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Commit 99ef4344 authored by Lee-Ping Wang's avatar Lee-Ping Wang
Browse files

Merge branch 'master' of github.com:SimTk/openmm

parents 471bea82 79fd69c3
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wrappers/python/simtk/openmm/__init__.py
View file @ 99ef4344
...@@ -13,7 +13,7 @@ It also tries to load any plugin modules it can find. ...@@ -13,7 +13,7 @@ It also tries to load any plugin modules it can find.
__author__ = "Randall J. Radmer" __author__ = "Randall J. Radmer"
import os, sys, glob import os, sys, glob, os.path
if sys.platform == "win32": if sys.platform == "win32":
libPrefix="" libPrefix=""
libExt="dll" libExt="dll"
...@@ -34,5 +34,9 @@ else: ...@@ -34,5 +34,9 @@ else:
from simtk.openmm.openmm import * from simtk.openmm.openmm import *
from simtk.openmm.vec3 import Vec3 from simtk.openmm.vec3 import Vec3
pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory()) from simtk.openmm import version
if os.getenv('OPENMM_PLUGIN_DIR') is None and os.path.isdir(version.openmm_library_path):
pluginLoadedLibNames = Platform.loadPluginsFromDirectory(os.path.join(version.openmm_library_path, 'plugins'))
else:
pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
__version__ = Platform.getOpenMMVersion() __version__ = Platform.getOpenMMVersion()
wrappers/python/simtk/openmm/app/__init__.py
View file @ 99ef4344
...@@ -24,6 +24,7 @@ from dcdreporter import DCDReporter ...@@ -24,6 +24,7 @@ from dcdreporter import DCDReporter
from modeller import Modeller from modeller import Modeller
from statedatareporter import StateDataReporter from statedatareporter import StateDataReporter
from element import Element from element import Element
from desmonddmsfile import DesmondDMSFile
# Enumerated values # Enumerated values
......
wrappers/python/simtk/openmm/app/amberprmtopfile.py
View file @ 99ef4344
...@@ -61,6 +61,11 @@ class GBn(object): ...@@ -61,6 +61,11 @@ class GBn(object):
return 'GBn' return 'GBn'
GBn = GBn() GBn = GBn()
class GBn2(object):
def __repr__(self):
return 'GBn2'
GBn2 = GBn2()
class AmberPrmtopFile(object): class AmberPrmtopFile(object):
"""AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it.""" """AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it."""
...@@ -69,6 +74,7 @@ class AmberPrmtopFile(object): ...@@ -69,6 +74,7 @@ class AmberPrmtopFile(object):
top = Topology() top = Topology()
## The Topology read from the prmtop file ## The Topology read from the prmtop file
self.topology = top self.topology = top
self.elements = []
# Load the prmtop file # Load the prmtop file
...@@ -96,21 +102,30 @@ class AmberPrmtopFile(object): ...@@ -96,21 +102,30 @@ class AmberPrmtopFile(object):
if atomName in atomReplacements: if atomName in atomReplacements:
atomName = atomReplacements[atomName] atomName = atomReplacements[atomName]
# Try to guess the element. # Get the element from the prmtop file if available
if prmtop.has_atomic_number:
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
else:
try: try:
element = elem.get_by_symbol(atomName[0]) element = elem.Element.getByAtomicNumber(int(prmtop._raw_data['ATOMIC_NUMBER'][index]))
except KeyError: except KeyError:
element = None element = None
else:
# Try to guess the element from the atom name.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
top.addAtom(atomName, element, r) top.addAtom(atomName, element, r)
self.elements.append(element)
# Add bonds to the topology # Add bonds to the topology
...@@ -137,7 +152,7 @@ class AmberPrmtopFile(object): ...@@ -137,7 +152,7 @@ class AmberPrmtopFile(object):
- constraints (object=None) Specifies which bonds angles should be implemented with constraints. - constraints (object=None) Specifies which bonds angles should be implemented with constraints.
Allowed values are None, HBonds, AllBonds, or HAngles. Allowed values are None, HBonds, AllBonds, or HAngles.
- rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument - rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
- implicitSolvent (object=None) If not None, the implicit solvent model to use. Allowed values are HCT, OBC1, OBC2, or GBn. - implicitSolvent (object=None) If not None, the implicit solvent model to use. Allowed values are HCT, OBC1, OBC2, GBn, or GBn2.
- soluteDielectric (float=1.0) The solute dielectric constant to use in the implicit solvent model. - soluteDielectric (float=1.0) The solute dielectric constant to use in the implicit solvent model.
- solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model. - solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model.
- removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
...@@ -167,19 +182,22 @@ class AmberPrmtopFile(object): ...@@ -167,19 +182,22 @@ class AmberPrmtopFile(object):
raise ValueError('Illegal value for constraints') raise ValueError('Illegal value for constraints')
if implicitSolvent is None: if implicitSolvent is None:
implicitString = None implicitString = None
elif implicitSolvent == HCT: elif implicitSolvent is HCT:
implicitString = 'HCT' implicitString = 'HCT'
elif implicitSolvent == OBC1: elif implicitSolvent is OBC1:
implicitString = 'OBC1' implicitString = 'OBC1'
elif implicitSolvent == OBC2: elif implicitSolvent is OBC2:
implicitString = 'OBC2' implicitString = 'OBC2'
elif implicitSolvent == GBn: elif implicitSolvent is GBn:
implicitString = 'GBn' implicitString = 'GBn'
elif implicitSolvent is GBn2:
implicitString = 'GBn2'
else: else:
raise ValueError('Illegal value for implicit solvent model') raise ValueError('Illegal value for implicit solvent model')
sys = amber_file_parser.readAmberSystem(prmtop_loader=self._prmtop, shake=constraintString, nonbondedCutoff=nonbondedCutoff, sys = amber_file_parser.readAmberSystem(prmtop_loader=self._prmtop, shake=constraintString, nonbondedCutoff=nonbondedCutoff,
nonbondedMethod=methodMap[nonbondedMethod], flexibleConstraints=False, gbmodel=implicitString, nonbondedMethod=methodMap[nonbondedMethod], flexibleConstraints=False, gbmodel=implicitString,
soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, rigidWater=rigidWater) soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, rigidWater=rigidWater,
elements=self.elements)
if hydrogenMass is not None: if hydrogenMass is not None:
for atom1, atom2 in self.topology.bonds(): for atom1, atom2 in self.topology.bonds():
if atom1.element == elem.hydrogen: if atom1.element == elem.hydrogen:
......
wrappers/python/simtk/openmm/app/desmonddmsfile.py 0 → 100644
View file @ 99ef4344
'''
desmonddmsfile.py: Load Desmond dms files
Portions copyright (c) 2013 Stanford University and the Authors
Authors: Robert McGibbon
Contributors:
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
'''
import os
import math
from simtk import openmm as mm
from simtk.openmm.app import forcefield as ff
from simtk.openmm.app import Element, Topology, PDBFile
from simtk.openmm.app.element import hydrogen
from simtk.unit import (nanometer, angstrom, dalton, radian,
kilocalorie_per_mole, kilojoule_per_mole,
degree, elementary_charge)
class DesmondDMSFile(object):
'''DesmondDMSFile parses a Desmond DMS (desmond molecular system) and
constructs a topology and (optionally) an OpenMM System from it
'''
def __init__(self, file):
'''Load a DMS file
Parameters:
- file (string) the name of the file to load
'''
# sqlite3 is included in the standard lib, but at python
# compile time, you can disable support (I think), so it's
# not *guarenteed* to be available. Doing the import here
# means we only raise an ImportError if people try to use
# this class, so the module can be safely imported
import sqlite3
self._open = False
self._tables = None
if not os.path.exists(str(file)):
raise IOError("No such file or directory: '%s'" % str(file))
self._conn = sqlite3.connect(file)
self._open = True
self._readSchemas()
if len(self._tables) == 0:
raise IOError('DMS file was not loaded sucessfully. No tables found')
if 'nbtype' not in self._tables['particle']:
raise ValueError('No nonbonded parameters associated with this '
'DMS file. You can add a forcefield with the '
'viparr command line tool distributed with desmond')
# build the provenance string
provenance = []
q = '''SELECT id, user, timestamp, version, workdir, cmdline, executable
FROM provenance'''
#for id, user, timestamp, version, workdir, cmdline, executable in self._conn.execute(q):
for row in self._conn.execute('SELECT * FROM provenance'):
rowdict = dict(zip(self._tables['provenance'], row))
provenance.append('%(id)d) %(timestamp)s: %(user)s\n version: %(version)s\n '
'cmdline: %(cmdline)s\n executable: %(executable)s\n' % rowdict)
self.provenance = ''.join(provenance)
# Build the topology
self.topology, self.positions = self._createTopology()
self._topologyAtoms = list(self.topology.atoms())
self._atomBonds = [{} for x in range(len(self._topologyAtoms))]
self._angleConstraints = [{} for x in range(len(self._topologyAtoms))]
def getPositions(self):
'''Get the positions of each atom in the system
'''
return self.positions
def getTopology(self):
'''Get the topology of the system
'''
return self.topology
def getProvenance(self):
'''Get the provenance string of this system
'''
return self.provenance
def _createTopology(self):
'''Build the topology of the system
'''
top = Topology()
positions = []
boxVectors = []
for x, y, z in self._conn.execute('SELECT x, y, z FROM global_cell'):
boxVectors.append(mm.Vec3(x, y, z))
unitCellDimensions = [boxVectors[0][0], boxVectors[1][1], boxVectors[2][2]]
top.setUnitCellDimensions(unitCellDimensions*angstrom)
atoms = {}
lastChain = None
lastResId = None
c = top.addChain()
q = '''SELECT id, name, anum, resname, resid, chain, x, y, z
FROM particle'''
for (atomId, atomName, atomNumber, resName, resId, chain, x, y, z) in self._conn.execute(q):
newChain = False
if chain != lastChain:
lastChain = chain
c = top.addChain()
newChain = True
if resId != lastResId or newChain:
lastResId = resId
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
if atomNumber == 0 and atomName.startswith('Vrt'):
elem = None
else:
elem = Element.getByAtomicNumber(atomNumber)
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
atoms[atomId] = top.addAtom(atomName, elem, r)
positions.append(mm.Vec3(x, y, z))
for p0, p1 in self._conn.execute('SELECT p0, p1 FROM bond'):
top.addBond(atoms[p0], atoms[p1])
positions = positions*angstrom
return top, positions
def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*nanometer,
ewaldErrorTolerance=0.0005, removeCMMotion=True, hydrogenMass=None):
'''Construct an OpenMM System representing the topology described by this dms file
Parameters:
- nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions. Allowed values are
NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
- nonbondedCutoff (distance=1*nanometer) The cutoff distance to use for nonbonded interactions
- ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
- removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
- hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is
subtracted from the heavy atom to keep their total mass the same.
'''
self._checkForUnsupportedTerms()
sys = mm.System()
# Buld the box dimensions
sys = mm.System()
boxSize = self.topology.getUnitCellDimensions()
if boxSize is not None:
sys.setDefaultPeriodicBoxVectors((boxSize[0], 0, 0), (0, boxSize[1], 0), (0, 0, boxSize[2]))
elif nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME):
raise ValueError('Illegal nonbonded method for a non-periodic system')
# Create all of the particles
for mass in self._conn.execute('SELECT mass from particle'):
sys.addParticle(mass[0]*dalton)
# Add all of the forces
self._addBondsToSystem(sys)
self._addAnglesToSystem(sys)
self._addConstraintsToSystem(sys)
self._addPeriodicTorsionsToSystem(sys)
self._addImproperHarmonicTorsionsToSystem(sys)
self._addCMAPToSystem(sys)
self._addVirtualSitesToSystem(sys)
nb = self._addNonbondedForceToSystem(sys)
# Finish configuring the NonbondedForce.
methodMap = {ff.NoCutoff:mm.NonbondedForce.NoCutoff,
ff.CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic,
ff.CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic,
ff.Ewald:mm.NonbondedForce.Ewald,
ff.PME:mm.NonbondedForce.PME}
nb.setNonbondedMethod(methodMap[nonbondedMethod])
nb.setCutoffDistance(nonbondedCutoff)
nb.setEwaldErrorTolerance(ewaldErrorTolerance)
# Adjust masses.
if hydrogenMass is not None:
for atom1, atom2 in self.topology.bonds():
if atom1.element == hydrogen:
(atom1, atom2) = (atom2, atom1)
if atom2.element == hydrogen and atom1.element not in (hydrogen, None):
transferMass = hydrogenMass-sys.getParticleMass(atom2.index)
sys.setParticleMass(atom2.index, hydrogenMass)
sys.setParticleMass(atom1.index, sys.getParticleMass(atom1.index)-transferMass)
# Add a CMMotionRemover.
if removeCMMotion:
sys.addForce(mm.CMMotionRemover())
return sys
def _addBondsToSystem(self, sys):
'''Create the harmonic bonds
'''
bonds = mm.HarmonicBondForce()
sys.addForce(bonds)
q = '''SELECT p0, p1, r0, fc, constrained
FROM stretch_harm_term INNER JOIN stretch_harm_param
ON stretch_harm_term.param=stretch_harm_param.id'''
for p0, p1, r0, fc, constrained in self._conn.execute(q):
if constrained:
sys.addConstraint(p0, p1, r0*angstrom)
else:
# Desmond writes the harmonic bond force without 1/2
# so we need to to double the force constant
bonds.addBond(p0, p1, r0*angstrom, 2*fc*kilocalorie_per_mole/angstrom**2)
# Record information that will be needed for constraining angles.
self._atomBonds[p0][p1] = r0*angstrom
self._atomBonds[p1][p0] = r0*angstrom
return bonds
def _addAnglesToSystem(self, sys):
'''Create the harmonic angles
'''
angles = mm.HarmonicAngleForce()
sys.addForce(angles)
degToRad = math.pi/180
q = '''SELECT p0, p1, p2, theta0, fc, constrained
FROM angle_harm_term INNER JOIN angle_harm_param
ON angle_harm_term.param=angle_harm_param.id'''
for p0, p1, p2, theta0, fc, constrained in self._conn.execute(q):
if constrained:
l1 = self._atomBonds[p1][p0]
l2 = self._atomBonds[p1][p2]
length = (l1*l1 + l2*l2 - 2*l1*l2*math.cos(theta0*degToRad)).sqrt()
sys.addConstraint(p0, p2, length)
self._angleConstraints[p1][p0] = p2
self._angleConstraints[p1][p2] = p0
else:
# Desmond writes the harmonic angle force without 1/2
# so we need to to double the force constant
angles.addAngle(p0, p1, p2, theta0*degToRad, 2*fc*kilocalorie_per_mole/radian**2)
return angles
def _addConstraintsToSystem(self, sys):
'''Add constraints to system. Normally these should already be
added by the bonds table, but we want to make sure that there's
no extra information in the constraints table that we're not
including in the system'''
for term_table in [n for n in self._tables.keys() if n.startswith('constraint_a') and n.endswith('term')]:
param_table = term_table.replace('term', 'param')
q = '''SELECT p0, p1, r1
FROM %(term)s INNER JOIN %(param)s
ON %(term)s.param=%(param)s.id''' % \
{'term': term_table, 'param': param_table}
for p0, p1, r1 in self._conn.execute(q):
if not p1 in self._atomBonds[p0]:
sys.addConstraint(p0, p1, r1*angstrom)
self._atomBonds[p0][p1] = r1*angstrom
self._atomBonds[p1][p0] = r1*angstrom
if 'constraint_hoh_term' in self._tables:
degToRad = math.pi/180
q = '''SELECT p0, p1, p2, r1, r2, theta
FROM constraint_hoh_term INNER JOIN constraint_hoh_param
ON constraint_hoh_term.param=constraint_hoh_param.id'''
for p0, p1, p2, r1, r2, theta in self._conn.execute(q):
# Here, p0 is the heavy atom and p1 and p2 are the H1 and H2
# wihth O-H1 and O-H2 distances r1 and r2
if not (self._angleConstraints[p0].get(p1, None) == p2):
length = (r1*r1 + r2*r2 - 2*r1*r2*math.cos(theta*degToRad)).sqrt()
sys.addConstraint(p1, p2, length)
def _addPeriodicTorsionsToSystem(self, sys):
'''Create the torsion terms
'''
periodic = mm.PeriodicTorsionForce()
sys.addForce(periodic)
q = '''SELECT p0, p1, p2, p3, phi0, fc0, fc1, fc2, fc3, fc4, fc5, fc6
FROM dihedral_trig_term INNER JOIN dihedral_trig_param
ON dihedral_trig_term.param=dihedral_trig_param.id'''
for p0, p1, p2, p3, phi0, fc0, fc1, fc2, fc3, fc4, fc5, fc6 in self._conn.execute(q):
for order, fc in enumerate([fc0, fc1, fc2, fc3, fc4, fc5, fc6]):
if fc == 0:
continue
periodic.addTorsion(p0, p1, p2, p3, order, phi0*degree, fc*kilocalorie_per_mole)
def _addImproperHarmonicTorsionsToSystem(self, sys):
'''Create the improper harmonic torsion terms
'''
if not self._hasTable('improper_harm_term'):
return
harmonicTorsion = mm.CustomTorsionForce('k*(theta-theta0)^2')
harmonicTorsion.addPerTorsionParameter('theta0')
harmonicTorsion.addPerTorsionParameter('k')
sys.addForce(harmonicTorsion)
q = '''SELECT p0, p1, p2, p3, phi0, fc
FROM improper_harm_term INNER JOIN improper_harm_param
ON improper_harm_term.param=improper_harm_param.id'''
for p0, p1, p2, p3, phi0, fc in self._conn.execute(q):
harmonicTorsion.addTorsion(p0, p1, p2, p3, [phi0*degree, fc*kilocalorie_per_mole])
def _addCMAPToSystem(self, sys):
'''Create the CMAP terms
'''
if not self._hasTable('torsiontorsion_cmap_term'):
return
# Create CMAP torsion terms
cmap = mm.CMAPTorsionForce()
sys.addForce(cmap)
cmap_indices = {}
for name in [k for k in self._tables.keys() if k.startswith('cmap')]:
size2 = self._conn.execute('SELECT COUNT(*) FROM %s' % name).fetchone()[0]
fsize = math.sqrt(size2)
if fsize != int(fsize):
raise ValueError('Non-square CMAPs are not supported')
size = int(fsize)
map = [0 for i in range(size2)]
for phi, psi, energy in self._conn.execute("SELECT phi, psi, energy FROM %s" % name):
i = int((phi % 360) / (360.0 / size))
j = int((psi % 360) / (360.0 / size))
map[i+size*j] = energy
index = cmap.addMap(size, map*kilocalorie_per_mole)
cmap_indices[name] = index
q = '''SELECT p0, p1, p2, p3, p4, p5, p6, p7, cmapid
FROM torsiontorsion_cmap_term INNER JOIN torsiontorsion_cmap_param
ON torsiontorsion_cmap_term.param=torsiontorsion_cmap_param.id'''
for p0, p1, p2, p3, p4, p5, p6, p7, cmapid in self._conn.execute(q):
cmap.addTorsion(cmap_indices[cmapid], p0, p1, p2, p3, p4, p5, p6, p7)
def _addNonbondedForceToSystem(self, sys):
'''Create the nonbonded force
'''
nb = mm.NonbondedForce()
sys.addForce(nb)
q = '''SELECT charge, sigma, epsilon
FROM particle INNER JOIN nonbonded_param
ON particle.nbtype=nonbonded_param.id'''
for charge, sigma, epsilon in self._conn.execute(q):
nb.addParticle(charge, sigma*angstrom, epsilon*kilocalorie_per_mole)
for p0, p1 in self._conn.execute('SELECT p0, p1 FROM exclusion'):
nb.addException(p0, p1, 0.0, 1.0, 0.0)
q = '''SELECT p0, p1, aij, bij, qij
FROM pair_12_6_es_term INNER JOIN pair_12_6_es_param
ON pair_12_6_es_term.param=pair_12_6_es_param.id;'''
for p0, p1, a_ij, b_ij, q_ij in self._conn.execute(q):
a_ij = (a_ij*kilocalorie_per_mole*(angstrom**12)).in_units_of(kilojoule_per_mole*(nanometer**12))
b_ij = (b_ij*kilocalorie_per_mole*(angstrom**6)).in_units_of(kilojoule_per_mole*(nanometer**6))
q_ij = q_ij*elementary_charge**2
if (b_ij._value == 0.0) or (a_ij._value == 0.0):
new_epsilon = 0
new_sigma = 1
else:
new_epsilon = b_ij**2/(4*a_ij)
new_sigma = (a_ij / b_ij)**(1.0/6.0)
nb.addException(p0, p1, q_ij, new_sigma, new_epsilon, True)
n_total = self._conn.execute('''SELECT COUNT(*) FROM pair_12_6_es_term''').fetchone()
n_in_exclusions = self._conn.execute('''SELECT COUNT(*)
FROM exclusion INNER JOIN pair_12_6_es_term
ON exclusion.p0==pair_12_6_es_term.p0 AND exclusion.p1==pair_12_6_es_term.p1''').fetchone()
if not n_total == n_in_exclusions:
raise NotImplementedError('All pair_12_6_es_terms must have a corresponding exclusion')
return nb
def _addVirtualSitesToSystem(self, sys):
'''Create any virtual sites in the systempy
'''
if not any(t.startswith('virtual_') for t in self._tables.keys()):
return
if 'virtual_lc2_term' in self._tables:
q = '''SELECT p0, p1, p2, c1
FROM virtual_lc2_term INNER JOIN virtual_lc2_param
ON virtual_lc2_term.param=virtual_lc2_param.id'''
for p0, p1, p2, c1 in self._conn.execute(q):
vsite = mm.TwoParticleAverageSite(p1, p2, (1-c1), c1)
sys.setVirtualSite(p0, vsite)
if 'virtual_lc3_term' in self._tables:
q = '''SELECT p0, p1, p2, p3, c1, c2
FROM virtual_lc3_term INNER JOIN virtual_lc3_param
ON virtual_lc3_term.param=virtual_lc3_param.id'''
for p0, p1, p2, p3, c1, c2 in self._conn.execute(q):
vsite = mm.ThreeParticleAverageSite(p1, p2, p3, (1-c1-c2), c1, c2)
sys.setVirtualSite(p0, vsite)
if 'virtual_out3_term' in self._tables:
q = '''SELECT p0, p1, p2, p3, c1, c2, c3
FROM virtual_out3_term INNER JOIN virtual_out3_param
ON virtual_out3_term.param=virtual_out3_param.id'''
for p0, p1, p2, p3, c1, c2, c3 in self._conn.execute(q):
vsite = mm.OutOfPlaneSite(p1, p2, p3, c1, c2, c3)
sys.setVirtualSite(p0, vsite)
if 'virtual_fdat3_term' in self._tables:
raise NotImplementedError('OpenMM does not currently support '
'fdat3-style virtual sites')
def _hasTable(self, table_name):
'''Does our DMS file contain this table?
'''
return table_name in self._tables
def _readSchemas(self):
'''Read the schemas of each of the tables in the dms file, populating
the `_tables` instance attribute
'''
tables = {}
for table in self._conn.execute("SELECT name FROM sqlite_master WHERE type='table'"):
names = []
for e in self._conn.execute('PRAGMA table_info(%s)' % table):
names.append(str(e[1]))
tables[str(table[0])] = names
self._tables = tables
def _checkForUnsupportedTerms(self):
'''Check the file for forcefield terms that are not currenty supported,
raising a NotImplementedError
'''
if 'posre_harm_term' in self._tables:
raise NotImplementedError('Position restraints are not implemented.')
flat_bottom_potential_terms = ['stretch_fbhw_term', 'angle_fbhw_term',
'improper_fbhw_term', 'posre_fbhw_term']
if any((t in self._tables) for t in flat_bottom_potential_terms):
raise NotImplementedError('Flat bottom potential terms '
'are not implemeneted')
nbinfo = dict(zip(self._tables['nonbonded_info'],
self._conn.execute('SELECT * FROM nonbonded_info').fetchone()))
if nbinfo['vdw_funct'] != u'vdw_12_6':
raise NotImplementedError('Only Leonard-Jones van der Waals '
'interactions are currently supported')
if nbinfo['vdw_rule'] != u'arithmetic/geometric':
raise NotImplementedError('Only Lorentz-Berthelot nonbonded '
'combining rules are currently supported')
if 'nonbonded_combined_param' in self._tables:
raise NotImplementedError('nonbonded_combined_param interactions '
'are not currently supported')
if 'alchemical_particle' in self._tables:
raise NotImplementedError('Alchemical particles are not supported')
if 'alchemical_stretch_harm' in self._tables:
raise NotImplementedError('Alchemical bonds are not supported')
if 'polar_term' in self._tables:
if self._conn.execute("SELECT COUNT(*) FROM polar_term").fetchone()[0] != 0:
raise NotImplementedError('Drude particles are not currently supported')
def close(self):
'''Close the SQL connection
'''
if self._open:
self._conn.close()
def __del__(self):
self.close()
wrappers/python/simtk/openmm/app/element.py
View file @ 99ef4344
...@@ -44,6 +44,7 @@ class Element: ...@@ -44,6 +44,7 @@ class Element:
look up the Element with a particular chemical symbol.""" look up the Element with a particular chemical symbol."""
_elements_by_symbol = {} _elements_by_symbol = {}
_elements_by_atomic_number = {}
def __init__(self, number, name, symbol, mass): def __init__(self, number, name, symbol, mass):
## The atomic number of the element ## The atomic number of the element
...@@ -58,6 +59,16 @@ class Element: ...@@ -58,6 +59,16 @@ class Element:
s = symbol.strip().upper() s = symbol.strip().upper()
assert s not in Element._elements_by_symbol assert s not in Element._elements_by_symbol
Element._elements_by_symbol[s] = self Element._elements_by_symbol[s] = self
if number in Element._elements_by_atomic_number:
other_element = Element._elements_by_atomic_number[number]
if mass < other_element.mass:
# If two "elements" share the same atomic number, they're
# probably hydrogen and deuterium, and we want to choose
# the lighter one to put in the table by atomic_number,
# since it's the "canonical" element.
Element._elements_by_atomic_number[number] = self
else:
Element._elements_by_atomic_number[number] = self
@staticmethod @staticmethod
def getBySymbol(symbol): def getBySymbol(symbol):
...@@ -65,6 +76,10 @@ class Element: ...@@ -65,6 +76,10 @@ class Element:
s = symbol.strip().upper() s = symbol.strip().upper()
return Element._elements_by_symbol[s] return Element._elements_by_symbol[s]
@staticmethod
def getByAtomicNumber(atomic_number):
return Element._elements_by_atomic_number[atomic_number]
# This is for backward compatibility. # This is for backward compatibility.
def get_by_symbol(symbol): def get_by_symbol(symbol):
s = symbol.strip().upper() s = symbol.strip().upper()
...@@ -188,3 +203,8 @@ ununtrium = Element(113, "ununtrium", "Uut", 284*daltons) ...@@ -188,3 +203,8 @@ ununtrium = Element(113, "ununtrium", "Uut", 284*daltons)
ununquadium = Element(114, "ununquadium", "Uuq", 289*daltons) ununquadium = Element(114, "ununquadium", "Uuq", 289*daltons)
ununpentium = Element(115, "ununpentium", "Uup", 288*daltons) ununpentium = Element(115, "ununpentium", "Uup", 288*daltons)
ununhexium = Element(116, "ununhexium", "Uuh", 292*daltons) ununhexium = Element(116, "ununhexium", "Uuh", 292*daltons)
# Aliases to recognize common alternative spellings. Both the '==' and 'is'
# relational operators will work with any chosen name
sulphur = sulfur
aluminium = aluminum
wrappers/python/simtk/openmm/app/gromacstopfile.py
View file @ 99ef4344
...@@ -40,6 +40,7 @@ import simtk.unit as unit ...@@ -40,6 +40,7 @@ import simtk.unit as unit
import simtk.openmm as mm import simtk.openmm as mm
import math import math
import os import os
import distutils
HBonds = ff.HBonds HBonds = ff.HBonds
AllBonds = ff.AllBonds AllBonds = ff.AllBonds
...@@ -90,6 +91,9 @@ class GromacsTopFile(object): ...@@ -90,6 +91,9 @@ class GromacsTopFile(object):
# A preprocessor command. # A preprocessor command.
fields = stripped.split() fields = stripped.split()
command = fields[0] command = fields[0]
if len(self._ifStack) != len(self._elseStack):
raise RuntimeError('#if/#else stack out of sync')
if command == '#include' and not ignore: if command == '#include' and not ignore:
# Locate the file to include # Locate the file to include
name = stripped[len(command):].strip(' \t"<>') name = stripped[len(command):].strip(' \t"<>')
...@@ -116,17 +120,29 @@ class GromacsTopFile(object): ...@@ -116,17 +120,29 @@ class GromacsTopFile(object):
raise ValueError('Illegal line in .top file: '+line) raise ValueError('Illegal line in .top file: '+line)
name = fields[1] name = fields[1]
self._ifStack.append(name in self._defines) self._ifStack.append(name in self._defines)
self._elseStack.append(False)
elif command == '#ifndef': elif command == '#ifndef':
# See whether this block should be ignored. # See whether this block should be ignored.
if len(fields) < 2: if len(fields) < 2:
raise ValueError('Illegal line in .top file: '+line) raise ValueError('Illegal line in .top file: '+line)
name = fields[1] name = fields[1]
self._ifStack.append(name not in self._defines) self._ifStack.append(name not in self._defines)
self._elseStack.append(False)
elif command == '#endif': elif command == '#endif':
# Pop an entry off the if stack. # Pop an entry off the if stack.
if len(self._ifStack) == 0: if len(self._ifStack) == 0:
raise ValueError('Unexpected line in .top file: '+line) raise ValueError('Unexpected line in .top file: '+line)
del(self._ifStack[-1]) del(self._ifStack[-1])
del(self._elseStack[-1])
elif command == '#else':
# Reverse the last entry on the if stack
if len(self._ifStack) == 0:
raise ValueError('Unexpected line in .top file: '+line)
if self._elseStack[-1]:
raise ValueError('Unexpected line in .top file: '
'#else has already been used ' + line)
self._ifStack[-1] = (not self._ifStack[-1])
self._elseStack[-1] = True
elif not ignore: elif not ignore:
# A line of data for the current category # A line of data for the current category
...@@ -342,16 +358,20 @@ class GromacsTopFile(object): ...@@ -342,16 +358,20 @@ class GromacsTopFile(object):
raise ValueError('Unsupported function type in [ cmaptypes ] line: '+line); raise ValueError('Unsupported function type in [ cmaptypes ] line: '+line);
self._cmapTypes[tuple(fields[:5])] = fields self._cmapTypes[tuple(fields[:5])] = fields
def __init__(self, file, unitCellDimensions=None, includeDir='/usr/local/gromacs/share/gromacs/top', defines={}): def __init__(self, file, unitCellDimensions=None, includeDir=None, defines={}):
"""Load a top file. """Load a top file.
Parameters: Parameters:
- file (string) the name of the file to load - file (string) the name of the file to load
- unitCellDimensions (Vec3=None) the dimensions of the crystallographic unit cell - unitCellDimensions (Vec3=None) the dimensions of the crystallographic unit cell
- includeDir (string=/usr/local/gromacs/share/gromacs/top) a directory in which to look for other files - includeDir (string=None) A directory in which to look for other files
included from the top file included from the top file. If not specified, we will attempt to locate a gromacs
installation on your system. When gromacs is installed in /usr/local, this will resolve
to /usr/local/gromacs/share/gromacs/top
- defines (map={}) preprocessor definitions that should be predefined when parsing the file - defines (map={}) preprocessor definitions that should be predefined when parsing the file
""" """
if includeDir is None:
includeDir = _defaultGromacsIncludeDir()
self._includeDirs = (os.path.dirname(file), includeDir) self._includeDirs = (os.path.dirname(file), includeDir)
self._defines = defines self._defines = defines
...@@ -359,6 +379,7 @@ class GromacsTopFile(object): ...@@ -359,6 +379,7 @@ class GromacsTopFile(object):
self._currentCategory = None self._currentCategory = None
self._ifStack = [] self._ifStack = []
self._elseStack = []
self._moleculeTypes = {} self._moleculeTypes = {}
self._molecules = [] self._molecules = []
self._currentMoleculeType = None self._currentMoleculeType = None
...@@ -752,3 +773,19 @@ class GromacsTopFile(object): ...@@ -752,3 +773,19 @@ class GromacsTopFile(object):
if removeCMMotion: if removeCMMotion:
sys.addForce(mm.CMMotionRemover()) sys.addForce(mm.CMMotionRemover())
return sys return sys
def _defaultGromacsIncludeDir():
"""Find the location where gromacs #include files are referenced from, by
searching for (1) gromacs environment variables, (2) for the gromacs binary
'pdb2gmx' in the PATH, or (3) just using the default gromacs install
location, /usr/local/gromacs/share/gromacs/top """
if 'GMXDATA' in os.environ:
return os.path.join(os.environ['GMXDATA'], 'top')
if 'GMXBIN' in os.environ:
return os.path.abspath(os.path.join(os.environ['GMXBIN'], '..', 'share', 'gromacs', 'top'))
pdb2gmx_path = distutils.spawn.find_executable('pdb2gmx')
if pdb2gmx_path is not None:
return os.path.abspath(os.path.join(os.path.dirname(pdb2gmx_path), '..', 'share', 'gromacs', 'top'))
return '/usr/local/gromacs/share/gromacs/top'
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ 99ef4344
...@@ -41,9 +41,9 @@ USE OR OTHER DEALINGS IN THE SOFTWARE. ...@@ -41,9 +41,9 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
import os import os
import os.path import os.path
import copy
import re import re
import math import math
import warnings
try: try:
import numpy import numpy
...@@ -52,6 +52,7 @@ except: ...@@ -52,6 +52,7 @@ except:
import simtk.unit as units import simtk.unit as units
import simtk.openmm import simtk.openmm
from simtk.openmm.app import element as elem
import customgbforces as customgb import customgbforces as customgb
#============================================================================================= #=============================================================================================
...@@ -428,15 +429,25 @@ class PrmtopLoader(object): ...@@ -428,15 +429,25 @@ class PrmtopLoader(object):
charges=self.getCharges() charges=self.getCharges()
nonbondTerms = self.getNonbondTerms() nonbondTerms = self.getNonbondTerms()
for ii in range(0,len(dihedralPointers),5): for ii in range(0,len(dihedralPointers),5):
if int(dihedralPointers[ii+2])>0 and int(dihedralPointers[ii+3])>0: if int(dihedralPointers[ii+2])>0 and int(dihedralPointers[ii+3])>0:
iAtom = int(dihedralPointers[ii])//3 iAtom = int(dihedralPointers[ii])//3
lAtom = int(dihedralPointers[ii+3])//3 lAtom = int(dihedralPointers[ii+3])//3
chargeProd = charges[iAtom]*charges[lAtom] iidx = int(dihedralPointers[ii+4]) - 1
(rVdwI, epsilonI) = nonbondTerms[iAtom] chargeProd = charges[iAtom]*charges[lAtom]
(rVdwL, epsilonL) = nonbondTerms[lAtom] (rVdwI, epsilonI) = nonbondTerms[iAtom]
rMin = (rVdwI+rVdwL) (rVdwL, epsilonL) = nonbondTerms[lAtom]
epsilon = math.sqrt(epsilonI*epsilonL) rMin = (rVdwI+rVdwL)
returnList.append((iAtom, lAtom, chargeProd, rMin, epsilon)) epsilon = math.sqrt(epsilonI*epsilonL)
try:
iScee = float(self._raw_data["SCEE_SCALE_FACTOR"][iidx])
except KeyError:
iScee = 1.2
try:
iScnb = float(self._raw_data["SCNB_SCALE_FACTOR"][iidx])
except KeyError:
iScnb = 2.0
returnList.append((iAtom, lAtom, chargeProd, rMin, epsilon, iScee, iScnb))
return returnList return returnList
def getExcludedAtoms(self): def getExcludedAtoms(self):
...@@ -462,34 +473,74 @@ class PrmtopLoader(object): ...@@ -462,34 +473,74 @@ class PrmtopLoader(object):
self._excludedAtoms.append(atomList) self._excludedAtoms.append(atomList)
return self._excludedAtoms return self._excludedAtoms
def getGBParms(self, symbls=None): def getGBParms(self, gbmodel, elements):
"""Return list giving GB params, Radius and screening factor""" """Return list giving GB params, Radius and screening factor"""
try: gb_List=[]
return self._gb_List radii=[float(r) for r in self._raw_data["RADII"]]
except AttributeError: screen=[float(s) for s in self._raw_data["SCREEN"]]
pass if gbmodel == 'GBn2':
self._gb_List=[] alpha = [0 for i in self._raw_data['RADII']]
radii=self._raw_data["RADII"] beta = [0 for i in self._raw_data['RADII']]
screen=self._raw_data["SCREEN"] gamma = [0 for i in self._raw_data['RADII']]
# Update screening parameters for GBn if specified # Update screening parameters for GBn if specified
if symbls: if gbmodel == 'GBn':
for (i, symbl) in enumerate(symbls): if elements is None:
if symbl[0] == ('c' or 'C'): raise Exception('GBn model requires element information')
for i, element in enumerate(elements):
if element is elem.carbon:
screen[i] = 0.48435382330 screen[i] = 0.48435382330
elif symbl[0] == ('h' or 'H'): elif element is elem.hydrogen:
screen[i] = 1.09085413633 screen[i] = 1.09085413633
elif symbl[0] == ('n' or 'N'): elif element is elem.nitrogen:
screen[i] = 0.700147318409 screen[i] = 0.700147318409
elif symbl[0] == ('o' or 'O'): elif element is elem.oxygen:
screen[i] = 1.06557401132 screen[i] = 1.06557401132
elif symbl[0] == ('s' or 'S'): elif element is elem.sulfur:
screen[i] = 0.602256336067 screen[i] = 0.602256336067
else: else:
screen[i] = 0.5 screen[i] = 0.5
if gbmodel == 'GBn2':
if elements is None:
raise Exception('GBn2 model requires element information')
for i, element in enumerate(elements):
if element is elem.carbon:
screen[i] = 1.058554
alpha[i] = 0.733756
beta[i] = 0.506378
gamma[i] = 0.205844
elif element is elem.hydrogen:
screen[i] = 1.425952
alpha[i] = 0.788440
beta[i] = 0.798699
gamma[i] = 0.437334
elif element is elem.nitrogen:
screen[i] = 0.733599
alpha[i] = 0.503364
beta[i] = 0.316828
gamma[i] = 0.192915
elif element is elem.oxygen:
screen[i] = 1.061039
alpha[i] = 0.867814
beta[i] = 0.876635
gamma[i] = 0.387882
elif element is elem.sulfur:
screen[i] = -0.703469
alpha[i] = 0.867814
beta[i] = 0.876635
gamma[i] = 0.387882
else: # not optimized
screen[i] = 0.5
alpha[i] = 1.0
beta[i] = 0.8
gamma[i] = 4.85
lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer) lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer)
for iAtom in range(len(radii)): if gbmodel == 'GBn2':
self._gb_List.append((float(radii[iAtom])*lengthConversionFactor, float(screen[iAtom]))) for rad, scr, alp, bet, gam in zip(radii, screen, alpha, beta, gamma):
return self._gb_List gb_List.append((rad*lengthConversionFactor, scr, alp, bet, gam))
else:
for rad, scr in zip(radii, screen):
gb_List.append((rad*lengthConversionFactor, scr))
return gb_List
def getBoxBetaAndDimensions(self): def getBoxBetaAndDimensions(self):
"""Return periodic boundary box beta angle and dimensions""" """Return periodic boundary box beta angle and dimensions"""
...@@ -502,11 +553,21 @@ class PrmtopLoader(object): ...@@ -502,11 +553,21 @@ class PrmtopLoader(object):
units.Quantity(y, units.angstrom), units.Quantity(y, units.angstrom),
units.Quantity(z, units.angstrom)) units.Quantity(z, units.angstrom))
@property
def has_scee_scnb(self):
return ("SCEE_SCALE_FACTOR" in self._raw_data and "SCNB_SCALE_FACTOR" in self._raw_data)
@property
def has_atomic_number(self):
return 'ATOMIC_NUMBER' in self._raw_data
#============================================================================================= #=============================================================================================
# AMBER System builder (based on, but not identical to, systemManager from 'zander') # AMBER System builder (based on, but not identical to, systemManager from 'zander')
#============================================================================================= #=============================================================================================
def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None, soluteDielectric=1.0, solventDielectric=78.5, nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=1.2, scnb=2.0, mm=None, verbose=False, EwaldErrorTolerance=None, flexibleConstraints=True, rigidWater=True): def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None, soluteDielectric=1.0, solventDielectric=78.5,
nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=None, scnb=None, mm=None, verbose=False,
EwaldErrorTolerance=None, flexibleConstraints=True, rigidWater=True, elements=None):
""" """
Create an OpenMM System from an Amber prmtop file. Create an OpenMM System from an Amber prmtop file.
...@@ -520,8 +581,8 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode ...@@ -520,8 +581,8 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
soluteDielectric (float) - The solute dielectric constant to use in the implicit solvent model (default: 1.0) soluteDielectric (float) - The solute dielectric constant to use in the implicit solvent model (default: 1.0)
solventDielectric (float) - The solvent dielectric constant to use in the implicit solvent model (default: 78.5) solventDielectric (float) - The solvent dielectric constant to use in the implicit solvent model (default: 78.5)
nonbondedCutoff (float) - if specified, will set nonbondedCutoff (default: None) nonbondedCutoff (float) - if specified, will set nonbondedCutoff (default: None)
scnb (float) - 1-4 Lennard-Jones scaling factor (default: 1.2) scnb (float) - 1-4 Lennard-Jones scaling factor (default: taken from prmtop or 1.2 if not present there)
scee (float) - 1-4 electrostatics scaling factor (default: 2.0) scee (float) - 1-4 electrostatics scaling factor (default: taken from prmtop or 2.0 if not present there)
mm - if specified, this module will be used in place of pyopenmm (default: None) mm - if specified, this module will be used in place of pyopenmm (default: None)
verbose (boolean) - if True, print out information on progress (default: False) verbose (boolean) - if True, print out information on progress (default: False)
flexibleConstraints (boolean) - if True, flexible bonds will be added in addition ot constrained bonds flexibleConstraints (boolean) - if True, flexible bonds will be added in addition ot constrained bonds
...@@ -571,6 +632,10 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode ...@@ -571,6 +632,10 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
if prmtop.getIfBox()>1: if prmtop.getIfBox()>1:
raise Exception("only standard periodic boxes are currently supported") raise Exception("only standard periodic boxes are currently supported")
if prmtop.has_scee_scnb and (scee is not None or scnb is not None):
warnings.warn("1-4 scaling parameters in topology file are being ignored. "
"This is not recommended unless you know what you are doing.")
# Use pyopenmm implementation of OpenMM by default. # Use pyopenmm implementation of OpenMM by default.
if mm is None: if mm is None:
mm = simtk.openmm mm = simtk.openmm
...@@ -615,7 +680,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode ...@@ -615,7 +680,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
if shake == 'h-angles': if shake == 'h-angles':
numConstrainedBonds = system.getNumConstraints() numConstrainedBonds = system.getNumConstraints()
atomConstraints = [[]]*system.getNumParticles() atomConstraints = [[]]*system.getNumParticles()
for i in range(system.getNumConstraints()): for i in range(numConstrainedBonds):
c = system.getConstraintParameters(i) c = system.getConstraintParameters(i)
distance = c[2].value_in_unit(units.nanometer) distance = c[2].value_in_unit(units.nanometer)
atomConstraints[c[0]].append((c[1], distance)) atomConstraints[c[0]].append((c[1], distance))
...@@ -712,9 +777,12 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode ...@@ -712,9 +777,12 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
# Add 1-4 Interactions # Add 1-4 Interactions
excludedAtomPairs = set() excludedAtomPairs = set()
sigmaScale = 2**(-1./6.) sigmaScale = 2**(-1./6.)
for (iAtom, lAtom, chargeProd, rMin, epsilon) in prmtop.get14Interactions(): _scee, _scnb = scee, scnb
chargeProd /= scee for (iAtom, lAtom, chargeProd, rMin, epsilon, iScee, iScnb) in prmtop.get14Interactions():
epsilon /= scnb if scee is None: _scee = iScee
if scnb is None: _scnb = iScnb
chargeProd /= _scee
epsilon /= _scnb
sigma = rMin * sigmaScale sigma = rMin * sigmaScale
force.addException(iAtom, lAtom, chargeProd, sigma, epsilon) force.addException(iAtom, lAtom, chargeProd, sigma, epsilon)
excludedAtomPairs.add(min((iAtom, lAtom), (lAtom, iAtom))) excludedAtomPairs.add(min((iAtom, lAtom), (lAtom, iAtom)))
...@@ -792,15 +860,12 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode ...@@ -792,15 +860,12 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
if gbmodel is not None: if gbmodel is not None:
if verbose: print "Adding GB parameters..." if verbose: print "Adding GB parameters..."
charges = prmtop.getCharges() charges = prmtop.getCharges()
symbls = None
cutoff = None cutoff = None
if nonbondedMethod != 'NoCutoff': if nonbondedMethod != 'NoCutoff':
cutoff = nonbondedCutoff cutoff = nonbondedCutoff
if units.is_quantity(cutoff): if units.is_quantity(cutoff):
cutoff = cutoff.value_in_unit(units.nanometers) cutoff = cutoff.value_in_unit(units.nanometers)
if gbmodel == 'GBn': gb_parms = prmtop.getGBParms(gbmodel, elements)
symbls = prmtop.getAtomTypes()
gb_parms = prmtop.getGBParms(symbls)
if gbmodel == 'HCT': if gbmodel == 'HCT':
gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE', cutoff) gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE', cutoff)
elif gbmodel == 'OBC1': elif gbmodel == 'OBC1':
...@@ -811,11 +876,16 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode ...@@ -811,11 +876,16 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
gb.setSolventDielectric(solventDielectric) gb.setSolventDielectric(solventDielectric)
elif gbmodel == 'GBn': elif gbmodel == 'GBn':
gb = customgb.GBSAGBnForce(solventDielectric, soluteDielectric, 'ACE', cutoff) gb = customgb.GBSAGBnForce(solventDielectric, soluteDielectric, 'ACE', cutoff)
elif gbmodel == 'GBn2':
gb = customgb.GBSAGBn2Force(solventDielectric, soluteDielectric, 'ACE', cutoff)
else: else:
raise Exception("Illegal value specified for implicit solvent model") raise Exception("Illegal value specified for implicit solvent model")
for iAtom in range(prmtop.getNumAtoms()): for iAtom in range(prmtop.getNumAtoms()):
if gbmodel == 'OBC2': if gbmodel == 'OBC2':
gb.addParticle(charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1]) gb.addParticle(charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1])
elif gbmodel == 'GBn2':
gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1],
gb_parms[iAtom][2], gb_parms[iAtom][3], gb_parms[iAtom][4]])
else: else:
gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1]]) gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1]])
system.addForce(gb) system.addForce(gb)
...@@ -829,6 +899,8 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode ...@@ -829,6 +899,8 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
gb.setCutoffDistance(nonbondedCutoff) gb.setCutoffDistance(nonbondedCutoff)
else: else:
raise Exception("Illegal nonbonded method for use with GBSA") raise Exception("Illegal nonbonded method for use with GBSA")
# This applies the reaction field dielectric to the NonbondedForce
# created above. Do not bind force to another name before this!
force.setReactionFieldDielectric(1.0) force.setReactionFieldDielectric(1.0)
# TODO: Add GBVI terms? # TODO: Add GBVI terms?
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ 99ef4344
...@@ -8,7 +8,7 @@ Medical Research, grant U54 GM072970. See https://simtk.org. ...@@ -8,7 +8,7 @@ Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012 University of Virginia and the Authors. Portions copyright (c) 2012 University of Virginia and the Authors.
Authors: Christoph Klein, Michael R. Shirts Authors: Christoph Klein, Michael R. Shirts
Contributors: Contributors: Jason M. Swails
Permission is hereby granted, free of charge, to any person obtaining a Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"), copy of this software and associated documentation files (the "Software"),
...@@ -29,8 +29,9 @@ OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE ...@@ -29,8 +29,9 @@ OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE. USE OR OTHER DEALINGS IN THE SOFTWARE.
""" """
from __future__ import division
from simtk.openmm import CustomGBForce from simtk.openmm import CustomGBForce
import sys, pdb, pickle
d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444, d0=[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, 2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196,
...@@ -212,11 +213,11 @@ def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non ...@@ -212,11 +213,11 @@ def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non
custom = CustomGBForce() custom = CustomGBForce()
custom.addPerParticleParameter("q"); custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius"); custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale"); custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric); custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric); custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009) custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;" "U=r+sr2;"
...@@ -237,11 +238,11 @@ def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=No ...@@ -237,11 +238,11 @@ def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=No
custom = CustomGBForce() custom = CustomGBForce()
custom.addPerParticleParameter("q"); custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius"); custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale"); custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric); custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric); custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009) custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;" "U=r+sr2;"
...@@ -262,11 +263,11 @@ def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=No ...@@ -262,11 +263,11 @@ def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=No
custom = CustomGBForce() custom = CustomGBForce()
custom.addPerParticleParameter("q"); custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius"); custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale"); custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric); custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric); custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009) custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;" "U=r+sr2;"
...@@ -296,12 +297,12 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non ...@@ -296,12 +297,12 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non
custom = CustomGBForce() custom = CustomGBForce()
custom.addPerParticleParameter("q"); custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius"); custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale"); custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric); custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric); custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009) custom.addGlobalParameter("offset", 0.009)
custom.addGlobalParameter("neckScale", 0.361825) custom.addGlobalParameter("neckScale", 0.361825)
custom.addGlobalParameter("neckCut", 0.68) custom.addGlobalParameter("neckCut", 0.68)
...@@ -323,3 +324,50 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non ...@@ -323,3 +324,50 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=Non
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle) "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff) _createEnergyTerms(custom, SA, cutoff)
return custom return custom
"""
Amber Equivalents: igb = 8
"""
def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):
"""
Indexing for tables:
input: radius1, radius2
index = (radius2*200-20)*21 + (radius1*200-20)
output: index of desired value in row-by-row, 1D version of Tables 3 & 4
"""
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addPerParticleParameter("alpha")
custom.addPerParticleParameter("beta")
custom.addPerParticleParameter("gamma")
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.0195141)
custom.addGlobalParameter("neckScale", 0.826836)
custom.addGlobalParameter("neckCut", 0.68)
custom.addFunction("getd0", d0, 0, 440)
custom.addFunction("getm0", m0, 0, 440)
custom.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
"index = (radius2*200-20)*21 + (radius1*200-20);"
"Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff)
return custom
wrappers/python/simtk/openmm/app/internal/pdbstructure.py
View file @ 99ef4344
...@@ -436,7 +436,7 @@ class Chain(object): ...@@ -436,7 +436,7 @@ class Chain(object):
self._finalize() self._finalize()
def get_residue(self, residue_number, insertion_code=' '): def get_residue(self, residue_number, insertion_code=' '):
return residues_by_num_icode[str(residue_number) + insertion_code] return self.residues_by_num_icode[str(residue_number) + insertion_code]
def __contains__(self, residue_number): def __contains__(self, residue_number):
return self.residues_by_number.__contains__(residue_number) return self.residues_by_number.__contains__(residue_number)
...@@ -916,7 +916,6 @@ if __name__=='__main__': ...@@ -916,7 +916,6 @@ if __name__=='__main__':
import doctest, sys import doctest, sys
doctest.testmod(sys.modules[__name__]) doctest.testmod(sys.modules[__name__])
import sys
import os import os
import gzip import gzip
import re import re
......
wrappers/python/simtk/openmm/app/pdbfile.py
View file @ 99ef4344
...@@ -287,11 +287,15 @@ class PDBFile(object): ...@@ -287,11 +287,15 @@ class PDBFile(object):
else: else:
atomName = atom.name atomName = atom.name
coords = positions[posIndex] coords = positions[posIndex]
line = "ATOM %5d %-4s %3s %s%4d %s%s%s 1.00 0.00" % ( if atom.element is not None:
symbol = atom.element.symbol
else:
symbol = ' '
line = "ATOM %5d %-4s %3s %s%4d %s%s%s 1.00 0.00 %2s " % (
atomIndex%100000, atomName, resName, chainName, atomIndex%100000, atomName, resName, chainName,
(resIndex+1)%10000, _format_83(coords[0]), (resIndex+1)%10000, _format_83(coords[0]),
_format_83(coords[1]), _format_83(coords[2])) _format_83(coords[1]), _format_83(coords[2]), symbol)
assert len(line) == 66, 'Fixed width overflow detected' assert len(line) == 80, 'Fixed width overflow detected'
print >>file, line print >>file, line
posIndex += 1 posIndex += 1
atomIndex += 1 atomIndex += 1
...@@ -309,6 +313,56 @@ class PDBFile(object): ...@@ -309,6 +313,56 @@ class PDBFile(object):
- topology (Topology) The Topology defining the molecular system being written - topology (Topology) The Topology defining the molecular system being written
- file (file=stdout) A file to write the file to - file (file=stdout) A file to write the file to
""" """
# Identify bonds that should be listed as CONECT records.
standardResidues = ['ALA', 'ASN', 'CYS', 'GLU', 'HIS', 'LEU', 'MET', 'PRO', 'THR', 'TYR',
'ARG', 'ASP', 'GLN', 'GLY', 'ILE', 'LYS', 'PHE', 'SER', 'TRP', 'VAL',
'A', 'G', 'C', 'U', 'I', 'DA', 'DG', 'DC', 'DT', 'DI', 'HOH']
conectBonds = []
for atom1, atom2 in topology.bonds():
if atom1.residue.name not in standardResidues or atom2.residue.name not in standardResidues:
conectBonds.append((atom1, atom2))
elif atom1.name == 'SG' and atom2.name == 'SG' and atom1.residue.name == 'CYS' and atom2.residue.name == 'CYS':
conectBonds.append((atom1, atom2))
if len(conectBonds) > 0:
# Work out the index used in the PDB file for each atom.
atomIndex = {}
nextAtomIndex = 0
prevChain = None
for chain in topology.chains():
for atom in chain.atoms():
if atom.residue.chain != prevChain:
nextAtomIndex += 1
prevChain = atom.residue.chain
atomIndex[atom] = nextAtomIndex
nextAtomIndex += 1
# Record which other atoms each atom is bonded to.
atomBonds = {}
for atom1, atom2 in conectBonds:
index1 = atomIndex[atom1]
index2 = atomIndex[atom2]
if index1 not in atomBonds:
atomBonds[index1] = []
if index2 not in atomBonds:
atomBonds[index2] = []
atomBonds[index1].append(index2)
atomBonds[index2].append(index1)
# Write the CONECT records.
for index1 in sorted(atomBonds):
bonded = atomBonds[index1]
while len(bonded) > 4:
print >>file, "CONECT%5d%5d%5d%5d" % (index1, bonded[0], bonded[1], bonded[2])
del bonded[:4]
line = "CONECT%5d" % index1
for index2 in bonded:
line = "%s%5d" % (line, index2)
print >>file, line
print >>file, "END" print >>file, "END"
......
wrappers/python/simtk/openmm/app/pdbreporter.py
View file @ 99ef4344
...@@ -79,5 +79,6 @@ class PDBReporter(object): ...@@ -79,5 +79,6 @@ class PDBReporter(object):
self._nextModel += 1 self._nextModel += 1
def __del__(self): def __del__(self):
PDBFile.writeFooter(self._topology, self._out) if self._topology is not None:
PDBFile.writeFooter(self._topology, self._out)
self._out.close() self._out.close()
wrappers/python/simtk/openmm/app/statedatareporter.py
View file @ 99ef4344
...@@ -31,9 +31,10 @@ USE OR OTHER DEALINGS IN THE SOFTWARE. ...@@ -31,9 +31,10 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
__author__ = "Peter Eastman" __author__ = "Peter Eastman"
__version__ = "1.0" __version__ = "1.0"
import bz2
import gzip
import simtk.openmm as mm import simtk.openmm as mm
import simtk.unit as unit import simtk.unit as unit
from simtk.openmm.app import PDBFile
import math import math
class StateDataReporter(object): class StateDataReporter(object):
...@@ -67,7 +68,14 @@ class StateDataReporter(object): ...@@ -67,7 +68,14 @@ class StateDataReporter(object):
self._reportInterval = reportInterval self._reportInterval = reportInterval
self._openedFile = isinstance(file, str) self._openedFile = isinstance(file, str)
if self._openedFile: if self._openedFile:
self._out = open(file, 'w', 0) # Detect the desired compression scheme from the filename extension
# and open all files unbuffered
if file.endswith('.gz'):
self._out = gzip.GzipFile(fileobj=open(file, 'wb', 0))
elif file.endswith('.bz2'):
self._out = bz2.BZ2File(file, 'w', 0)
else:
self._out = open(file, 'w', 0)
else: else:
self._out = file self._out = file
self._step = step self._step = step
...@@ -109,7 +117,10 @@ class StateDataReporter(object): ...@@ -109,7 +117,10 @@ class StateDataReporter(object):
self._initializeConstants(simulation) self._initializeConstants(simulation)
headers = self._constructHeaders() headers = self._constructHeaders()
print >>self._out, '#"%s"' % ('"'+self._separator+'"').join(headers) print >>self._out, '#"%s"' % ('"'+self._separator+'"').join(headers)
self._out.flush() try:
self._out.flush()
except AttributeError:
pass
self._hasInitialized = True self._hasInitialized = True
# Check for errors. # Check for errors.
...@@ -120,7 +131,10 @@ class StateDataReporter(object): ...@@ -120,7 +131,10 @@ class StateDataReporter(object):
# Write the values. # Write the values.
print >>self._out, self._separator.join(str(v) for v in values) print >>self._out, self._separator.join(str(v) for v in values)
self._out.flush() try:
self._out.flush()
except AttributeError:
pass
def _constructReportValues(self, simulation, state): def _constructReportValues(self, simulation, state):
"""Query the simulation for the current state of our observables of interest. """Query the simulation for the current state of our observables of interest.
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ 99ef4344
...@@ -145,6 +145,8 @@ SKIP_METHODS = [('State',), ...@@ -145,6 +145,8 @@ SKIP_METHODS = [('State',),
('IntegrateDrudeSCFStepKernel',), ('IntegrateDrudeSCFStepKernel',),
('XmlSerializer', 'serialize'), ('XmlSerializer', 'serialize'),
('XmlSerializer', 'deserialize'), ('XmlSerializer', 'deserialize'),
('fvec4',),
('ivec4',),
] ]
# The build script assumes method args that are non-const references are # The build script assumes method args that are non-const references are
......
wrappers/python/tests/TestDesmondDMSFile.py 0 → 100644
View file @ 99ef4344
import os
import unittest
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
import simtk.openmm.app.element as elem
class TestDesmondDMSFile(unittest.TestCase):
def setUp(self):
"""Set up the tests by loading the input files."""
# alanine dipeptide with explicit water
path = os.path.join(os.path.dirname(__file__), 'systems/alanine-dipeptide-explicit-amber99SBILDN-tip3p.dms')
self.dms = DesmondDMSFile(path)
def test_NonbondedMethod(self):
"""Test all five options for the nonbondedMethod parameter."""
methodMap = {NoCutoff:NonbondedForce.NoCutoff,
CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic,
CutoffPeriodic:NonbondedForce.CutoffPeriodic,
Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
for method in methodMap:
system = self.dms.createSystem(nonbondedMethod=method)
forces = system.getForces()
self.assertTrue(any(isinstance(f, NonbondedForce) and
f.getNonbondedMethod()==methodMap[method]
for f in forces))
def test_Cutoff(self):
"""Test to make sure the nonbondedCutoff parameter is passed correctly."""
for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
system = self.dms.createSystem(nonbondedMethod=method,
nonbondedCutoff=2*nanometer)
cutoff_distance = 0.0*nanometer
cutoff_check = 2.0*nanometer
for force in system.getForces():
if isinstance(force, NonbondedForce):
cutoff_distance = force.getCutoffDistance()
self.assertEqual(cutoff_distance, cutoff_check)
def test_EwaldErrorTolerance(self):
"""Test to make sure the ewaldErrorTolerance parameter is passed correctly."""
for method in [Ewald, PME]:
system = self.dms.createSystem(nonbondedMethod=method,
ewaldErrorTolerance=1e-6)
tolerance = 0
tolerance_check = 1e-6
for force in system.getForces():
if isinstance(force, NonbondedForce):
tolerance = force.getEwaldErrorTolerance()
self.assertEqual(tolerance, tolerance_check)
def test_RemoveCMMotion(self):
"""Test both options (True and False) for the removeCMMotion parameter."""
for b in [True, False]:
system = self.dms.createSystem(removeCMMotion=b)
self.assertEqual(any(isinstance(f, CMMotionRemover) for f in system.getForces()), b)
def test_HydrogenMass(self):
"""Test that altering the mass of hydrogens works correctly."""
topology = self.dms.topology
hydrogenMass = 4*amu
system1 = self.dms.createSystem()
system2 = self.dms.createSystem(hydrogenMass=hydrogenMass)
for atom in topology.atoms():
if atom.element == elem.hydrogen:
self.assertNotEqual(hydrogenMass, system1.getParticleMass(atom.index))
self.assertEqual(hydrogenMass, system2.getParticleMass(atom.index))
totalMass1 = sum([system1.getParticleMass(i) for i in range(system1.getNumParticles())]).value_in_unit(amu)
totalMass2 = sum([system2.getParticleMass(i) for i in range(system2.getNumParticles())]).value_in_unit(amu)
self.assertAlmostEqual(totalMass1, totalMass2)
wrappers/python/tests/systems/alanine-dipeptide-explicit.pdb
View file @ 99ef4344
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