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Commit 94d6275b authored by joaorodrigues's avatar joaorodrigues
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Forgot to undo my test optimization...

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wrappers/python/tests/TestModeller.py
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......@@ -29,1052 +29,1052 @@ class TestModeller(unittest.TestCase):
self.topology_start3 = self.pdb3.topology
self.positions3 = self.pdb3.positions
# def test_deleteWater(self):
# """ Test the deleteWater() method. """
# # build the chain dictionary
# chain_dict = {0:0}
# # 749 water chains are deleted
# chain_delta = -749
# # Build the residue and atom dictionaries for validate_preserved.
# # Also, count the number of deleted residues and atoms.
# residues_preserved = 0
# residue_delta = 0
# residue_dict = {}
# atoms_preserved = 0
# atom_delta = 0
# atom_dict = {}
# for residue in self.topology_start.residues():
# if residue.name!='HOH' and residue.name!='WAT':
# residue_dict[residue.index] = residues_preserved
# residues_preserved += 1
# for atom in residue.atoms():
# atom_dict[atom.index] = atoms_preserved
# atoms_preserved += 1
# else:
# residue_delta -= 1
# for atom in residue.atoms():
# atom_delta -= 1
# modeller = Modeller(self.topology_start, self.positions)
# modeller.deleteWater()
# topology_after = modeller.getTopology()
# validate_preserved(self, self.topology_start, topology_after,
# chain_dict, residue_dict, atom_dict)
# validate_deltas(self, self.topology_start, topology_after,
# chain_delta, residue_delta, atom_delta)
# def test_delete(self):
# """ Test the delete() method. """
# modeller = Modeller(self.topology_start, self.positions)
# topology_before = modeller.getTopology()
# # Create the list of items to be deleted.
# # Start with the first 50 water chains
# chains = [chain for chain in topology_before.chains()]
# toDelete = chains[1:51]
# # Next add water residues 103->152 to the list of items to be deleted
# residues = [residue for residue in topology_before.residues()]
# toDelete.extend(residues[103:153])
# # Finally add water atoms 622->771 to the list of items to be deleted
# atoms = [atom for atom in topology_before.atoms()]
# toDelete.extend(atoms[622:772])
# modeller.delete(toDelete)
# topology_after = modeller.getTopology()
# # build the chain dictionary
# chain_dict = {0:0}
# for i in range(1,51):
# chain_dict[i+50] = i
# for i in range(51,101):
# chain_dict[i+100] = i
# for i in range(101, 600):
# chain_dict[i+150] = i
# # build the residue dictionary
# residue_dict = {}
# for i in range(3):
# residue_dict[i] = i
# for i in range(3,53):
# residue_dict[i+50] = i
# for i in range(53, 103):
# residue_dict[i+100] = i
# for i in range(103, 602):
# residue_dict[i+150] = i
# # build the atom dictionary
# atom_dict = {}
# for i in range(22):
# atom_dict[i] = i
# for i in range(22,172):
# atom_dict[i+150] = i
# for i in range(172,322):
# atom_dict[i+300] = i
# for i in range(322,1819):
# atom_dict[i+450] = i
# validate_preserved(self, topology_before, topology_after, chain_dict, residue_dict, atom_dict)
# chain_delta = -150
# residue_delta = -150
# atom_delta = -450
# validate_deltas(self, topology_before, topology_after, chain_delta, residue_delta, atom_delta)
# def test_add(self):
# """ Test the add() method. """
# # load the methanol-box pdb file
# pdb2 = PDBFile('systems/methanol-box.pdb')
# topology_toAdd = pdb2.topology
# positions_toAdd = pdb2.positions
# modeller = Modeller(self.topology_start, self.positions)
# modeller.deleteWater()
# topology_before = modeller.getTopology()
# modeller.add(topology_toAdd, positions_toAdd)
# topology_after = modeller.getTopology()
# # build the first chain dictionary for the first call of validate_preserved()
# chain_counter = 0
# chain_dict = {}
# for chain in topology_before.chains():
# chain_dict[chain.index] = chain_counter
# chain_counter += 1
# # build the residue and atom dictionaries for the first call of validate_preserved()
# residue_counter = 0
# residue_dict = {}
# atom_counter = 0
# atom_dict = {}
# for residue in topology_before.residues():
# residue_dict[residue.index] = residue_counter
# residue_counter += 1
# for atom in residue.atoms():
# atom_dict[atom.index] = atom_counter
# atom_counter += 1
# # Validate that the items from the before topology are preserved after addition of items.
# validate_preserved(self, topology_before, topology_after, chain_dict, residue_dict, atom_dict)
# # Next, we build another set of dictionaries to validate that the items added are
# # preserved. Also, we calculate the number of chains, residues, and atoms added.
# # build the chain dictionary
# chain_delta = 0
# chain_dict = {}
# for chain in topology_toAdd.chains():
# chain_dict[chain.index] = chain_counter
# chain_counter += 1
# chain_delta += 1
# # build the residue and atom dictionaries for the second call of validate_preserved
# residue_delta = 0
# residue_dict = {}
# atom_delta = 0
# atom_dict = {}
# for residue in topology_toAdd.residues():
# residue_dict[residue.index] = residue_counter
# residue_counter += 1
# residue_delta += 1
# for atom in residue.atoms():
# atom_dict[atom.index] = atom_counter
# atom_counter += 1
# atom_delta += 1
# # validate that the items in the added topology are preserved
# validate_preserved(self, topology_toAdd, topology_after, chain_dict, residue_dict, atom_dict)
# # validate that the final topology has the correct number of items
# validate_deltas(self, topology_before, topology_after, chain_delta, residue_delta, atom_delta)
# def test_convertWater(self):
# """ Test the convertWater() method. """
# for model in ['tip3p', 'spce', 'tip4pew', 'tip5p']:
# if model == 'tip5p':
# firstmodel = 'tip4pew'
# else:
# firstmodel = 'tip5p'
# modeller = Modeller(self.topology_start, self.positions)
# modeller.convertWater(model=firstmodel)
# modeller.convertWater(model=model)
# topology_after = modeller.getTopology()
# for residue in topology_after.residues():
# if residue.name == "HOH":
# oatom = [atom for atom in residue.atoms() if atom.element == element.oxygen]
# hatoms = [atom for atom in residue.atoms() if atom.element == element.hydrogen]
# matoms = [atom for atom in residue.atoms() if atom.name == 'M']
# m1atoms = [atom for atom in residue.atoms() if atom.name == 'M1']
# m2atoms = [atom for atom in residue.atoms() if atom.name == 'M2']
# self.assertTrue(len(oatom)==1 and len(hatoms)==2)
# if model=='tip3p' or model=='spce':
# self.assertTrue(len(matoms)==0 and len(m1atoms)==0 and len(m2atoms)==0)
# elif model=='tip4pew':
# self.assertTrue(len(matoms)==1 and len(m1atoms)==0 and len(m2atoms)==0)
# elif model=='tip5p':
# self.assertTrue(len(matoms)==0 and len(m1atoms)==1 and len(m2atoms)==1)
# # build the chain dictionary for validate_preserved
# chain_counter = 0
# chain_dict = {}
# chain_delta = 0
# for chain in self.topology_start.chains():
# chain_dict[chain.index] = chain_counter
# chain_counter += 1
# # build the residue and atom dictionaries for validate_preserved
# residue_counter = 0
# residue_dict = {}
# residue_delta = 0
# atom_counter = 0
# atom_dict = {}
# atom_delta = 0
# for residue in self.topology_start.residues():
# residue_dict[residue.index] = residue_counter
# residue_counter += 1
# for atom in residue.atoms():
# atom_dict[atom.index] = atom_counter
# atom_counter += 1
# if residue.name == 'HOH' and model == 'tip4pew':
# atom_counter += 1
# atom_delta += 1
# if residue.name == 'HOH' and model == 'tip5p':
# atom_counter += 2
# atom_delta += 2
# validate_preserved(self, self.topology_start, topology_after,
# chain_dict, residue_dict, atom_dict)
# validate_deltas(self, self.topology_start, topology_after,
# chain_delta, residue_delta, atom_delta)
# def test_addSolventWaterModels(self):
# """ Test all addSolvent() method with all possible water models. """
# topology_start = self.pdb.topology
# topology_start.setUnitCellDimensions(Vec3(3.5, 3.5, 3.5)*nanometers)
# for model in ['tip3p', 'spce', 'tip4pew', 'tip5p']:
# forcefield = ForceField('amber10.xml', model + '.xml')
# modeller = Modeller(topology_start, self.positions)
# # delete water to get the "before" topology
# modeller.deleteWater()
# topology_before = modeller.getTopology()
# # add the solvent to get the "after" topology
# modeller.addSolvent(forcefield, model=model)
# topology_after = modeller.getTopology()
# # First, check that everything that was there before has been preserved.
# # build the chain dictionary for validate_preserved
# chain_counter = 0
# chain_dict = {0:0}
# for chain in topology_before.chains():
# chain_dict[chain.index] = chain_counter
# chain_counter += 1
# # build the residue and atom dictionaries for validate_preserved
# residue_counter = 0
# residue_dict = {}
# atom_counter = 0
# atom_dict = {}
# for residue in topology_before.residues():
# residue_dict[residue.index] = residue_counter
# residue_counter += 1
# for atom in residue.atoms():
# atom_dict[atom.index] = atom_counter
# atom_counter += 1
# # validate that the items in the before topology remain after solvent is added
# validate_preserved(self, topology_before, topology_after, chain_dict, residue_dict, atom_dict)
# # Make sure water that was added was the correct model
# for residue in topology_after.residues():
# if residue.name == 'HOH':
# oatom = [atom for atom in residue.atoms() if atom.element == element.oxygen]
# hatoms = [atom for atom in residue.atoms() if atom.element == element.hydrogen]
# matoms = [atom for atom in residue.atoms() if atom.name == 'M']
# m1atoms = [atom for atom in residue.atoms() if atom.name == 'M1']
# m2atoms = [atom for atom in residue.atoms() if atom.name == 'M2']
# self.assertTrue(len(oatom)==1 and len(hatoms)==2)
# if model=='tip3p' or model=='spce':
# self.assertTrue(len(matoms)==0 and len(m1atoms)==0 and len(m2atoms)==0)
# elif model=='tip4pew':
# self.assertTrue(len(matoms)==1 and len(m1atoms)==0 and len(m2atoms)==0)
# elif model=='tip5p':
# self.assertTrue(len(matoms)==0 and len(m1atoms)==1 and len(m2atoms)==1)
# def test_addSolventPeriodicBox(self):
# """ Test the addSolvent() method; test that the five ways of passing in the periodic box all work. """
# # 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.getPeriodicBoxVectors()
# 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 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.getPeriodicBoxVectors()
# 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 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.getPeriodicBoxVectors()
# 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))
# # Fifth way: specify a number of molecules to add instead of a box size
# topology_start = self.pdb.topology
# modeller = Modeller(topology_start, self.positions)
# modeller.deleteWater()
# numInitial = len(list(modeller.topology.residues()))
# modeller.addSolvent(self.forcefield, numAdded=1000)
# self.assertEqual(numInitial+1000, len(list(modeller.topology.residues())))
# 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
# for residue in topology_after.residues():
# if residue.name=='HOH':
# water_count += 1
# elif residue.name=='NA':
# 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+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. """
# 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()
# # add 5 Cl- ions to the original topology
# topology_toAdd = Topology()
# newChain = topology_toAdd.addChain()
# for i in range(5):
# topology_toAdd.addResidue('CL', newChain)
# residues = [residue for residue in topology_toAdd.residues()]
# for i in range(5):
# topology_toAdd.addAtom('Cl',Element.getBySymbol('Cl'), 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
# modeller.add(topology_toAdd, positions_toAdd)
# modeller.addSolvent(self.forcefield, ionicStrength=1.0*molar, neutralize=neutralize)
# topology_after = modeller.getTopology()
# water_count = 0
# sodium_count = 0
# chlorine_count = 0
# for residue in topology_after.residues():
# if residue.name=='HOH':
# water_count += 1
# elif residue.name=='NA':
# 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_chlorine = math.floor((total_water_ions-10)*expected_ion_fraction+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. """
# 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()
# # add 5 Na+ ions to the original topology
# topology_toAdd = Topology()
# newChain = topology_toAdd.addChain()
# for i in range(5):
# topology_toAdd.addResidue('NA', newChain)
# residues = [residue for residue in topology_toAdd.residues()]
# for i in range(5):
# 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, neutralize=neutralize)
# topology_after = modeller.getTopology()
# water_count = 0
# sodium_count = 0
# chlorine_count = 0
# for residue in topology_after.residues():
# if residue.name=='HOH':
# water_count += 1
# elif residue.name=='NA':
# 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_sodium = math.floor((total_water_ions-10)*expected_ion_fraction+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. """
# 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+']:
# ionName = positiveIon[:-1].upper()
# 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
# for residue in topology_after.residues():
# if residue.name=='HOH':
# water_count += 1
# elif residue.name==ionName:
# 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+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
# for residue in topology_after.residues():
# if residue.name=='HOH':
# water_count += 1
# elif residue.name=='NA':
# sodium_count += 1
# elif residue.name==ionName:
# negative_ion_count += 1
# total_added = water_count+sodium_count+negative_ion_count
# self.assertEqual(total_added, 1364)
# expected_ions = math.floor(total_added*expected_ion_fraction+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. """
# # build the Modeller
# 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)
# # For this protein, when you add hydrogens, the hydrogen is added to the delta nitrogen.
# # 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. """
# # build the Modeller
# 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)
# # For this protein, when you add hydrogens, the hydrogen is added to the delta nitrogen.
# # 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]
# atoms = [atom for atom in topology_ASH.atoms()]
# toDelete2 = []
# for index in index_list_ASH:
# self.assertTrue(atoms[index].element.symbol=='H')
# 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()]
# toDelete2 = []
# for index in index_list_CYS:
# self.assertTrue(atoms[index].element.symbol=='H')
# 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)
# # For this protein, when you add hydrogens, the hydrogen is added to the delta nitrogen.
# # 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]
# atoms = [atom for atom in topology_GLH.atoms()]
# toDelete2 = []
# for index in index_list_GLH:
# self.assertTrue(atoms[index].element.symbol=='H')
# 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)
# # For this protein, when you add hydrogens, the hydrogen is added to the delta nitrogen.
# # 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()]
# toDelete2 = []
# 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_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)
# # For this protein, when you add hydrogens, the hydrogen is added to the delta nitrogen.
# # 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]
# index_list_GLH = [85, 193, 389, 733, 996, 1022, 1726, 2051]
# atoms = [atom for atom in topology_ASH_GLH.atoms()]
# toDelete2 = []
# for index in index_list_ASH:
# self.assertTrue(atoms[index].element.symbol=='H')
# toDelete2.append(atoms[index])
# for index in index_list_GLH:
# self.assertTrue(atoms[index].element.symbol=='H')
# 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()]
# toDelete2 = []
# for index in index_list_CYS:
# self.assertTrue(atoms[index].element.symbol=='H')
# 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)
# # For this protein, when you add hydrogens, the hydrogen is added to the delta nitrogen.
# # 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]
# atoms = [atom for atom in topology_start.atoms()]
# toDelete2 = []
# 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_removeExtraHydrogens(self):
# """Test that addHydrogens() can remove hydrogens that shouldn't be there. """
# topology_start = self.topology_start3
# positions = self.positions3
# modeller = Modeller(topology_start, positions)
# # Add hydrogens, forcing residue 1 to be ASH.
# variants = [None]*25
# variants[1] = 'ASH'
# modeller.addHydrogens(self.forcefield, variants=variants)
# residue = list(modeller.topology.residues())[1]
# self.assertTrue(any(a.name == 'HD2' for a in residue.atoms()))
# # Now force it to be ASP and see if HD2 gets removed.
# variants[1] = 'ASP'
# modeller.addHydrogens(self.forcefield, variants=variants)
# residue = list(modeller.topology.residues())[1]
# self.assertFalse(any(a.name == 'HD2' for a in residue.atoms()))
# 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():
# atoms = list(residue.atoms())
# self.assertEqual(4, len(atoms))
# ep = [atom for atom in atoms if atom.element is None]
# 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 test_deleteWater(self):
""" Test the deleteWater() method. """
# build the chain dictionary
chain_dict = {0:0}
# 749 water chains are deleted
chain_delta = -749
# Build the residue and atom dictionaries for validate_preserved.
# Also, count the number of deleted residues and atoms.
residues_preserved = 0
residue_delta = 0
residue_dict = {}
atoms_preserved = 0
atom_delta = 0
atom_dict = {}
for residue in self.topology_start.residues():
if residue.name!='HOH' and residue.name!='WAT':
residue_dict[residue.index] = residues_preserved
residues_preserved += 1
for atom in residue.atoms():
atom_dict[atom.index] = atoms_preserved
atoms_preserved += 1
else:
residue_delta -= 1
for atom in residue.atoms():
atom_delta -= 1
modeller = Modeller(self.topology_start, self.positions)
modeller.deleteWater()
topology_after = modeller.getTopology()
validate_preserved(self, self.topology_start, topology_after,
chain_dict, residue_dict, atom_dict)
validate_deltas(self, self.topology_start, topology_after,
chain_delta, residue_delta, atom_delta)
def test_delete(self):
""" Test the delete() method. """
modeller = Modeller(self.topology_start, self.positions)
topology_before = modeller.getTopology()
# Create the list of items to be deleted.
# Start with the first 50 water chains
chains = [chain for chain in topology_before.chains()]
toDelete = chains[1:51]
# Next add water residues 103->152 to the list of items to be deleted
residues = [residue for residue in topology_before.residues()]
toDelete.extend(residues[103:153])
# Finally add water atoms 622->771 to the list of items to be deleted
atoms = [atom for atom in topology_before.atoms()]
toDelete.extend(atoms[622:772])
modeller.delete(toDelete)
topology_after = modeller.getTopology()
# build the chain dictionary
chain_dict = {0:0}
for i in range(1,51):
chain_dict[i+50] = i
for i in range(51,101):
chain_dict[i+100] = i
for i in range(101, 600):
chain_dict[i+150] = i
# build the residue dictionary
residue_dict = {}
for i in range(3):
residue_dict[i] = i
for i in range(3,53):
residue_dict[i+50] = i
for i in range(53, 103):
residue_dict[i+100] = i
for i in range(103, 602):
residue_dict[i+150] = i
# build the atom dictionary
atom_dict = {}
for i in range(22):
atom_dict[i] = i
for i in range(22,172):
atom_dict[i+150] = i
for i in range(172,322):
atom_dict[i+300] = i
for i in range(322,1819):
atom_dict[i+450] = i
validate_preserved(self, topology_before, topology_after, chain_dict, residue_dict, atom_dict)
chain_delta = -150
residue_delta = -150
atom_delta = -450
validate_deltas(self, topology_before, topology_after, chain_delta, residue_delta, atom_delta)
def test_add(self):
""" Test the add() method. """
# load the methanol-box pdb file
pdb2 = PDBFile('systems/methanol-box.pdb')
topology_toAdd = pdb2.topology
positions_toAdd = pdb2.positions
modeller = Modeller(self.topology_start, self.positions)
modeller.deleteWater()
topology_before = modeller.getTopology()
modeller.add(topology_toAdd, positions_toAdd)
topology_after = modeller.getTopology()
# build the first chain dictionary for the first call of validate_preserved()
chain_counter = 0
chain_dict = {}
for chain in topology_before.chains():
chain_dict[chain.index] = chain_counter
chain_counter += 1
# build the residue and atom dictionaries for the first call of validate_preserved()
residue_counter = 0
residue_dict = {}
atom_counter = 0
atom_dict = {}
for residue in topology_before.residues():
residue_dict[residue.index] = residue_counter
residue_counter += 1
for atom in residue.atoms():
atom_dict[atom.index] = atom_counter
atom_counter += 1
# Validate that the items from the before topology are preserved after addition of items.
validate_preserved(self, topology_before, topology_after, chain_dict, residue_dict, atom_dict)
# Next, we build another set of dictionaries to validate that the items added are
# preserved. Also, we calculate the number of chains, residues, and atoms added.
# build the chain dictionary
chain_delta = 0
chain_dict = {}
for chain in topology_toAdd.chains():
chain_dict[chain.index] = chain_counter
chain_counter += 1
chain_delta += 1
# build the residue and atom dictionaries for the second call of validate_preserved
residue_delta = 0
residue_dict = {}
atom_delta = 0
atom_dict = {}
for residue in topology_toAdd.residues():
residue_dict[residue.index] = residue_counter
residue_counter += 1
residue_delta += 1
for atom in residue.atoms():
atom_dict[atom.index] = atom_counter
atom_counter += 1
atom_delta += 1
# validate that the items in the added topology are preserved
validate_preserved(self, topology_toAdd, topology_after, chain_dict, residue_dict, atom_dict)
# validate that the final topology has the correct number of items
validate_deltas(self, topology_before, topology_after, chain_delta, residue_delta, atom_delta)
def test_convertWater(self):
""" Test the convertWater() method. """
for model in ['tip3p', 'spce', 'tip4pew', 'tip5p']:
if model == 'tip5p':
firstmodel = 'tip4pew'
else:
firstmodel = 'tip5p'
modeller = Modeller(self.topology_start, self.positions)
modeller.convertWater(model=firstmodel)
modeller.convertWater(model=model)
topology_after = modeller.getTopology()
for residue in topology_after.residues():
if residue.name == "HOH":
oatom = [atom for atom in residue.atoms() if atom.element == element.oxygen]
hatoms = [atom for atom in residue.atoms() if atom.element == element.hydrogen]
matoms = [atom for atom in residue.atoms() if atom.name == 'M']
m1atoms = [atom for atom in residue.atoms() if atom.name == 'M1']
m2atoms = [atom for atom in residue.atoms() if atom.name == 'M2']
self.assertTrue(len(oatom)==1 and len(hatoms)==2)
if model=='tip3p' or model=='spce':
self.assertTrue(len(matoms)==0 and len(m1atoms)==0 and len(m2atoms)==0)
elif model=='tip4pew':
self.assertTrue(len(matoms)==1 and len(m1atoms)==0 and len(m2atoms)==0)
elif model=='tip5p':
self.assertTrue(len(matoms)==0 and len(m1atoms)==1 and len(m2atoms)==1)
# build the chain dictionary for validate_preserved
chain_counter = 0
chain_dict = {}
chain_delta = 0
for chain in self.topology_start.chains():
chain_dict[chain.index] = chain_counter
chain_counter += 1
# build the residue and atom dictionaries for validate_preserved
residue_counter = 0
residue_dict = {}
residue_delta = 0
atom_counter = 0
atom_dict = {}
atom_delta = 0
for residue in self.topology_start.residues():
residue_dict[residue.index] = residue_counter
residue_counter += 1
for atom in residue.atoms():
atom_dict[atom.index] = atom_counter
atom_counter += 1
if residue.name == 'HOH' and model == 'tip4pew':
atom_counter += 1
atom_delta += 1
if residue.name == 'HOH' and model == 'tip5p':
atom_counter += 2
atom_delta += 2
validate_preserved(self, self.topology_start, topology_after,
chain_dict, residue_dict, atom_dict)
validate_deltas(self, self.topology_start, topology_after,
chain_delta, residue_delta, atom_delta)
def test_addSolventWaterModels(self):
""" Test all addSolvent() method with all possible water models. """
topology_start = self.pdb.topology
topology_start.setUnitCellDimensions(Vec3(3.5, 3.5, 3.5)*nanometers)
for model in ['tip3p', 'spce', 'tip4pew', 'tip5p']:
forcefield = ForceField('amber10.xml', model + '.xml')
modeller = Modeller(topology_start, self.positions)
# delete water to get the "before" topology
modeller.deleteWater()
topology_before = modeller.getTopology()
# add the solvent to get the "after" topology
modeller.addSolvent(forcefield, model=model)
topology_after = modeller.getTopology()
# First, check that everything that was there before has been preserved.
# build the chain dictionary for validate_preserved
chain_counter = 0
chain_dict = {0:0}
for chain in topology_before.chains():
chain_dict[chain.index] = chain_counter
chain_counter += 1
# build the residue and atom dictionaries for validate_preserved
residue_counter = 0
residue_dict = {}
atom_counter = 0
atom_dict = {}
for residue in topology_before.residues():
residue_dict[residue.index] = residue_counter
residue_counter += 1
for atom in residue.atoms():
atom_dict[atom.index] = atom_counter
atom_counter += 1
# validate that the items in the before topology remain after solvent is added
validate_preserved(self, topology_before, topology_after, chain_dict, residue_dict, atom_dict)
# Make sure water that was added was the correct model
for residue in topology_after.residues():
if residue.name == 'HOH':
oatom = [atom for atom in residue.atoms() if atom.element == element.oxygen]
hatoms = [atom for atom in residue.atoms() if atom.element == element.hydrogen]
matoms = [atom for atom in residue.atoms() if atom.name == 'M']
m1atoms = [atom for atom in residue.atoms() if atom.name == 'M1']
m2atoms = [atom for atom in residue.atoms() if atom.name == 'M2']
self.assertTrue(len(oatom)==1 and len(hatoms)==2)
if model=='tip3p' or model=='spce':
self.assertTrue(len(matoms)==0 and len(m1atoms)==0 and len(m2atoms)==0)
elif model=='tip4pew':
self.assertTrue(len(matoms)==1 and len(m1atoms)==0 and len(m2atoms)==0)
elif model=='tip5p':
self.assertTrue(len(matoms)==0 and len(m1atoms)==1 and len(m2atoms)==1)
def test_addSolventPeriodicBox(self):
""" Test the addSolvent() method; test that the five ways of passing in the periodic box all work. """
# 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.getPeriodicBoxVectors()
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 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.getPeriodicBoxVectors()
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 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.getPeriodicBoxVectors()
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))
# Fifth way: specify a number of molecules to add instead of a box size
topology_start = self.pdb.topology
modeller = Modeller(topology_start, self.positions)
modeller.deleteWater()
numInitial = len(list(modeller.topology.residues()))
modeller.addSolvent(self.forcefield, numAdded=1000)
self.assertEqual(numInitial+1000, len(list(modeller.topology.residues())))
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
for residue in topology_after.residues():
if residue.name=='HOH':
water_count += 1
elif residue.name=='NA':
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+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. """
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()
# add 5 Cl- ions to the original topology
topology_toAdd = Topology()
newChain = topology_toAdd.addChain()
for i in range(5):
topology_toAdd.addResidue('CL', newChain)
residues = [residue for residue in topology_toAdd.residues()]
for i in range(5):
topology_toAdd.addAtom('Cl',Element.getBySymbol('Cl'), 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
modeller.add(topology_toAdd, positions_toAdd)
modeller.addSolvent(self.forcefield, ionicStrength=1.0*molar, neutralize=neutralize)
topology_after = modeller.getTopology()
water_count = 0
sodium_count = 0
chlorine_count = 0
for residue in topology_after.residues():
if residue.name=='HOH':
water_count += 1
elif residue.name=='NA':
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_chlorine = math.floor((total_water_ions-10)*expected_ion_fraction+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. """
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()
# add 5 Na+ ions to the original topology
topology_toAdd = Topology()
newChain = topology_toAdd.addChain()
for i in range(5):
topology_toAdd.addResidue('NA', newChain)
residues = [residue for residue in topology_toAdd.residues()]
for i in range(5):
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, neutralize=neutralize)
topology_after = modeller.getTopology()
water_count = 0
sodium_count = 0
chlorine_count = 0
for residue in topology_after.residues():
if residue.name=='HOH':
water_count += 1
elif residue.name=='NA':
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_sodium = math.floor((total_water_ions-10)*expected_ion_fraction+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. """
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+']:
ionName = positiveIon[:-1].upper()
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
for residue in topology_after.residues():
if residue.name=='HOH':
water_count += 1
elif residue.name==ionName:
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+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
for residue in topology_after.residues():
if residue.name=='HOH':
water_count += 1
elif residue.name=='NA':
sodium_count += 1
elif residue.name==ionName:
negative_ion_count += 1
total_added = water_count+sodium_count+negative_ion_count
self.assertEqual(total_added, 1364)
expected_ions = math.floor(total_added*expected_ion_fraction+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. """
# build the Modeller
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)
# For this protein, when you add hydrogens, the hydrogen is added to the delta nitrogen.
# 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. """
# build the Modeller
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)
# For this protein, when you add hydrogens, the hydrogen is added to the delta nitrogen.
# 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]
atoms = [atom for atom in topology_ASH.atoms()]
toDelete2 = []
for index in index_list_ASH:
self.assertTrue(atoms[index].element.symbol=='H')
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()]
toDelete2 = []
for index in index_list_CYS:
self.assertTrue(atoms[index].element.symbol=='H')
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)
# For this protein, when you add hydrogens, the hydrogen is added to the delta nitrogen.
# 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]
atoms = [atom for atom in topology_GLH.atoms()]
toDelete2 = []
for index in index_list_GLH:
self.assertTrue(atoms[index].element.symbol=='H')
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)
# For this protein, when you add hydrogens, the hydrogen is added to the delta nitrogen.
# 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()]
toDelete2 = []
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_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)
# For this protein, when you add hydrogens, the hydrogen is added to the delta nitrogen.
# 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]
index_list_GLH = [85, 193, 389, 733, 996, 1022, 1726, 2051]
atoms = [atom for atom in topology_ASH_GLH.atoms()]
toDelete2 = []
for index in index_list_ASH:
self.assertTrue(atoms[index].element.symbol=='H')
toDelete2.append(atoms[index])
for index in index_list_GLH:
self.assertTrue(atoms[index].element.symbol=='H')
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()]
toDelete2 = []
for index in index_list_CYS:
self.assertTrue(atoms[index].element.symbol=='H')
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)
# For this protein, when you add hydrogens, the hydrogen is added to the delta nitrogen.
# 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]
atoms = [atom for atom in topology_start.atoms()]
toDelete2 = []
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_removeExtraHydrogens(self):
"""Test that addHydrogens() can remove hydrogens that shouldn't be there. """
topology_start = self.topology_start3
positions = self.positions3
modeller = Modeller(topology_start, positions)
# Add hydrogens, forcing residue 1 to be ASH.
variants = [None]*25
variants[1] = 'ASH'
modeller.addHydrogens(self.forcefield, variants=variants)
residue = list(modeller.topology.residues())[1]
self.assertTrue(any(a.name == 'HD2' for a in residue.atoms()))
# Now force it to be ASP and see if HD2 gets removed.
variants[1] = 'ASP'
modeller.addHydrogens(self.forcefield, variants=variants)
residue = list(modeller.topology.residues())[1]
self.assertFalse(any(a.name == 'HD2' for a in residue.atoms()))
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():
atoms = list(residue.atoms())
self.assertEqual(4, len(atoms))
ep = [atom for atom in atoms if atom.element is None]
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 test_addMembrane(self):
......
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