35752,3.4136,
2.31191,2.37017,2.4283,2.48632,2.5442,2.60197,2.65961,2.71711,
......@@ -110,9 +112,11 @@ d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
4.04598,4.09974,4.15347,4.20715,4.26078,
3.22855,3.28307,3.33751,3.39188,3.4462,3.50046,3.55466,3.6088,
3.6629,3.71694,3.77095,3.82489,3.8788,3.93265,3.98646,4.04022,
4.09395,4.14762,4.20126,4.25485,4.3084]
4.09395,4.14762,4.20126,4.25485,4.3084],
numpy.double)
m0=[0.0381511,0.0338587,0.0301776,0.027003,0.0242506,0.0218529,
m0=numpy.array(
[0.0381511,0.0338587,0.0301776,0.027003,0.0242506,0.0218529,
0.0197547,0.0179109,0.0162844,0.0148442,0.0135647,0.0124243,
0.0114047,0.0104906,0.00966876,0.008928,0.0082587,0.00765255,
0.00710237,0.00660196,0.00614589,
......@@ -195,10 +199,11 @@ m0=[0.0381511,0.0338587,0.0301776,0.027003,0.0242506,0.0218529,
0.0609642,0.0546169,0.0491183,0.0443295,0.0401388,0.036455,
0.0332033,0.030322,0.0277596,0.0254732,0.0234266,0.0215892,
0.0199351,0.018442,0.0170909,0.0158654,0.0147514,0.0137365,
0.0128101,0.0119627,0.0111863]
0.0128101,0.0119627,0.0111863],
numpy.double)
# Rescale to nanometers
d0 = [d / 10. for d in d0]
m0 = [m * 10. for m in m0]
d0/=10
m0*=10
def _get_bonded_atom_list(topology):
......@@ -232,38 +237,45 @@ def _is_carboxylateO(atom, all_bonds):
def _bondi_radii(topology):
""" Sets the bondi radii """
radii = [0.0 for atom in topology.atoms()]
default_radius = 1.5
element_to_radius = {
E.carbon: 1.7,
E.hydrogen: 1.2,
E.deuterium: 1.2,
E.nitrogen: 1.55,
E.oxygen: 1.5,
E.fluorine: 1.5,
E.silicon: 2.1,
E.phosphorus: 1.85,
E.sulfur: 1.8,
E.chlorine: 1.5,
}
natoms = topology.getNumAtoms()
radii = numpy.empty(topology.getNumAtoms(), numpy.double)
for i, atom in enumerate(topology.atoms()):
if atom.element is E.carbon:
radii[i] = 1.7
elif atom.element in (E.hydrogen, E.deuterium):
radii[i] = 1.2
elif atom.element is E.nitrogen:
radii[i] = 1.55
elif atom.element is E.oxygen:
radii[i] = 1.5
elif atom.element is E.fluorine:
radii[i] = 1.5
elif atom.element is E.silicon:
radii[i] = 2.1
elif atom.element is E.phosphorus:
radii[i] = 1.85
elif atom.element is E.sulfur:
radii[i] = 1.8
elif atom.element is E.chlorine:
radii[i] = 1.5
else:
radii[i] = 1.5
radii[i] = element_to_radius.get(atom.element, default_radius)
return radii # converted to nanometers above
def _mbondi_radii(topology):
def _mbondi_radii(topology, all_bonds = None):
""" Sets the mbondi radii """
radii = [0.0 for atom in topology.atoms()]
all_bonds = _get_bonded_atom_list(topology)
default_radius = 1.5
element_to_const_radius = {
E.nitrogen: 1.55,
E.oxygen: 1.5,
E.fluorine: 1.5,
E.silicon: 2.1,
E.phosphorus: 1.85,
E.sulfur: 1.8,
E.chlorine: 1.5,
}
radii = numpy.empty(topology.getNumAtoms(), numpy.double)
if all_bonds is None:
all_bonds = _get_bonded_atom_list(topology)
for i, atom in enumerate(topology.atoms()):
# Radius of H atom depends on element it is bonded to
if atom.element in (E.hydrogen, E.deuterium):
element = atom.element
if element in (E.hydrogen, E.deuterium):
bondeds = all_bonds[atom]
if bondeds[0].element in (E.carbon, E.nitrogen):
radii[i] = 1.3
......@@ -272,67 +284,51 @@ def _mbondi_radii(topology):
else:
radii[i] = 1.2
# Radius of C atom depends on what type it is
elif atom.element is E.carbon:
elif element is E.carbon:
radii[i] = 1.7
# All other elements have fixed radii for all types/partners
elif atom.element is E.nitrogen:
radii[i] = 1.55
elif atom.element is E.oxygen:
radii[i] = 1.5
elif atom.element is E.fluorine:
radii[i] = 1.5
elif atom.element is E.silicon:
radii[i] = 2.1
elif atom.element is E.phosphorus:
radii[i] = 1.85
elif atom.element is E.sulfur:
radii[i] = 1.8
elif atom.element is E.chlorine:
radii[i] = 1.5
else:
radii[i] = 1.5
radii[i] = element_to_const_radius.get(element, default_radius)
return radii # converted to nanometers above
def _mbondi2_radii(topology):
def _mbondi2_radii(topology, all_bonds = None):
""" Sets the mbondi2 radii """
radii = [0.0 for atom in topology.atoms()]
all_bonds = _get_bonded_atom_list(topology)
default_radius = 1.5
element_to_const_radius = {
E.nitrogen: 1.55,
E.oxygen: 1.5,
E.fluorine: 1.5,
E.silicon: 2.1,
E.phosphorus: 1.85,
E.sulfur: 1.8,
E.chlorine: 1.5,
}
radii = numpy.empty(topology.getNumAtoms(), numpy.double)
if all_bonds is None:
all_bonds = _get_bonded_atom_list(topology)
for i, atom in enumerate(topology.atoms()):
element = atom.element
# Radius of H atom depends on element it is bonded to
if atom.element in (E.hydrogen, E.deuterium):
if element in (E.hydrogen, E.deuterium):
bondeds = all_bonds[atom]
if bondeds[0].element is E.nitrogen:
radii[i] = 1.3
else:
radii[i] = 1.2
# Radius of C atom depends on what type it is
elif atom.element is E.carbon:
elif element is E.carbon:
radii[i] = 1.7
# All other elements have fixed radii for all types/partners
elif atom.element is E.nitrogen:
radii[i] = 1.55
elif atom.element is E.oxygen:
radii[i] = 1.5
elif atom.element is E.fluorine:
radii[i] = 1.5
elif atom.element is E.silicon:
radii[i] = 2.1
elif atom.element == E.phosphorus:
radii[i] = 1.85
elif atom.element == E.sulfur:
radii[i] = 1.8
elif atom.element == E.chlorine:
radii[i] = 1.5
else:
radii[i] = 1.5
radii[i] = element_to_const_radius.get(element, default_radius)
return radii # Converted to nanometers above
def _mbondi3_radii(topology):
def _mbondi3_radii(topology, all_bonds = None):
""" Sets the mbondi3 radii """
radii = _mbondi2_radii(topology)
all_bonds = _get_bonded_atom_list(topology)
if all_bonds is None:
all_bonds = _get_bonded_atom_list(topology)
radii = _mbondi2_radii(topology, all_bonds=all_bonds)
for i, atom in enumerate(topology.atoms()):
# carboxylate and HH/HE (ARG)
if _is_carboxylateO(atom, all_bonds):
......@@ -391,12 +387,12 @@ _SCREEN_PARAMETERS = { # normal, GBn, GBn2
E.sulfur : (0.96, 0.602256336067, -0.703469),
None : (0.8, 0.5, 0.5) # default
}
for key, val in _SCREEN_PARAMETERS.items():
_SCREEN_PARAMETERS[key] = numpy.array(val, numpy.double)
_SCREEN_PARAMETERS[E.deuterium] = _SCREEN_PARAMETERS[E.hydrogen]
def _screen_parameter(atom):
if atom.element in _SCREEN_PARAMETERS:
return _SCREEN_PARAMETERS[atom.element]
return _SCREEN_PARAMETERS[None]
return _SCREEN_PARAMETERS.get(atom.element, _SCREEN_PARAMETERS[None])
class CustomAmberGBForceBase(CustomGBForce):
......@@ -439,6 +435,33 @@ class CustomAmberGBForceBase(CustomGBForce):
self.parameters.append(params)
return params
def addParticles(self, params):
"""Add a set of particles to the force
Particles are added in order. The total number of particles added to the
force must match the number of particles in the system.
Parameters
----------
params : list or numpy array
A (natoms * npar) dimensional array of parameters to add to the
force. The meaning of the parameters depends on the model. All
parameters should be simple floating-point values in OpenMM's
default units.
Returns
-------
None
"""
if isinstance(params, list):
params = numpy.array(params)
else:
params = copy.deepcopy(params)
params[:,self.RADIUS_ARG_POSITION] -= self.OFFSET
params[:,self.SCREEN_POSITION] *= params[:,self.RADIUS_ARG_POSITION]
self.parameters.extend(params.tolist())
@staticmethod
def getStandardParameters(topology):
""" Gets list of standard parameters for this GB model based on an input Topology
......@@ -528,9 +551,10 @@ class GBSAHCTForce(CustomAmberGBForceBase):
at the beginning of the list
"""
radii = [[x/10] for x in _mbondi_radii(topology)]
for i, atom in enumerate(topology.atoms()):
radii[i].append(_screen_parameter(atom)[0])
radii = numpy.empty((topology.getNumAtoms(), 2), numpy.double)
radii[:,0] = _mbondi_radii(topology)/10
for rad, atom in zip(radii, topology.atoms()):
rad[1] = _screen_parameter(atom)[0]
return radii
......@@ -590,9 +614,10 @@ class GBSAOBC1Force(CustomAmberGBForceBase):
at the beginning of the list
"""
radii = [[x/10] for x in _mbondi2_radii(topology)]
for i, atom in enumerate(topology.atoms()):
radii[i].append(_screen_parameter(atom)[0])
radii = numpy.empty((topology.getNumAtoms(), 2), numpy.double)
radii[:,0] = _mbondi2_radii(topology)/10
for rad, atom in zip(radii, topology.atoms()):
rad[1] = _screen_parameter(atom)[0]
return radii
......@@ -678,6 +703,14 @@ class GBSAGBnForce(CustomAmberGBForceBase):
if parameters[1] + self.OFFSET < 0.1 or parameters[1] + self.OFFSET > 0.2:
raise ValueError('Radii must be between 1 and 2 Angstroms for neck lookup')
def addParticles(self, parameters):
if isinstance(parameters, list):
parameters = numpy.array(parameters)
radii = parameters[:,1]
if numpy.any(numpy.logical_or(radii<0.1, radii>0.2)):
raise ValueError('Radii must be between 1 and 2 Angstroms for neck lookup')
CustomAmberGBForceBase.addParticles(self, parameters)
def finalize(self):
self._findUniqueRadii()
self._createRadiusToIndexMap()
......@@ -701,9 +734,10 @@ class GBSAGBnForce(CustomAmberGBForceBase):
at the beginning of the list
"""
radii = [[x/10] for x in _bondi_radii(topology)]
for i, atom in enumerate(topology.atoms()):
radii[i].append(_screen_parameter(atom)[1])
radii = numpy.empty((topology.getNumAtoms(), 2), numpy.double)
radii[:,0] = _bondi_radii(topology)/10
for rad, atom in zip(radii, topology.atoms()):
rad[1] = _screen_parameter(atom)[1]
return radii
def _findUniqueRadii(self):
......@@ -799,8 +833,57 @@ class GBSAGBn2Force(GBSAGBnForce):
def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None, kappa=0.0):
GBSAGBnForce.__init__(self, solventDielectric, soluteDielectric, SA, cutoff, kappa)
@staticmethod
def getStandardParameters(topology):
# @staticmethod
# def getStandardParameters(topology):
# """ Gets list of standard parameters for this GB model based on an input Topology
#
# Parameters
# ----------
# topology : simtk.openmm.app.Topology
# Topology of the system to get parameters for
#
# Returns
# -------
# list of float
# List of all parameters needed for this GB model. These can be passed
# to addParticle or setParticleParameters after the charge is inserted
# at the beginning of the list
#
# """
# import numpy
# natoms = topology.getNumAtoms()
# radii = numpy.empty((6,natoms), numpy.double)
# radii[:,0] = [[x/10] for x in _mbondi3_radii(topology)]
# for i, atom in enumerate(topology.atoms()):
# radii[i,1] = _screen_parameter(atom)[2]
# e = atom.element
# if e in (E.hydrogen, E.deuterium):
# radii[i, 2:]= [0.788440, 0.798699, 0.437334]
# elif atom.element is E.carbon:
# radii[i].extend([0.733756, 0.506378, 0.205844])
# elif atom.element is E.nitrogen:
# radii[i].extend([0.503364, 0.316828, 0.192915])
# elif atom.element is E.oxygen:
# radii[i].extend([0.867814, 0.876635, 0.387882])
# elif atom.element is E.sulfur:
# radii[i].extend([0.867814, 0.876635, 0.387882])
# else:
# radii[i].extend([0.8, 4.85, 0.5])
# return radii
_atom_params = {
E.hydrogen: numpy.array([0.788440, 0.798699, 0.437334]),
E.deuterium: numpy.array([0.788440, 0.798699, 0.437334]),
E.carbon: numpy.array([0.733756, 0.506378, 0.205844]),
E.nitrogen: numpy.array([0.503364, 0.316828, 0.192915]),
E.oxygen: numpy.array([0.867814, 0.876635, 0.387882]),
E.sulfur: numpy.array([0.867814, 0.876635, 0.387882]),
}
_default_atom_params = numpy.array([0.8, 4.85, 0.5]);
@classmethod
def getStandardParameters(cls, topology):
""" Gets list of standard parameters for this GB model based on an input Topology
Parameters
......@@ -816,21 +899,12 @@ class GBSAGBn2Force(GBSAGBnForce):
at the beginning of the list
"""
radii = [[x/10] for x in _mbondi3_radii(topology)]
for i, atom in enumerate(topology.atoms()):
radii[i].append(_screen_parameter(atom)[2])
if atom.element in (E.hydrogen, E.deuterium):
radii[i].extend([0.788440, 0.798699, 0.437334])
elif atom.element is E.carbon:
radii[i].extend([0.733756, 0.506378, 0.205844])
elif atom.element is E.nitrogen:
radii[i].extend([0.503364, 0.316828, 0.192915])
elif atom.element is E.oxygen:
radii[i].extend([0.867814, 0.876635, 0.387882])
elif atom.element is E.sulfur:
radii[i].extend([0.867814, 0.876635, 0.387882])
else:
radii[i].extend([0.8, 4.85, 0.5])
natoms = topology.getNumAtoms()
radii = numpy.empty([natoms,5], numpy.double)
radii[:,0] = _mbondi3_radii(topology)/10
for atom, rad in zip(topology.atoms(), radii):
rad[1] = _screen_parameter(atom)[2]
rad[2:] = cls._atom_params.get(atom.element, cls._default_atom_params)
return radii
def _addEnergyTerms(self):
......
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