def makeSim(system, ligand_mol, watersys):
"""Create simulation systems with and without the ligand and return those systems together
with the moves"""
stage1 = System("with_ligand")
stage2 = System("without_ligand")
if system.containsProperty("reflection center"):
reflection_center = system.property("reflection center").toVector()[0]
reflection_radius = float(
str(system.property("reflection sphere radius")))
stage1.setProperty("reflection center",
AtomCoords(CoordGroup(1, reflection_center)))
stage1.setProperty("reflection sphere radius",
VariantProperty(reflection_radius))
stage2.setProperty("reflection center",
AtomCoords(CoordGroup(1, reflection_center)))
stage2.setProperty("reflection sphere radius",
VariantProperty(reflection_radius))
# create a molecule group for fixed atoms (everything except the mobile water)
fixed_group = MoleculeGroup("fixed")
if MGName("fixed_molecules") in system.mgNames():
fixed_group.add(system[MGName("fixed_molecules")])
if MGName("mobile_solutes") in system.mgNames():
fixed_group.add(system[MGName("mobile_solutes")])
if MGName("protein_sidechains") in system.mgNames() or \
MGName("protein_backbones") in system.mgNames():
all_proteins = Molecules()
try:
protein_sidechains = system[MGName("protein_sidechains")]
all_proteins.add(protein_sidechains.molecules())
except:
pass
try:
protein_backbones = system[MGName("protein_backbones")]
all_proteins.add(protein_backbones.molecules())
except:
pass
try:
boundary_molecules = system[MGName("boundary_molecules")]
all_proteins.add(boundary_molecules.molecules())
except:
pass
for molnum in all_proteins.molNums():
protein_mol = Molecule.join(all_proteins[molnum])
fixed_group.add(protein_mol)
stage1_fixed_group = MoleculeGroup(fixed_group)
stage2_fixed_group = MoleculeGroup(fixed_group)
stage1_fixed_group.add(ligand_mol)
stage2_fixed_group.remove(ligand_mol)
mobile_group = MoleculeGroup("mobile_group")
if MGName("mobile_solvents") in system.mgNames():
mobile_group.add(system[MGName("mobile_solvents")])
stage1_mobile_group = MoleculeGroup(mobile_group)
stage2_mobile_group = MoleculeGroup(mobile_group)
# now find water molecules from the water system that can be substituted for the ligand
watermols = findOverlappingWaters(ligand_mol, watersys)
stage2_mobile_group.add(watermols)
print("The number of stage 1 fixed non-solvent molecules is %d." %
stage1_fixed_group.nMolecules())
print("The number of stage 1 mobile solvent molecules is %d." %
stage1_mobile_group.nMolecules())
print("The number of stage 2 fixed non-solvent molecules is %d." %
stage2_fixed_group.nMolecules())
print("The number of stage 2 mobile solvent molecules is %d." %
stage2_mobile_group.nMolecules())
# write a PDB of all of the fixed molecules
PDB().write(stage1_mobile_group, "stage1_mobile_atoms.pdb")
PDB().write(stage2_mobile_group, "stage2_mobile_atoms.pdb")
PDB().write(stage1_fixed_group, "stage1_fixed_atoms.pdb")
PDB().write(stage2_fixed_group, "stage2_fixed_atoms.pdb")
# create the forcefields
if use_fast_ff.val:
stage1_ff = InterFF("ff")
stage2_ff = InterFF("ff")
stage1_ff.setCLJFunction(
CLJShiftFunction(Cartesian(), coul_cutoff.val, lj_cutoff.val))
stage2_ff.setCLJFunction(
CLJShiftFunction(Cartesian(), coul_cutoff.val, lj_cutoff.val))
if disable_grid.val:
stage1_ff.disableGrid()
stage2_ff.disableGrid()
else:
stage1_ff.enableGrid()
stage1_ff.setGridSpacing(grid_spacing.val)
stage1_ff.setGridBuffer(grid_buffer.val)
stage2_ff.enableGrid()
stage2_ff.setGridSpacing(grid_spacing.val)
stage2_ff.setGridBuffer(grid_buffer.val)
stage1_ff.add(stage1_mobile_group)
stage1_ff.setFixedAtoms(stage1_fixed_group.molecules())
stage2_ff.add(stage2_mobile_group)
stage2_ff.setFixedAtoms(stage2_fixed_group.molecules())
stage1.add(stage1_ff)
stage1.setComponent(stage1.totalComponent(),
stage1_ff.components().total())
stage2.add(stage1_ff)
stage2.setComponent(stage2.totalComponent(),
stage2_ff.components().total())
else:
# forcefield holding the energy between the mobile atoms and
# the fixed atoms
if disable_grid.val:
stage1_mobile_fixed = InterGroupCLJFF("mobile-fixed")
stage1_mobile_fixed = setCLJProperties(stage1_mobile_fixed)
stage1_mobile_fixed = setFakeGridProperties(stage1_mobile_fixed)
stage1_mobile_fixed.add(stage1_mobile_group, MGIdx(0))
stage1_mobile_fixed.add(stage1_fixed_group, MGIdx(1))
stage2_mobile_fixed = InterGroupCLJFF("mobile-fixed")
stage2_mobile_fixed = setCLJProperties(stage2_mobile_fixed)
stage2_mobile_fixed = setFakeGridProperties(stage2_mobile_fixed)
stage2_mobile_fixed.add(stage2_mobile_group, MGIdx(0))
stage2_mobile_fixed.add(stage2_fixed_group, MGIdx(1))
else:
stage1_mobile_fixed = GridFF2("mobile-fixed")
stage1_mobile_fixed = setCLJProperties(stage1_mobile_fixed)
stage1_mobile_fixed = setGridProperties(stage1_mobile_fixed)
stage1_mobile_fixed.add(stage1_mobile_group, MGIdx(0))
stage1_mobile_fixed.addFixedAtoms(stage1_fixed_group)
stage2_mobile_fixed = GridFF2("mobile-fixed")
stage2_mobile_fixed = setCLJProperties(stage2_mobile_fixed)
stage2_mobile_fixed = setGridProperties(stage2_mobile_fixed)
stage2_mobile_fixed.add(stage2_mobile_group, MGIdx(0))
stage2_mobile_fixed.addFixedAtoms(stage2_fixed_group)
# forcefield holding the energy between fixed atoms
stage1_mobile_mobile = InterCLJFF("mobile-mobile")
stage1_mobile_mobile = setCLJProperties(stage1_mobile_mobile)
stage1_mobile_mobile.add(stage1_mobile_group)
stage2_mobile_mobile = InterCLJFF("mobile-mobile")
stage2_mobile_mobile = setCLJProperties(stage2_mobile_mobile)
stage2_mobile_mobile.add(stage2_mobile_group)
stage1.add(stage1_mobile_group)
stage1.add(stage1_mobile_fixed)
stage1.add(stage1_mobile_mobile)
stage2.add(stage2_mobile_group)
stage2.add(stage2_mobile_fixed)
stage2.add(stage2_mobile_mobile)
stage1.setComponent(
stage1.totalComponent(),
stage1_mobile_mobile.components().total() +
stage1_mobile_fixed.components().total())
stage2.setComponent(
stage2.totalComponent(),
stage2_mobile_mobile.components().total() +
stage2_mobile_fixed.components().total())
stage1.add(stage1_mobile_group)
stage2.add(stage2_mobile_group)
stage1.add("volume_map", VolMapMonitor(stage1_mobile_group), 1000)
stage2.add("volume_map", VolMapMonitor(stage2_mobile_group), 1000)
max_water_translation = 0.15 * angstroms
max_water_rotation = 15 * degrees
stage1_moves = WeightedMoves()
if stage1_mobile_group.nViews() > 0:
rb_moves = RigidBodyMC(stage1_mobile_group)
rb_moves.setMaximumTranslation(max_water_translation)
rb_moves.setMaximumRotation(max_water_rotation)
if stage1.containsProperty("reflection sphere radius"):
reflection_radius = float(
str(stage1.property("reflection sphere radius"))) * angstroms
reflection_center = stage1.property(
"reflection center").toVector()[0]
rb_moves.setReflectionSphere(reflection_center, reflection_radius)
stage1_moves.add(rb_moves, stage1_mobile_group.nViews())
stage2_moves = WeightedMoves()
if stage2_mobile_group.nViews() > 0:
rb_moves = RigidBodyMC(stage2_mobile_group)
rb_moves.setMaximumTranslation(max_water_translation)
rb_moves.setMaximumRotation(max_water_rotation)
if stage2.containsProperty("reflection sphere radius"):
reflection_radius = float(
str(stage2.property("reflection sphere radius"))) * angstroms
reflection_center = stage2.property(
"reflection center").toVector()[0]
rb_moves.setReflectionSphere(reflection_center, reflection_radius)
stage2_moves.add(rb_moves, stage2_mobile_group.nViews())
stage1_moves.setTemperature(temperature.val)
stage2_moves.setTemperature(temperature.val)
seed = random_seed.val
if seed is None:
seed = RanGenerator().randInt(100000, 1000000)
print("Using generated random number seed %d" % seed)
else:
print("Using supplied random number seed %d" % seed)
stage1_moves.setGenerator(RanGenerator(seed))
stage2_moves.setGenerator(RanGenerator(seed + 7))
return ((stage1, stage1_moves), (stage2, stage2_moves))
def test_props(verbose=False):
sys = System()
box0 = PeriodicBox( Vector(10.0,10.0,10.0) )
box1 = PeriodicBox( Vector(20.0,20.0,20.0) )
if verbose:
print(box0)
print(box0.volume())
print(box1.volume())
assert(not sys.containsProperty("space"))
sys.add( InterCLJFF("cljff") )
if verbose:
print(sys)
print(sys.property("space"))
print(sys.userProperties().propertyKeys())
print(sys.builtinProperties().propertyKeys())
assert(sys.containsProperty("space"))
assert_equal( sys.property("space"), Cartesian() )
sys.setProperty( "space0", LinkToProperty("space", FFIdx(0)) )
if verbose:
print(sys.property("space0"))
assert(sys.containsProperty("space0"))
sys.setProperty("space0", box0)
if verbose:
print(sys.property("space"))
assert_equal(sys.property("space0"), box0)
sys.setProperty("space1", box1)
sys.setProperty("combined_space", CombineSpaces("space0", "space1"))
assert_equal(sys.property("space1"), box1)
if verbose:
print(sys.properties().propertyKeys())
print(sys.property("combined_space"))
print(sys.property("combined_space").volume())
assert_almost_equal( sys.property("combined_space").volume().value(),
sys.property("space0").volume().value() + sys.property("space1").volume().value(), 5 )
space3 = PeriodicBox( Vector(5,5,5) )
sys.setProperty("space0", space3)
assert_equal( sys.property("space0"), space3 )
if verbose:
print(sys.property("combined_space"))
print(sys.property("combined_space").volume())
assert_almost_equal( sys.property("combined_space").volume().value(),
sys.property("space0").volume().value() + sys.property("space1").volume().value(), 5 )
sys.removeProperty("space0")
if verbose:
print(sys.properties().propertyKeys())
assert( not sys.containsProperty("space0") )
def makeSim(system, ligand_mol, watersys):
"""Create simulation systems with and without the ligand and return those systems together
with the moves"""
stage1 = System("with_ligand")
stage2 = System("without_ligand")
if system.containsProperty("reflection center"):
reflection_center = system.property("reflection center").toVector()[0]
reflection_radius = float(str(system.property("reflection sphere radius")))
stage1.setProperty("reflection center", AtomCoords(CoordGroup(1,reflection_center)))
stage1.setProperty("reflection sphere radius", VariantProperty(reflection_radius))
stage2.setProperty("reflection center", AtomCoords(CoordGroup(1,reflection_center)))
stage2.setProperty("reflection sphere radius", VariantProperty(reflection_radius))
# create a molecule group for fixed atoms (everything except the mobile water)
fixed_group = MoleculeGroup("fixed")
if MGName("fixed_molecules") in system.mgNames():
fixed_group.add( system[ MGName("fixed_molecules") ] )
if MGName("mobile_solutes") in system.mgNames():
fixed_group.add( system[MGName("mobile_solutes")] )
if MGName("protein_sidechains") in system.mgNames() or \
MGName("protein_backbones") in system.mgNames():
all_proteins = Molecules()
try:
protein_sidechains = system[MGName("protein_sidechains")]
all_proteins.add(protein_sidechains.molecules())
except:
pass
try:
protein_backbones = system[MGName("protein_backbones")]
all_proteins.add(protein_backbones.molecules())
except:
pass
try:
boundary_molecules = system[MGName("boundary_molecules")]
all_proteins.add(boundary_molecules.molecules())
except:
pass
for molnum in all_proteins.molNums():
protein_mol = all_proteins[molnum].join()
fixed_group.add(protein_mol)
stage1_fixed_group = MoleculeGroup(fixed_group)
stage2_fixed_group = MoleculeGroup(fixed_group)
stage1_fixed_group.add(ligand_mol)
stage2_fixed_group.remove(ligand_mol)
mobile_group = MoleculeGroup("mobile_group")
if MGName("mobile_solvents") in system.mgNames():
mobile_group.add( system[MGName("mobile_solvents")] )
stage1_mobile_group = MoleculeGroup(mobile_group)
stage2_mobile_group = MoleculeGroup(mobile_group)
# now find water molecules from the water system that can be substituted for the ligand
watermols = findOverlappingWaters(ligand_mol, watersys)
stage2_mobile_group.add(watermols)
print("The number of stage 1 fixed non-solvent molecules is %d." % stage1_fixed_group.nMolecules())
print("The number of stage 1 mobile solvent molecules is %d." % stage1_mobile_group.nMolecules())
print("The number of stage 2 fixed non-solvent molecules is %d." % stage2_fixed_group.nMolecules())
print("The number of stage 2 mobile solvent molecules is %d." % stage2_mobile_group.nMolecules())
# write a PDB of all of the fixed molecules
PDB().write(stage1_mobile_group, "stage1_mobile_atoms.pdb")
PDB().write(stage2_mobile_group, "stage2_mobile_atoms.pdb")
PDB().write(stage1_fixed_group, "stage1_fixed_atoms.pdb")
PDB().write(stage2_fixed_group, "stage2_fixed_atoms.pdb")
# create the forcefields
if use_fast_ff.val:
stage1_ff = InterFF("ff")
stage2_ff = InterFF("ff")
stage1_ff.setCLJFunction( CLJShiftFunction(Cartesian(), coul_cutoff.val, lj_cutoff.val) )
stage2_ff.setCLJFunction( CLJShiftFunction(Cartesian(), coul_cutoff.val, lj_cutoff.val) )
if disable_grid.val:
stage1_ff.disableGrid()
stage2_ff.disableGrid()
else:
stage1_ff.enableGrid()
stage1_ff.setGridSpacing(grid_spacing.val)
stage1_ff.setGridBuffer(grid_buffer.val)
stage2_ff.enableGrid()
stage2_ff.setGridSpacing(grid_spacing.val)
stage2_ff.setGridBuffer(grid_buffer.val)
stage1_ff.add(stage1_mobile_group)
stage1_ff.setFixedAtoms(stage1_fixed_group.molecules())
stage2_ff.add(stage2_mobile_group)
stage2_ff.setFixedAtoms(stage2_fixed_group.molecules())
stage1.add(stage1_ff)
stage1.setComponent(stage1.totalComponent(), stage1_ff.components().total())
stage2.add(stage1_ff)
stage2.setComponent(stage2.totalComponent(), stage2_ff.components().total())
else:
# forcefield holding the energy between the mobile atoms and
# the fixed atoms
if disable_grid.val:
stage1_mobile_fixed = InterGroupCLJFF("mobile-fixed")
stage1_mobile_fixed = setCLJProperties(stage1_mobile_fixed)
stage1_mobile_fixed = setFakeGridProperties(stage1_mobile_fixed)
stage1_mobile_fixed.add(stage1_mobile_group, MGIdx(0))
stage1_mobile_fixed.add(stage1_fixed_group, MGIdx(1))
stage2_mobile_fixed = InterGroupCLJFF("mobile-fixed")
stage2_mobile_fixed = setCLJProperties(stage2_mobile_fixed)
stage2_mobile_fixed = setFakeGridProperties(stage2_mobile_fixed)
stage2_mobile_fixed.add(stage2_mobile_group, MGIdx(0))
stage2_mobile_fixed.add(stage2_fixed_group, MGIdx(1))
else:
stage1_mobile_fixed = GridFF("mobile-fixed")
stage1_mobile_fixed = setCLJProperties(stage1_mobile_fixed)
stage1_mobile_fixed = setGridProperties(stage1_mobile_fixed)
stage1_mobile_fixed.add(stage1_mobile_group, MGIdx(0))
stage1_mobile_fixed.addFixedAtoms(stage1_fixed_group)
stage2_mobile_fixed = GridFF("mobile-fixed")
stage2_mobile_fixed = setCLJProperties(stage2_mobile_fixed)
stage2_mobile_fixed = setGridProperties(stage2_mobile_fixed)
stage2_mobile_fixed.add(stage2_mobile_group, MGIdx(0))
stage2_mobile_fixed.addFixedAtoms(stage2_fixed_group)
# forcefield holding the energy between fixed atoms
stage1_mobile_mobile = InterCLJFF("mobile-mobile")
stage1_mobile_mobile = setCLJProperties(stage1_mobile_mobile)
stage1_mobile_mobile.add(stage1_mobile_group)
stage2_mobile_mobile = InterCLJFF("mobile-mobile")
stage2_mobile_mobile = setCLJProperties(stage2_mobile_mobile)
stage2_mobile_mobile.add(stage2_mobile_group)
stage1.add(stage1_mobile_group)
stage1.add(stage1_mobile_fixed)
stage1.add(stage1_mobile_mobile)
stage2.add(stage2_mobile_group)
stage2.add(stage2_mobile_fixed)
stage2.add(stage2_mobile_mobile)
stage1.setComponent(stage1.totalComponent(), stage1_mobile_mobile.components().total() + stage1_mobile_fixed.components().total())
stage2.setComponent(stage2.totalComponent(), stage2_mobile_mobile.components().total() + stage2_mobile_fixed.components().total())
stage1.add(stage1_mobile_group)
stage2.add(stage2_mobile_group)
stage1.add("volume_map", VolMapMonitor(stage1_mobile_group), 1000)
stage2.add("volume_map", VolMapMonitor(stage2_mobile_group), 1000)
max_water_translation = 0.15 * angstroms
max_water_rotation = 15 * degrees
stage1_moves = WeightedMoves()
if stage1_mobile_group.nViews() > 0:
rb_moves = RigidBodyMC(stage1_mobile_group)
rb_moves.setMaximumTranslation(max_water_translation)
rb_moves.setMaximumRotation(max_water_rotation)
if stage1.containsProperty("reflection sphere radius"):
reflection_radius = float(str(stage1.property("reflection sphere radius"))) * angstroms
reflection_center = stage1.property("reflection center").toVector()[0]
rb_moves.setReflectionSphere(reflection_center, reflection_radius)
stage1_moves.add(rb_moves, stage1_mobile_group.nViews())
stage2_moves = WeightedMoves()
if stage2_mobile_group.nViews() > 0:
rb_moves = RigidBodyMC(stage2_mobile_group)
rb_moves.setMaximumTranslation(max_water_translation)
rb_moves.setMaximumRotation(max_water_rotation)
if stage2.containsProperty("reflection sphere radius"):
reflection_radius = float(str(stage2.property("reflection sphere radius"))) * angstroms
reflection_center = stage2.property("reflection center").toVector()[0]
rb_moves.setReflectionSphere(reflection_center, reflection_radius)
stage2_moves.add(rb_moves, stage2_mobile_group.nViews())
stage1_moves.setTemperature(temperature.val)
stage2_moves.setTemperature(temperature.val)
seed = random_seed.val
if seed is None:
seed = RanGenerator().randInt(100000,1000000)
print("Using generated random number seed %d" % seed)
else:
print("Using supplied random number seed %d" % seed)
stage1_moves.setGenerator( RanGenerator(seed) )
stage2_moves.setGenerator( RanGenerator(seed+7) )
return ( (stage1,stage1_moves), (stage2,stage2_moves) )
