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Commit 51b7f9e2 authored by Robert McGibbon's avatar Robert McGibbon
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Merge master

parents 85bfd73c be0387b6
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Showing with 258 additions and 120 deletions
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ 51b7f9e2
......@@ -141,6 +141,7 @@ STEAL_OWNERSHIP = {("Platform", "registerPlatform") : [0],
("CustomHbondForce", "addTabulatedFunction") : [1],
("CustomCompoundBondForce", "addTabulatedFunction") : [1],
("CustomManyParticleForce", "addTabulatedFunction") : [1],
("CompoundIntegrator", "addIntegrator") : [0],
}
# This is a list of units to attach to return values and method args.
......@@ -308,6 +309,7 @@ UNITS = {
("AmoebaWcaDispersionForce", "getShctd") : ( None, ()),
("Context", "getParameter") : (None, ()),
("Context", "getParameters") : (None, ()),
("Context", "getMolecules") : (None, ()),
("CMAPTorsionForce", "getMapParameters") : (None, (None, 'unit.kilojoule_per_mole')),
("CMAPTorsionForce", "getTorsionParameters") : (None, ()),
......
wrappers/python/src/swig_doxygen/swig_lib/python/extend.i
View file @ 51b7f9e2
......@@ -51,33 +51,33 @@
%pythoncode %{
def getState(self,
getPositions=False,
getVelocities=False,
getForces=False,
getEnergy=False,
getParameters=False,
enforcePeriodicBox=False,
groups=-1):
"""
getState(self, getPositions=False, getVelocities=False, getForces=False,
getEnergy=False, getParameters=False, enforcePeriodicBox=False,
groups=-1) -> State
Get a State object recording the current state information stored in this context.
Parameters:
- getPositions (bool=False) whether to store particle positions in the State
- getVelocities (bool=False) whether to store particle velocities in the State
- getForces (bool=False) whether to store the forces acting on particles in the State
- getEnergy (bool=False) whether to store potential and kinetic energy in the State
- getParameter (bool=False) whether to store context parameters in the State
- enforcePeriodicBox (bool=False) if false, the position of each particle will be whatever position is stored in the Context, regardless of periodic boundary conditions. If true, particle positions will be translated so the center of every molecule lies in the same periodic box.
- groups (set={0,1,2,...,31}) a set of indices for which force groups
to include when computing forces and energies. The default value
includes all groups. groups can also be passed as an unsigned integer
interpreted as a bitmask, in which case group i will be included if
(groups&(1<<i)) != 0.
def getState(self, getPositions=False, getVelocities=False,
getForces=False, getEnergy=False, getParameters=False,
enforcePeriodicBox=False, groups=-1):
"""Get a State object recording the current state information stored in this context.
Parameters
----------
getPositions : bool=False
whether to store particle positions in the State
getVelocities : bool=False
whether to store particle velocities in the State
getForces : bool=False
whether to store the forces acting on particles in the State
getEnergy : bool=False
whether to store potential and kinetic energy in the State
getParameter : bool=False
whether to store context parameters in the State
enforcePeriodicBox : bool=False
if false, the position of each particle will be whatever position
is stored in the Context, regardless of periodic boundary conditions.
If true, particle positions will be translated so the center of
every molecule lies in the same periodic box.
groups : set={0,1,2,...,31}
a set of indices for which force groups to include when computing
forces and energies. The default value includes all groups. groups
can also be passed as an unsigned integer interpreted as a bitmask,
in which case group i will be included if (groups&(1<<i)) != 0.
"""
getP, getV, getF, getE, getPa, enforcePeriodic = map(bool,
(getPositions, getVelocities, getForces, getEnergy, getParameters,
......@@ -208,33 +208,32 @@ Parameters:
getParameters=False,
enforcePeriodicBox=False,
groups=-1):
"""
getState(self,
copy,
getPositions = False,
getVelocities = False,
getForces = False,
getEnergy = False,
getParameters = False,
enforcePeriodicBox = False,
groups = -1)
-> State
Get a State object recording the current state information about one copy of the system.
Parameters:
- copy (int) the index of the copy for which to retrieve state information
- getPositions (bool=False) whether to store particle positions in the State
- getVelocities (bool=False) whether to store particle velocities in the State
- getForces (bool=False) whether to store the forces acting on particles in the State
- getEnergy (bool=False) whether to store potential and kinetic energy in the State
- getParameter (bool=False) whether to store context parameters in the State
- enforcePeriodicBox (bool=False) if false, the position of each particle will be whatever position is stored in the Context, regardless of periodic boundary conditions. If true, particle positions will be translated so the center of every molecule lies in the same periodic box.
- groups (set={0,1,2,...,31}) a set of indices for which force groups
to include when computing forces and energies. The default value
includes all groups. groups can also be passed as an unsigned integer
interpreted as a bitmask, in which case group i will be included if
(groups&(1<<i)) != 0.
"""Get a State object recording the current state information about one copy of the system.
Parameters
----------
copy : int
the index of the copy for which to retrieve state information
getPositions : bool=False
whether to store particle positions in the State
getVelocities : bool=False
whether to store particle velocities in the State
getForces : bool=False
whether to store the forces acting on particles in the State
getEnergy : bool=False
whether to store potential and kinetic energy in the State
getParameter : bool=False
whether to store context parameters in the State
enforcePeriodicBox : bool=False
if false, the position of each particle will be whatever position
is stored in the Context, regardless of periodic boundary conditions.
If true, particle positions will be translated so the center of
every molecule lies in the same periodic box.
groups : set={0,1,2,...,31}
a set of indices for which force groups to include when computing
forces and energies. The default value includes all groups. groups
can also be passed as an unsigned integer interpreted as a bitmask,
in which case group i will be included if (groups&(1<<i)) != 0.
"""
getP, getV, getF, getE, getPa, enforcePeriodic = map(bool,
(getPositions, getVelocities, getForces, getEnergy, getParameters,
......
wrappers/python/tests/TestModeller.py
View file @ 51b7f9e2
......@@ -3,6 +3,10 @@ from validateModeller import *
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
if sys.version_info >= (3, 0):
from io import StringIO
else:
from cStringIO import StringIO
class TestModeller(unittest.TestCase):
""" Test the Modeller class. """
......@@ -401,6 +405,7 @@ class TestModeller(unittest.TestCase):
topology_start = self.pdb.topology
topology_start.setUnitCellDimensions(Vec3(3.5, 3.5, 3.5)*nanometers)
for neutralize in (True, False):
# set up modeller with no solvent
modeller = Modeller(topology_start, self.positions)
modeller.deleteWater()
......@@ -416,7 +421,7 @@ class TestModeller(unittest.TestCase):
positions_toAdd = [Vec3(1.0,1.2,1.5), Vec3(1.7,1.0,1.4), Vec3(1.5,2.0,1.0),
Vec3(2.0,2.0,2.0), Vec3(2.0,1.5,1.0)]*nanometers
modeller.add(topology_toAdd, positions_toAdd)
modeller.addSolvent(self.forcefield, ionicStrength=1.0*molar)
modeller.addSolvent(self.forcefield, ionicStrength=1.0*molar, neutralize=neutralize)
topology_after = modeller.getTopology()
water_count = 0
......@@ -432,9 +437,10 @@ class TestModeller(unittest.TestCase):
total_water_ions = water_count+sodium_count+chlorine_count
expected_ion_fraction = 1.0*molar/(55.4*molar)
expected_ions = math.floor((total_water_ions-10)*expected_ion_fraction/2+0.5)+5
self.assertEqual(sodium_count, expected_ions)
self.assertEqual(chlorine_count, expected_ions)
expected_chlorine = math.floor((total_water_ions-10)*expected_ion_fraction/2+0.5)+5
expected_sodium = expected_chlorine if neutralize else expected_chlorine-5
self.assertEqual(sodium_count, expected_sodium)
self.assertEqual(chlorine_count, expected_chlorine)
def test_addSolventPositiveSolvent(self):
""" Test the addSolvent() method; test adding ions to a positively charged solvent. """
......@@ -442,6 +448,7 @@ class TestModeller(unittest.TestCase):
topology_start = self.pdb.topology
topology_start.setUnitCellDimensions(Vec3(3.5, 3.5, 3.5)*nanometers)
for neutralize in (True, False):
# set up modeller with no solvent
modeller = Modeller(topology_start, self.positions)
modeller.deleteWater()
......@@ -459,7 +466,7 @@ class TestModeller(unittest.TestCase):
# positions_toAdd doesn't need to change
modeller.add(topology_toAdd, positions_toAdd)
modeller.addSolvent(self.forcefield, ionicStrength=1.0*molar)
modeller.addSolvent(self.forcefield, ionicStrength=1.0*molar, neutralize=neutralize)
topology_after = modeller.getTopology()
water_count = 0
......@@ -475,9 +482,10 @@ class TestModeller(unittest.TestCase):
total_water_ions = water_count+sodium_count+chlorine_count
expected_ion_fraction = 1.0*molar/(55.4*molar)
expected_ions = math.floor((total_water_ions-10)*expected_ion_fraction/2+0.5)+5
self.assertEqual(sodium_count, expected_ions)
self.assertEqual(chlorine_count, expected_ions)
expected_sodium = math.floor((total_water_ions-10)*expected_ion_fraction/2+0.5)+5
expected_chlorine = expected_sodium if neutralize else expected_sodium-5
self.assertEqual(sodium_count, expected_sodium)
self.assertEqual(chlorine_count, expected_chlorine)
def test_addSolventIons(self):
""" Test the addSolvent() method with all possible choices for positive and negative ions. """
......@@ -915,6 +923,135 @@ class TestModeller(unittest.TestCase):
self.assertEqual(1, len(ep))
def test_addVirtualSites(self):
"""Test adding extra particles defined by virtual sites."""
xml = """
<ForceField>
<AtomTypes>
<Type name="C" class="C" element="C" mass="10"/>
<Type name="N" class="N" element="N" mass="10"/>
<Type name="O" class="O" element="O" mass="10"/>
<Type name="V" class="V" mass="0.0"/>
</AtomTypes>
<Residues>
<Residue name="Test">
<Atom name="C" type="C"/>
<Atom name="N" type="N"/>
<Atom name="O" type="O"/>
<Atom name="V1" type="V"/>
<Atom name="V2" type="V"/>
<Atom name="V3" type="V"/>
<Atom name="V4" type="V"/>
<VirtualSite type="average2" index="3" atom1="0" atom2="1" weight1="0.7" weight2="0.3"/>
<VirtualSite type="average3" index="4" atom1="0" atom2="1" atom3="2" weight1="0.2" weight2="0.3" weight3="0.5"/>
<VirtualSite type="outOfPlane" index="5" atom1="0" atom2="1" atom3="2" weight12="0.1" weight13="-0.2" weightCross="0.8"/>
<VirtualSite type="localCoords" index="6" atom1="0" atom2="1" atom3="2" wo1="0.1" wo2="0.5" wo3="0.4" wx1="1" wx2="-0.6" wx3="-0.4" wy1="0.1" wy2="0.9" wy3="-1" p1="-0.5" p2="0.4" p3="1.1"/>
</Residue>
</Residues>
</ForceField>"""
ff = ForceField(StringIO(xml))
# Create the three real atoms.
topology = Topology()
chain = topology.addChain()
residue = topology.addResidue('Test', chain)
topology.addAtom('C', element.carbon, residue)
topology.addAtom('N', element.nitrogen, residue)
topology.addAtom('V', element.oxygen, residue)
# Add the virtual sites.
modeller = Modeller(topology, [Vec3(0.1, 0.2, 0.3), Vec3(1.0, 0.9, 0.8), Vec3(1.5, 1.1, 0.7)]*nanometers)
modeller.addExtraParticles(ff)
top = modeller.topology
pos = modeller.positions
# Check that the correct particles were added.
self.assertEqual(len(pos), 7)
for atom, elem in zip(top.atoms(), [element.carbon, element.nitrogen, element.oxygen, None, None, None, None]):
self.assertEqual(elem, atom.element)
# Check that the positions were calculated correctly.
system = ff.createSystem(top)
integ = VerletIntegrator(1.0)
context = Context(system, integ)
context.setPositions(pos)
context.computeVirtualSites()
state = context.getState(getPositions=True)
for p1, p2 in zip (pos, state.getPositions()):
self.assertVecAlmostEqual(p1.value_in_unit(nanometers), p2.value_in_unit(nanometers), 1e-6)
def test_multiSiteIon(self):
"""Test adding extra particles whose positions are determined based on bonds."""
xml = """
<ForceField>
<AtomTypes>
<Type name="Zn" class="Zn" element="Zn" mass="53.380"/>
<Type name="DA" class="DA" mass="3.0"/>
</AtomTypes>
<Residues>
<Residue name="ZN">
<Atom name="ZN" type="Zn"/>
<Atom name="D1" type="DA"/>
<Atom name="D2" type="DA"/>
<Atom name="D3" type="DA"/>
<Atom name="D4" type="DA"/>
<Bond from="0" to="2"/>
<Bond from="0" to="1"/>
<Bond from="0" to="3"/>
<Bond from="0" to="4"/>
<Bond from="1" to="2"/>
<Bond from="1" to="3"/>
<Bond from="1" to="4"/>
<Bond from="2" to="4"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond class1="DA" class2="Zn" length="0.09" k="535552.0"/>
<Bond class1="DA" class2="DA" length="0.147" k="535552.0"/>
</HarmonicBondForce>
</ForceField>"""
ff = ForceField(StringIO(xml))
# Create two zinc atoms.
topology = Topology()
chain = topology.addChain()
residue = topology.addResidue('ZN', chain)
topology.addAtom('ZN', element.zinc, residue)
residue = topology.addResidue('ZN', chain)
topology.addAtom('ZN', element.zinc, residue)
# Add the extra particles.
modeller = Modeller(topology, [Vec3(0.5, 1.0, 1.5), Vec3(2.0, 2.0, 0.0)]*nanometers)
modeller.addExtraParticles(ff)
top = modeller.topology
pos = modeller.positions
# Check that the correct particles were added.
self.assertEqual(len(pos), 10)
for i, atom in enumerate(top.atoms()):
self.assertEqual(element.zinc if i in (0,5) else None, atom.element)
# Check that the positions in the first residue are reasonable.
center = Vec3(0.5, 1.0, 1.5)*nanometers
self.assertEqual(center, modeller.positions[0])
for i in range(1, 5):
for j in range(i):
dist = norm(pos[i]-pos[j])
expectedDist = 0.09 if j == 0 else 0.147
self.assertTrue(dist > (expectedDist-0.01)*nanometers and dist < (expectedDist+0.01)*nanometers)
def assertVecAlmostEqual(self, p1, p2, tol=1e-7):
scale = max(1.0, norm(p1),)
for i in range(3):
......
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