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Commit 21a39eaf authored by Peter Eastman's avatar Peter Eastman
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Modeller supports triclinic boxes

parent 0a0f0214
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Showing with 65 additions and 34 deletions
wrappers/python/simtk/openmm/app/modeller.py
View file @ 21a39eaf
......@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012-2013 Stanford University and the Authors.
Portions copyright (c) 2012-2015 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
......@@ -94,7 +94,7 @@ class Modeller(object):
# Copy over the existing model.
newTopology = Topology()
newTopology.setUnitCellDimensions(self.topology.getUnitCellDimensions())
newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
newAtoms = {}
newPositions = []*nanometer
for chain in self.topology.chains():
......@@ -140,7 +140,7 @@ class Modeller(object):
- toDelete (list) a list of Atoms, Residues, Chains, and bonds (specified as tuples of Atoms) to delete
"""
newTopology = Topology()
newTopology.setUnitCellDimensions(self.topology.getUnitCellDimensions())
newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
newAtoms = {}
newPositions = []*nanometer
deleteSet = set(toDelete)
......@@ -189,7 +189,7 @@ class Modeller(object):
else:
raise ValueError('Unknown water model: %s' % model)
newTopology = Topology()
newTopology.setUnitCellDimensions(self.topology.getUnitCellDimensions())
newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
newAtoms = {}
newPositions = []*nanometer
for chain in self.topology.chains():
......@@ -240,7 +240,7 @@ class Modeller(object):
self.topology = newTopology
self.positions = newPositions
def addSolvent(self, forcefield, model='tip3p', boxSize=None, padding=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar):
def addSolvent(self, forcefield, model='tip3p', boxSize=None, boxVectors=None, padding=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar):
"""Add solvent (both water and ions) to the model to fill a rectangular box.
The algorithm works as follows:
......@@ -250,15 +250,17 @@ class Modeller(object):
randomly selecting a water molecule and replacing it with the ion.
4. Ion pairs are added to give the requested total ionic strength.
The box size can be specified in three ways. First, you can explicitly give a box size to use. Alternatively, you can
The box size can be specified in four ways. First, you can explicitly give the vectors defining the periodic box to
use. Alternatively, for a rectangular box you can simply give the dimensions of the unit cell. Third, you can
give a padding distance. The largest dimension of the solute (along the x, y, or z axis) is determined, and a cubic
box of size (largest dimension)+2*padding is used. Finally, if neither a box size nor a padding distance is specified,
the existing Topology's unit cell dimensions are used.
box of size (largest dimension)+2*padding is used. Finally, if neither box vectors, box size, nor padding distance is specified,
the existing Topology's box vectors are used.
Parameters:
- forcefield (ForceField) the ForceField to use for determining van der Waals radii and atomic charges
- model (string='tip3p') the water model to use. Supported values are 'tip3p', 'spce', 'tip4pew', and 'tip5p'.
- boxSize (Vec3=None) the size of the box to fill with water
- boxVectors (tuple of Vec3=None) the vectors defining the periodic box to fill with water
- padding (distance=None) the padding distance to use
- positiveIon (string='Na+') the type of positive ion to add. Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'
- negativeIon (string='Cl-') the type of negative ion to add. Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'. Be aware
......@@ -268,18 +270,28 @@ class Modeller(object):
"""
# Pick a unit cell size.
if boxSize is not None:
if boxVectors is not None:
if is_quantity(boxVectors[0]):
boxVectors = (boxVectors[0].value_in_unit(nanometer), boxVectors[1].value_in_unit(nanometer), boxVectors[2].value_in_unit(nanometer))
box = Vec3(boxVectors[0][0], boxVectors[1][1], boxVectors[2][2])
vectors = boxVectors
elif boxSize is not None:
if is_quantity(boxSize):
boxSize = boxSize.value_in_unit(nanometer)
box = Vec3(boxSize[0], boxSize[1], boxSize[2])*nanometer
box = Vec3(boxSize[0], boxSize[1], boxSize[2])
vectors = (Vec3(boxSize[0], 0, 0), Vec3(0, boxSize[1], 0), Vec3(0, 0, boxSize[2]))
elif padding is not None:
if is_quantity(padding):
padding = padding.value_in_unit(nanometer)
maxSize = max(max((pos[i] for pos in self.positions))-min((pos[i] for pos in self.positions)) for i in range(3))
maxSize = maxSize.value_in_unit(nanometer)
box = (maxSize+2*padding)*Vec3(1, 1, 1)
vectors = (Vec3(maxSize+2*padding, 0, 0), Vec3(0, maxSize+2*padding, 0), Vec3(0, 0, maxSize+2*padding))
else:
box = self.topology.getUnitCellDimensions()
box = self.topology.getUnitCellDimensions().value_in_unit(nanometer)
vectors = self.topology.getPeriodicBoxVectors().value_in_unit(nanometer)
if box is None:
raise ValueError('Neither the box size nor padding was specified, and the Topology does not define unit cell dimensions')
box = box.value_in_unit(nanometer)
raise ValueError('Neither the box size, box vectors, nor padding was specified, and the Topology does not define unit cell dimensions')
invBox = Vec3(1.0/box[0], 1.0/box[1], 1.0/box[2])
# Identify the ion types.
......@@ -331,7 +343,7 @@ class Modeller(object):
# Copy the solute over.
newTopology = Topology()
newTopology.setUnitCellDimensions(box)
newTopology.setPeriodicBoxVectors(vectors*nanometer)
newAtoms = {}
newPositions = []*nanometer
for chain in self.topology.chains():
......@@ -378,7 +390,9 @@ class Modeller(object):
def periodicDistance(pos1, pos2):
delta = pos1-pos2
delta = [delta[i]-floor(delta[i]*invBox[i]+0.5)*box[i] for i in range(3)]
delta -= vectors[2]*floor(delta[2]*invBox[2]+0.5)
delta -= vectors[1]*floor(delta[1]*invBox[1]+0.5)
delta -= vectors[0]*floor(delta[0]*invBox[0]+0.5)
return norm(delta)
# Find the list of water molecules to add.
......@@ -472,7 +486,6 @@ class Modeller(object):
for atom2 in molAtoms:
if atom2.element == elem.hydrogen:
newTopology.addBond(atom1, atom2)
newTopology.setUnitCellDimensions(box*nanometer)
self.topology = newTopology
self.positions = newPositions
......@@ -610,7 +623,7 @@ class Modeller(object):
# Loop over residues.
newTopology = Topology()
newTopology.setUnitCellDimensions(self.topology.getUnitCellDimensions())
newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
newAtoms = {}
newPositions = []*nanometer
newIndices = []
......@@ -883,7 +896,7 @@ class Modeller(object):
# Create the new Topology.
newTopology = Topology()
newTopology.setUnitCellDimensions(self.topology.getUnitCellDimensions())
newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
newAtoms = {}
newPositions = []*nanometer
for chain in self.topology.chains():
......
wrappers/python/tests/TestModeller.py
View file @ 21a39eaf
......@@ -308,44 +308,56 @@ class TestModeller(unittest.TestCase):
self.assertTrue(len(matoms)==0 and len(m1atoms)==1 and len(m2atoms)==1)
def test_addSolventPeriodicBox(self):
""" Test the addSolvent() method; test that the three ways of passing in the periodic box all work. """
""" Test the addSolvent() method; test that the four ways of passing in the periodic box all work. """
# First way of passing in periodic box dimensions: set it in the original topology.
# First way of passing in periodic box vectors: set it in the original topology.
topology_start = self.pdb.topology
topology_start.setUnitCellDimensions(Vec3(3.5, 4.5, 5.5)*nanometers)
modeller = Modeller(topology_start, self.positions)
modeller.deleteWater()
modeller.addSolvent(self.forcefield)
topology_after = modeller.getTopology()
dim3 = topology_after.getUnitCellDimensions()
dim3 = topology_after.getPeriodicBoxVectors()
self.assertAlmostEqual(dim3[0]/nanometers, 3.5)
self.assertAlmostEqual(dim3[1]/nanometers, 4.5)
self.assertAlmostEqual(dim3[2]/nanometers, 5.5)
self.assertVecAlmostEqual(dim3[0]/nanometers, Vec3(3.5, 0, 0))
self.assertVecAlmostEqual(dim3[1]/nanometers, Vec3(0, 4.5, 0))
self.assertVecAlmostEqual(dim3[2]/nanometers, Vec3(0, 0, 5.5))
# Second way of passing in the periodic box dimensions: as a parameter to addSolvent()
# Second way of passing in the periodic box vectors: with the boxSize parameter to addSolvent()
topology_start = self.pdb.topology
modeller = Modeller(topology_start, self.positions)
modeller.deleteWater()
modeller.addSolvent(self.forcefield, boxSize = Vec3(3.6, 4.6, 5.6)*nanometers)
topology_after = modeller.getTopology()
dim3 = topology_after.getUnitCellDimensions()
dim3 = topology_after.getPeriodicBoxVectors()
self.assertAlmostEqual(dim3[0]/nanometers, 3.6)
self.assertAlmostEqual(dim3[1]/nanometers, 4.6)
self.assertAlmostEqual(dim3[2]/nanometers, 5.6)
self.assertVecAlmostEqual(dim3[0]/nanometers, Vec3(3.6, 0, 0))
self.assertVecAlmostEqual(dim3[1]/nanometers, Vec3(0, 4.6, 0))
self.assertVecAlmostEqual(dim3[2]/nanometers, Vec3(0, 0, 5.6))
# Third way of passing in the periodic box dimensions: pass a 'padding' value to addSolvent()
# Third way of passing in the periodic box vectors: with the boxVectors parameter to addSolvent()
topology_start = self.pdb.topology
modeller = Modeller(topology_start, self.positions)
modeller.deleteWater()
modeller.addSolvent(self.forcefield, boxVectors = (Vec3(3.4, 0, 0), Vec3(0.5, 4.4, 0), Vec3(-1.0, -1.5, 5.4))*nanometers)
topology_after = modeller.getTopology()
dim3 = topology_after.getPeriodicBoxVectors()
self.assertVecAlmostEqual(dim3[0]/nanometers, Vec3(3.4, 0, 0))
self.assertVecAlmostEqual(dim3[1]/nanometers, Vec3(0.5, 4.4, 0))
self.assertVecAlmostEqual(dim3[2]/nanometers, Vec3(-1.0, -1.5, 5.4))
# Fourth way of passing in the periodic box vectors: pass a 'padding' value to addSolvent()
topology_start = self.pdb.topology
modeller = Modeller(topology_start, self.positions)
modeller.deleteWater()
modeller.addSolvent(self.forcefield, padding = 1.0*nanometers)
topology_after = modeller.getTopology()
dim3 = topology_after.getUnitCellDimensions()
dim3 = topology_after.getPeriodicBoxVectors()
self.assertAlmostEqual(dim3[0]/nanometers, 2.8802)
self.assertAlmostEqual(dim3[1]/nanometers, 2.8802)
self.assertAlmostEqual(dim3[2]/nanometers, 2.8802)
self.assertVecAlmostEqual(dim3[0]/nanometers, Vec3(2.8802, 0, 0))
self.assertVecAlmostEqual(dim3[1]/nanometers, Vec3(0, 2.8802, 0))
self.assertVecAlmostEqual(dim3[2]/nanometers, Vec3(0, 0, 2.8802))
def test_addSolventNeutralSolvent(self):
""" Test the addSolvent() method; test adding ions to neutral solvent. """
......@@ -874,6 +886,12 @@ class TestModeller(unittest.TestCase):
validate_equivalence(self, topology_LYN, topology_after)
def assertVecAlmostEqual(self, p1, p2, tol=1e-7):
scale = max(1.0, norm(p1),)
for i in range(3):
diff = abs(p1[i]-p2[i])/scale
self.assertTrue(diff < tol)
if __name__ == '__main__':
unittest.main()
......
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