def test_cleanup(urea, water):
mixture = mdapackmol.packmol([
mdapackmol.PackmolStructure(
water,
number=2,
instructions=['inside box 0. 0. 0. 40. 40. 40.'],
),
mdapackmol.PackmolStructure(
urea,
number=2,
instructions=['inside box 0. 0. 0. 40. 40. 40.'],
),
])
assert not os.path.exists(mdapackmol.mdapackmol.PACKMOL_INP)
assert not os.path.exists('output.pdb')
def mixture(in_tmpdir, water, urea):
# PS(ag, number, instructions)
mixture = mdapackmol.packmol([
mdapackmol.PackmolStructure(
water,
number=1000,
instructions=['inside box 0. 0. 0. 40. 40. 40.'],
),
mdapackmol.PackmolStructure(
urea,
number=400,
instructions=['inside box 0. 0. 0. 40. 40. 40.'],
),
])
return mixture
def test_bonds(urea, water):
urea.atoms.guess_bonds()
water.atoms.guess_bonds()
mixture = mdapackmol.packmol([
mdapackmol.PackmolStructure(
water,
number=50,
instructions=['inside box 0. 0. 0. 40. 40. 40.'],
),
mdapackmol.PackmolStructure(
urea,
number=50,
instructions=['inside box 0. 0. 0. 40. 40. 40.'],
),
])
assert hasattr(mixture, 'bonds')
assert len(mixture.bonds) == len(water.bonds) * 50 + len(urea.bonds) * 50
def set_positions(self, simulation, *args):
import MDAnalysis as mda
import mdapackmol
# Get topology options
topology_options = args[0]
# Create default instructions
box_vectors = simulation.context.getState().getPeriodicBoxVectors()
a = box_vectors[0][0].value_in_unit(angstrom)
b = box_vectors[1][1].value_in_unit(angstrom)
c = box_vectors[2][2].value_in_unit(angstrom)
default_instructions = ["inside box 0. 0. 0. {:.1f} {:.1f} {:.1f}".format(a, b, c)]
# Create input for packmol
mdapackmol_input = []
for chain_options in topology_options.chains:
instructions = chain_options.instructions
if instructions is None:
instructions = default_instructions
chain_filepath = "data/{}.pdb".format(chain_options.sequence_str)
if topology_options.forceField_str == 'OPLS-AA':
chain_filepath = "data/{}_aa.pdb".format(chain_options.sequence_str)
molecule = mda.Universe(
os.path.join(os.path.dirname(__file__), chain_filepath)
)
packmol_structure = mdapackmol.PackmolStructure(
molecule, number=chain_options.num,
instructions=instructions
)
mdapackmol_input.append(packmol_structure)
for branched_chain_options in topology_options.branched_chains:
instructions = branched_chain_options.instructions
if instructions is None:
instructions = default_instructions
molecule = mda.Universe(
branched_chain_options.pdb
)
packmol_structure = mdapackmol.PackmolStructure(
molecule, number=branched_chain_options.num,
instructions=instructions
)
mdapackmol_input.append(packmol_structure)
if topology_options.numDodecane > 0:
instructions = topology_options.dodecaneInstructions
if instructions is None:
instructions = default_instructions
dodecane_pdb_filepath = "data/C12.pdb"
if topology_options.forceField_str == 'OPLS-AA':
dodecane_pdb_filepath = "data/C12_aa.pdb"
molecule = mda.Universe(
os.path.join(os.path.dirname(__file__), dodecane_pdb_filepath)
)
packmol_structure = mdapackmol.PackmolStructure(
molecule, number=topology_options.numDodecane,
instructions=instructions
)
mdapackmol_input.append(packmol_structure)
if topology_options.numSqualane > 0:
instructions = default_instructions
if topology_options.forceField_str == 'TraPPE-UA':
squalane_pdb_filepath = "data/squalane_ua.pdb"
else:
raise NotImplementedError("force field not implemented for squalane")
molecule = mda.Universe(
os.path.join(os.path.dirname(__file__), squalane_pdb_filepath)
)
packmol_structure = mdapackmol.PackmolStructure(
molecule, number=topology_options.numSqualane,
instructions=instructions
)
mdapackmol_input.append(packmol_structure)
# Call Packmol
system = mdapackmol.packmol(mdapackmol_input)
# Set positions to simulation
positions = system.coord.positions/10.0
simulation.context.setPositions(positions)
# Save to PDB file
if self.file is not None:
PDBReporter(self.file, 1).report(simulation, simulation.context.getState(getPositions=True))
PDBFile.writeFile(
simulation.topology, state.getPositions(), outfile)
###
# Mutant
###
""" Model components """
water = mda.Universe(f'{PDB_DIR}/water.pdb').select_atoms('resname *')
ligand = mda.Universe('selex.00.pdb').select_atoms('resname UNL')
protein = mda.Universe('selex.00.pdb').select_atoms('protein')
""" Crteate the solvent box """
num,rho = pkm.tools.molecules_for_target_density(
{protein:1, ligand:1}, water, SOLVENT_BOX_RHO, SOLVENT_BOX_DIM)
solvent = pkm.packmol([
pkm.PackmolStructure(water, num, [SOLVENT_BOX_CMD])])
""" Center components """
complejo = mda.Merge(ligand, protein)
protein = complejo.select_atoms('protein')
ligand = complejo.select_atoms('resname UNL')
point = [d/2 for d in SOLVENT_BOX_DIM]
complejo.trajectory.add_transformations(
mtx.center_in_box(complejo.atoms, point=point, wrap=False))
""" Dissolve complex """
uni_selex00 = mda.Merge(complejo.atoms, solvent.atoms)
""" Construct mutation strings by chain for PDBFixer """
wtgroup_A = uni_selex00.select_atoms('segid A and (around 3.0 resname UNL)')