def testLoadStruct(self):
""" Test load_rosetta against read_PDB"""
init()
pose = pose_from_sequence(3*'A')
struct = load_rosetta(pose)
pdb = read_PDB(get_fn('ala_ala_ala.pdb'))
self.assertEqual(len(struct.atoms), len(pdb.atoms))
self.assertEqual(len(struct.residues), len(pdb.residues))
def test_loaded_topology(self):
""" Test load_rosetta against OpenMM topology"""
init()
pose = pose_from_sequence(3 * 'A')
struct = load_rosetta(pose)
pdb = PDBFile(get_fn('ala_ala_ala.pdb'))
self.assertEqual(len(list(struct.topology.atoms())),
len(list(pdb.topology.atoms())))
self.assertEqual(len(list(struct.topology.bonds())),
len(list(pdb.topology.bonds())))
self.assertEqual(len(list(struct.topology.residues())),
len(list(pdb.topology.residues())))
def test_loaded_positions(self):
""" Test that positions were properly loaded"""
init()
seq = 3 * 'A'
pose = pose_from_sequence(seq)
struct = load_rosetta(pose)
posexyz = list(
chain(*[[tuple(atom.xyz()) for atom in res.atoms()] for res in
[pose.residue(idx) for idx in range(1,
len(seq) + 1)]]))
structxyz = [(atom.xx, atom.xy, atom.xz) for atom in struct.atoms]
self.assertEqual(posexyz, structxyz)
def testLoadedTopology(self):
""" Test load_rosetta against OpenMM topology"""
init()
pose = pose_from_sequence(3*'A')
struct = load_rosetta(pose)
pdb = PDBFile(get_fn('ala_ala_ala.pdb'))
self.assertEqual(_unpackLen(struct.topology.atoms()),
_unpackLen(pdb.topology.atoms()))
self.assertEqual(_unpackLen(struct.topology.bonds()),
_unpackLen(pdb.topology.bonds()))
self.assertEqual(_unpackLen(struct.topology.residues()),
_unpackLen(pdb.topology.residues()))
def testLoadedPositions(self):
""" Test that positions were properly loaded"""
init()
seq = 3*'A'
pose = pose_from_sequence(seq)
struct = load_rosetta(pose)
posexyz = list(
chain(*[[tuple(atom.xyz()) for atom in res.atoms()]
for res in [pose.residue(idx)
for idx in range(1, len(seq)+1)]]))
structxyz = [(atom.xx, atom.xy, atom.xz) for atom in struct.atoms]
self.assertEqual(posexyz, structxyz)
# Initialize PyRosetta
init()
# Create Ala12
print('Creating Ala12...')
seq = 12*'A'
pose = pose_from_sequence(seq)
# Mutate residue 5 to K
print('Mutating Fifth Ala to Lys...')
mutant = mutate_residue(pose, 5, 'K')
# Load mutant into ParmEd
print('Loading into ParmEd...')
struct = load_rosetta(mutant)
# Load AMBER-99SBildn and TIP3P parameters
print('Loading AMBER parameters...')
ff = ForceField('amber99sbildn.xml', 'tip3p.xml')
# Solvate Structure
print('Solvating...')
mod = Modeller(struct.topology, struct.positions)
mod.addSolvent(ff, model='tip3p', boxSize=Vec3(4, 4, 4)*nanometers,
positiveIon='Na+', negativeIon='Cl-',
ionicStrength=0.1*molar)
# Create OpenMM System
print('Creating OpenMM System...')
system = ff.createSystem(mod.topology, nonbondedMethod=PME,
