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Commit ffc96cc6 authored by peastman's avatar peastman
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wrappers/python/tests/TestModeller.py
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......@@ -369,14 +369,14 @@ class TestModeller(unittest.TestCase):
def test_addSolventNeutralSolvent(self):
""" Test the addSolvent() method; test adding ions to neutral solvent. """
topology_start = self.pdb.topology
topology_start.setUnitCellDimensions(Vec3(3.5, 3.5, 3.5)*nanometers)
modeller = Modeller(topology_start, self.positions)
modeller.deleteWater()
modeller.addSolvent(self.forcefield, ionicStrength = 2.0*molar)
topology_after = modeller.getTopology()
water_count=0
sodium_count=0
chlorine_count=0
......@@ -387,14 +387,14 @@ class TestModeller(unittest.TestCase):
sodium_count += 1
elif residue.name=='CL':
chlorine_count += 1
total_added = water_count+sodium_count+chlorine_count
self.assertEqual(total_added, 1364)
expected_ion_fraction = 2.0*molar/(55.4*molar)
expected_ions = math.floor(total_added*expected_ion_fraction/2+0.5)
self.assertEqual(sodium_count, expected_ions)
self.assertEqual(chlorine_count, expected_ions)
def test_addSolventNegativeSolvent(self):
""" Test the addSolvent() method; test adding ions to a negatively charged solvent. """
......@@ -404,7 +404,7 @@ class TestModeller(unittest.TestCase):
# set up modeller with no solvent
modeller = Modeller(topology_start, self.positions)
modeller.deleteWater()
# add 5 Cl- ions to the original topology
topology_toAdd = Topology()
newChain = topology_toAdd.addChain()
......@@ -418,7 +418,7 @@ class TestModeller(unittest.TestCase):
modeller.add(topology_toAdd, positions_toAdd)
modeller.addSolvent(self.forcefield, ionicStrength=1.0*molar)
topology_after = modeller.getTopology()
water_count = 0
sodium_count = 0
chlorine_count = 0
......@@ -429,23 +429,23 @@ class TestModeller(unittest.TestCase):
sodium_count += 1
elif residue.name=='CL':
chlorine_count += 1
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)
def test_addSolventPositiveSolvent(self):
""" Test the addSolvent() method; test adding ions to a positively charged solvent. """
topology_start = self.pdb.topology
topology_start.setUnitCellDimensions(Vec3(3.5, 3.5, 3.5)*nanometers)
# set up modeller with no solvent
modeller = Modeller(topology_start, self.positions)
modeller.deleteWater()
# add 5 Na+ ions to the original topology
topology_toAdd = Topology()
newChain = topology_toAdd.addChain()
......@@ -456,12 +456,12 @@ class TestModeller(unittest.TestCase):
topology_toAdd.addAtom('Na',Element.getBySymbol('Na'), residues[i])
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
# positions_toAdd doesn't need to change
modeller.add(topology_toAdd, positions_toAdd)
modeller.addSolvent(self.forcefield, ionicStrength=1.0*molar)
topology_after = modeller.getTopology()
water_count = 0
sodium_count = 0
chlorine_count = 0
......@@ -472,25 +472,25 @@ class TestModeller(unittest.TestCase):
sodium_count += 1
elif residue.name=='CL':
chlorine_count += 1
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)
def test_addSolventIons(self):
""" Test the addSolvent() method with all possible choices for positive and negative ions. """
topology_start = self.pdb.topology
topology_start.setUnitCellDimensions(Vec3(3.5, 3.5, 3.5)*nanometers)
# set up modeller with no solvent
modeller = Modeller(topology_start, self.positions)
modeller.deleteWater()
topology_nowater = modeller.getTopology()
positions_nowater = modeller.getPositions()
expected_ion_fraction = 1.0*molar/(55.4*molar)
for positiveIon in ['Cs+', 'K+', 'Li+', 'Na+', 'Rb+']:
......@@ -498,7 +498,7 @@ class TestModeller(unittest.TestCase):
modeller = Modeller(topology_nowater, positions_nowater)
modeller.addSolvent(self.forcefield, positiveIon=positiveIon, ionicStrength=1.0*molar)
topology_after = modeller.getTopology()
water_count = 0
positive_ion_count = 0
chlorine_count = 0
......@@ -509,20 +509,20 @@ class TestModeller(unittest.TestCase):
positive_ion_count += 1
elif residue.name=='CL':
chlorine_count += 1
total_added = water_count+positive_ion_count+chlorine_count
self.assertEqual(total_added, 1364)
expected_ions = math.floor(total_added*expected_ion_fraction/2+0.5)
self.assertEqual(positive_ion_count, expected_ions)
self.assertEqual(chlorine_count, expected_ions)
for negativeIon in ['Cl-', 'Br-', 'F-', 'I-']:
ionName = negativeIon[:-1].upper()
modeller = Modeller(topology_nowater, positions_nowater)
modeller.addSolvent(self.forcefield, negativeIon=negativeIon, ionicStrength=1.0*molar)
topology_after = modeller.getTopology()
water_count = 0
sodium_count = 0
negative_ion_count = 0
......@@ -539,7 +539,7 @@ class TestModeller(unittest.TestCase):
expected_ions = math.floor(total_added*expected_ion_fraction/2+0.5)
self.assertEqual(positive_ion_count, expected_ions)
self.assertEqual(chlorine_count, expected_ions)
def test_addHydrogensPdb2(self):
""" Test the addHydrogens() method on the T4-lysozyme-L99A pdb file. """
......@@ -547,11 +547,11 @@ class TestModeller(unittest.TestCase):
topology_start = self.topology_start2
positions = self.positions2
modeller = Modeller(topology_start, positions)
# remove hydrogens from the topology
toDelete = [atom for atom in topology_start.atoms() if atom.element==Element.getBySymbol('H')]
modeller.delete(toDelete)
# Create a variants list to force the one histidine to be of the right variation.
residues = [residue for residue in topology_start.residues()]
variants = [None]*len(residues)
......@@ -559,13 +559,13 @@ class TestModeller(unittest.TestCase):
# By setting variants[30] to 'HIE', we force the hydrogen onto the epsilon nitrogen, so
# that it will match the topology in topology_start.
variants[30] = 'HIE'
# add the hydrogens back
modeller.addHydrogens(self.forcefield, variants=variants)
topology_after = modeller.getTopology()
validate_equivalence(self, topology_start, topology_after)
def test_addHydrogensPdb3(self):
""" Test the addHydrogens() method on the metallothionein pdb file. """
......@@ -573,31 +573,31 @@ class TestModeller(unittest.TestCase):
topology_start = self.topology_start3
positions = self.positions3
modeller = Modeller(topology_start, positions)
# remove hydrogens from the topology
toDelete = [atom for atom in topology_start.atoms() if atom.element==Element.getBySymbol('H')]
modeller.delete(toDelete)
# add the hydrogens back
modeller.addHydrogens(self.forcefield)
topology_after = modeller.getTopology()
validate_equivalence(self, topology_start, topology_after)
def test_addHydrogensASH(self):
""" Test of addHydrogens() in which we force ASH to be a variant using the variants parameter. """
# use the T4-lysozyme-L99A pdb file
topology_start = self.topology_start2
positions = self.positions2
# build the Modeller
modeller = Modeller(topology_start, positions)
# remove hydrogens from the topology
toDelete = [atom for atom in topology_start.atoms() if atom.element==Element.getBySymbol('H')]
modeller.delete(toDelete)
# Create a variants list to force the one histidine to be of the right variation.
residues = [residue for residue in topology_start.residues()]
variants = [None]*len(residues)
......@@ -605,15 +605,15 @@ class TestModeller(unittest.TestCase):
# By setting variants[30] to 'HIE', we force the hydrogen onto the epsilon nitrogen, so
# that it will match the topology in topology_start.
variants[30] = 'HIE'
ASP_residue_list = [9,19,46,60,69,71,88,91,126,158]
for residue_index in ASP_residue_list:
variants[residue_index] = 'ASH'
# add the hydrogens back, using the variants list we just built
modeller.addHydrogens(self.forcefield, variants=variants)
topology_ASH = modeller.getTopology()
# There should be extra hydrogens on the ASP residues. Assert that they exist,
# then we delete them and validate that the topology matches what we started with.
index_list_ASH = [176, 357, 761, 976, 1121, 1150, 1430, 1473, 2028, 2556]
......@@ -624,41 +624,41 @@ class TestModeller(unittest.TestCase):
toDelete2.append(atoms[index])
modeller.delete(toDelete2)
topology_ASP = modeller.getTopology()
validate_equivalence(self, topology_ASP, topology_start)
def test_addHydrogensCYX(self):
""" Test of addHydrogens() in which we force CYX to be a variant using the variants parameter. """
# use the metallothionein pdb file
topology_start = self.topology_start3
positions = self.positions3
# build the Modeller
modeller = Modeller(topology_start, positions)
# remove hydrogens from the topology
toDelete = [atom for atom in topology_start.atoms() if atom.element==Element.getBySymbol('H')]
modeller.delete(toDelete)
# Create a variants list to force the cysteins to be of the CYX variety.
residues = [residue for residue in topology_start.residues()]
variants = [None]*len(residues)
CYS_residues = [2,4,10,12,16,18,21]
for index in CYS_residues:
variants[index] = 'CYX'
# add the hydrogens
modeller.addHydrogens(self.forcefield, variants=variants)
topology_CYX = modeller.getTopology()
# create a second modeller that we will attempt to match with topology_CYX
modeller2 = Modeller(topology_start, positions)
topology2 = modeller2.getTopology()
# There should be extra hydrogens on the CYS residues. Assert that they exist
# on modeller2, then delete them and validate that the topologies match.
# These are the indices of the hydrogens to delete from CYS to make CYX.
index_list_CYS = [31, 49, 110, 135, 171, 193, 229]
atoms = [atom for atom in topology2.atoms()]
......@@ -668,23 +668,23 @@ class TestModeller(unittest.TestCase):
toDelete2.append(atoms[index])
modeller2.delete(toDelete2)
topology_after = modeller2.getTopology()
validate_equivalence(self, topology_CYX, topology_after)
def test_addHydrogensGLH(self):
""" Test of addHydrogens() in which we force GLH to be a variant using the variants parameter. """
# use the T4-lysozyme-L99A pdb file
topology_start = self.topology_start2
positions = self.positions2
# build the Modeller
modeller = Modeller(topology_start, positions)
# remove hydrogens from the topology
toDelete = [atom for atom in topology_start.atoms() if atom.element==Element.getBySymbol('H')]
modeller.delete(toDelete)
# Create a variants list to force the one histidine to be of the right variation.
residues = [residue for residue in topology_start.residues()]
variants = [None]*len(residues)
......@@ -692,15 +692,15 @@ class TestModeller(unittest.TestCase):
# By setting variants[30] to 'HIE', we force the hydrogen onto the epsilon nitrogen, so
# that it will match the topology in topology_start.
variants[30] = 'HIE'
GLU_residue_list = [4,10,21,44,61,63,107,127]
for residue_index in GLU_residue_list:
variants[residue_index] = 'GLH'
# add the hydrogens back, this time with the GLH variant in place of GLU
modeller.addHydrogens(self.forcefield, variants=variants)
topology_GLH = modeller.getTopology()
# There should be extra hydrogens on the GLU residues. Assert that they exist,
# then we delete them and validate that the topology matches what we started with.
index_list_GLH = [85, 192, 387, 731, 992, 1018, 1718, 2042]
......@@ -711,23 +711,23 @@ class TestModeller(unittest.TestCase):
toDelete2.append(atoms[index])
modeller.delete(toDelete2)
topology_GLU = modeller.getTopology()
validate_equivalence(self, topology_GLU, topology_start)
def test_addHydrogensLYN(self):
""" Test of addHydrogens() in which we force LYN to be a variant using the variants parameter. """
# use the T4-lysozyme-L99A pdb file
topology_start = self.topology_start2
positions = self.positions2
# build the Modeller
modeller = Modeller(topology_start, positions)
# remove hydrogens from topology
toDelete = [atom for atom in topology_start.atoms() if atom.element==Element.getBySymbol('H')]
modeller.delete(toDelete)
# Create a variants list to force the one histidine to be of the right variation.
residues = [residue for residue in topology_start.residues()]
variants = [None]*len(residues)
......@@ -735,25 +735,25 @@ class TestModeller(unittest.TestCase):
# By setting variants[30] to 'HIE', we force the hydrogen onto the epsilon nitrogen, so
# that it will match the topology in topology_start.
variants[30] = 'HIE'
# Here we add the residues in which LYS is present to the variant list. The final
# LYS residue, 161, is not on the list because Amber force fields do not have an
# entry for a terminal LYN residue.
residue_list_LYS = [15,18,34,42,47,59,64,82,84,123,134,146]
for residue_index in residue_list_LYS:
variants[residue_index] = 'LYN'
# add the hydrogens back, using the variants list we just built
modeller.addHydrogens(self.forcefield, variants=variants)
topology_LYN = modeller.getTopology()
# create a second modeller that we will attempt to match with topology_LYN
modeller2 = Modeller(topology_start, positions)
# There should be extra hydrogens on the LYS residues. Assert that they exist
# on modeller2, then delete them and validate that the topologies match.
# These are the indices of the hydrogens to delete from LYN to make LYS.
index_list_LYN = [281,343,590,701,780,960,1034,1319,1360,1959,2135,2344]
atoms = [atom for atom in topology_start.atoms()]
......@@ -763,23 +763,23 @@ class TestModeller(unittest.TestCase):
toDelete2.append(atoms[index])
modeller2.delete(toDelete2)
topology_after = modeller2.getTopology()
validate_equivalence(self, topology_LYN, topology_after)
def test_addHydrogenspH4(self):
""" Test of addHydrogens() with pH=4. """
# use the T4-lysozyme-L99A pdb file
topology_start = self.topology_start2
positions = self.positions2
# build the Modeller
modeller = Modeller(topology_start, positions)
# remove hydrogens from the topology
toDelete = [atom for atom in topology_start.atoms() if atom.element==Element.getBySymbol('H')]
modeller.delete(toDelete)
# Create a variants list to force the one histidine to be of the right variation.
residues = [residue for residue in topology_start.residues()]
variants = [None]*len(residues)
......@@ -787,12 +787,12 @@ class TestModeller(unittest.TestCase):
# By setting variants[30] to 'HIE', we force the hydrogen onto the epsilon nitrogen, so
# that it will match the topology in topology_start.
variants[30] = 'HIE'
# add the hydrogens back, this time at a lower pH
modeller.addHydrogens(self.forcefield, variants=variants, pH=4.0)
topology_ASH_GLH = modeller.getTopology()
# There should be extra hydrogens on the ASP and GLU residues. Assert that they exist,
# then we delete them and validate that the topology matches what we started with.
index_list_ASH = [177, 359, 765, 980, 1127, 1156, 1436, 1479, 2035, 2564]
......@@ -807,34 +807,34 @@ class TestModeller(unittest.TestCase):
toDelete2.append(atoms[index])
modeller.delete(toDelete2)
topology_ASP_GLU = modeller.getTopology()
validate_equivalence(self, topology_ASP_GLU, topology_start)
def test_addHydrogenspH9(self):
""" Test of addHydrogens() with pH=9. """
# use the metallothionein pdb file
topology_start = self.topology_start3
positions = self.positions3
# build the Modeller
modeller = Modeller(topology_start, positions)
# remove hydrogens from topology
toDelete = [atom for atom in topology_start.atoms() if atom.element==Element.getBySymbol('H')]
modeller.delete(toDelete)
# add hydrogens with pH=9, so that the variation CYX will be chosen
modeller.addHydrogens(self.forcefield, pH=9.0)
topology_CYX = modeller.getTopology()
# create a second modeller that we will attempt to match with topology_CYX
modeller2 = Modeller(topology_start, positions)
topology2 = modeller2.getTopology()
# There should be extra hydrogens on the CYS residues. Assert that they exist
# on modeller2, then delete them and validate that the topologies match.
# These are the indices of the hydrogens to delete from CYS to make CYX.
index_list_CYS = [31, 49, 110, 135, 171, 193, 229]
atoms = [atom for atom in topology2.atoms()]
......@@ -844,23 +844,23 @@ class TestModeller(unittest.TestCase):
toDelete2.append(atoms[index])
modeller2.delete(toDelete2)
topology_after = modeller2.getTopology()
validate_equivalence(self, topology_CYX, topology_after)
def test_addHydrogenspH11(self):
""" Test of addHydrogens() with pH=11. """
# use the T4-lysozyme-L99A pdb file
topology_start = self.topology_start2
positions = self.positions2
# build the Modeller
modeller = Modeller(topology_start, positions)
# remove hydrogens from topology
toDelete = [atom for atom in topology_start.atoms() if atom.element==Element.getBySymbol('H')]
modeller.delete(toDelete)
# Create a variants list to force the one histidine to be of the right variation.
residues = [residue for residue in topology_start.residues()]
variants = [None]*len(residues)
......@@ -868,18 +868,18 @@ class TestModeller(unittest.TestCase):
# By setting variants[30] to 'HIE', we force the hydrogen onto the epsilon nitrogen, so
# that it will match the topology in topology_start.
variants[30] = 'HIE'
# The Amber force fields do not have an entry for terminal LYN residues, so we need to
# force residue 161 to be the LYS variant.
variants[161] = 'LYS'
# add the hydrogens back at pH = 11
modeller.addHydrogens(self.forcefield, variants=variants, pH=11.0)
topology_LYN = modeller.getTopology()
# create a second modeller that we will attempt to match with topology_LYN
modeller2 = Modeller(topology_start, positions)
# There should be extra hydrogens on the LYS residues. Assert that they exist
# on modeller2, then delete them and validate that the topologies match.
index_list_LYN = [281,343,590,701,780,960,1034,1319,1360,1959,2135,2344]
......@@ -888,24 +888,24 @@ class TestModeller(unittest.TestCase):
for index in index_list_LYN:
self.assertTrue(atoms[index].element.symbol=='H')
toDelete2.append(atoms[index])
modeller2.delete(toDelete2)
topology_after = modeller2.getTopology()
validate_equivalence(self, topology_LYN, topology_after)
def test_addExtraParticles(self):
"""Test addExtraParticles()."""
# Create a box of water.
ff1 = ForceField('tip3p.xml')
modeller = Modeller(Topology(), []*nanometers)
modeller.addSolvent(ff1, 'tip3p', boxSize=Vec3(2,2,2)*nanometers)
# Now convert the water to TIP4P.
ff2 = ForceField('tip4pew.xml')
modeller.addExtraParticles(ff2)
for residue in modeller.topology.residues():
......
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