guest_wall_targets = [11.3, 13.3, 80.0]
else:
guest_wall_targets = [12.5, 14.5, 80.0]
guest_wall_restraints = setup_guest_wall_restraints(
guest_wall_template,
guest_wall_targets,
structure,
resname="MGO",
angle_fc=500.0,
distance_fc=50.0,
)
restraints = (static_restraints + conformational_restraints +
guest_restraints + guest_wall_restraints)
window_list = create_window_list(guest_restraints)
print("Writing restratint file in each window...")
for window in window_list:
if not os.path.exists(os.path.join("..", system, window)):
os.makedirs(os.path.join("..", system, window))
with open(os.path.join("..", system, window, "disang.rest"),
"w") as file:
if window[0] == "a":
phase = "attach"
restraints = (static_restraints + guest_restraints +
conformational_restraints +
guest_wall_restraints)
if window[0] == "p":
phase = "pull"
restraints = (static_restraints + conformational_restraints +
def populate_window_list(self, input_pdb):
logger.debug("Setting up dummy restraint to build window list.")
_dummy_restraint = self._create_dummy_restraint(
initial_structure=str(input_pdb), )
self.window_list = create_window_list([_dummy_restraint])
return _dummy_restraint
def test_amber_single_window_gbmin(clean_files):
# Distance restraint
restraint = restraints.DAT_restraint()
restraint.continuous_apr = True
restraint.amber_index = True
restraint.topology = os.path.join(
os.path.dirname(__file__), "../data/k-cl/k-cl.pdb"
)
restraint.mask1 = ":K+"
restraint.mask2 = ":Cl-"
restraint.attach["target"] = 4.5
restraint.attach["fraction_list"] = [0.00, 0.04, 0.181, 0.496, 1.000]
restraint.attach["fc_final"] = 5.0
restraint.pull["fc"] = restraint.attach["fc_final"]
restraint.pull["target_initial"] = restraint.attach["target"]
restraint.pull["target_final"] = 18.5
restraint.pull["num_windows"] = 5
restraint.initialize()
windows_directory = os.path.join("tmp", "k-cl", "windows")
window_list = create_window_list([restraint])
for window in window_list:
os.makedirs(os.path.join(windows_directory, window))
with open(
os.path.join(windows_directory, window, "restraints.in"), "a"
) as file:
string = amber.amber_restraint_line(restraint, window)
file.write(string)
for window in window_list:
if window[0] == "a":
structure = pmd.load_file(
os.path.join(os.path.dirname(__file__), "../data/k-cl/k-cl-sol.prmtop"),
os.path.join(os.path.dirname(__file__), "../data/k-cl/k-cl-sol.rst7"),
structure=True,
)
for atom in structure.atoms:
if atom.name == "Cl-":
atom.xz = 2.65
structure.save(
os.path.join(windows_directory, window, "k-cl.prmtop"), overwrite=True
)
structure.save(
os.path.join(windows_directory, window, "k-cl.rst7"), overwrite=True
)
structure.save(
os.path.join(windows_directory, window, "k-cl.pdb"), overwrite=True
)
elif window[0] == "p":
structure = pmd.load_file(
os.path.join(os.path.dirname(__file__), "../data/k-cl/k-cl-sol.prmtop"),
os.path.join(os.path.dirname(__file__), "../data/k-cl/k-cl-sol.rst7"),
structure=True,
)
target_difference = (
restraint.phase["pull"]["targets"][int(window[1:])]
- restraint.phase["pull"]["targets"][0]
)
for atom in structure.atoms:
if atom.name == "Cl-":
atom.xz += target_difference
structure.save(
os.path.join(windows_directory, window, "k-cl.prmtop"), overwrite=True
)
structure.save(
os.path.join(windows_directory, window, "k-cl.rst7"), overwrite=True
)
structure.save(
os.path.join(windows_directory, window, "k-cl.pdb"), overwrite=True
)
gbsim = AMBER()
gbsim.path = os.path.join("tmp", "k-cl", "windows", "a003")
gbsim.executable = "sander"
gbsim.topology = "k-cl.prmtop"
gbsim.prefix = "minimize"
gbsim.coordinates = "k-cl.rst7"
gbsim.config_gb_min()
gbsim.cntrl["maxcyc"] = 1
gbsim.cntrl["ncyc"] = 1
gbsim.run()
gbsim.config_gb_md()
gbsim.prefix = "md"
gbsim.coordinates = "minimize.rst7"
gbsim.cntrl["nstlim"] = 1
gbsim.cntrl["ntwe"] = 1
gbsim.cntrl["ntpr"] = 1
gbsim.cntrl["ig"] = 777
gbsim.run()
mden = parse_mden(os.path.join("tmp", "k-cl", "windows", "a003", "md.mden"))
assert pytest.approx(mden["Bond"][0]) == 0
assert pytest.approx(mden["Angle"][0]) == 0
assert pytest.approx(mden["Dihedral"][0]) == 0
assert pytest.approx(mden["V14"][0]) == 0
assert pytest.approx(mden["E14"][0]) == 0
assert pytest.approx(mden["VDW"][0], 0.1) == 25956.13225
assert pytest.approx(mden["Ele"][0], 0.1) == -18828.99631
assert pytest.approx(mden["Total"][0], 0.1) == 7127.13594
def test_DAT_restraint():
# Method 1
logger.info("### Testing restraint 1, Method 1")
rest1 = DAT_restraint()
rest1.amber_index = True
rest1.continuous_apr = False
rest1.auto_apr = False
rest1.topology = os.path.join(os.path.dirname(__file__),
"../data/cb6-but/cb6-but-notcentered.pdb")
rest1.mask1 = ":CB6@O,O2,O4,O6,O8,O10"
rest1.mask2 = ":BUT@C3"
rest1.attach["target"] = 3.0
rest1.attach["num_windows"] = 4
rest1.attach["fc_initial"] = 0.0
rest1.attach["fc_final"] = 3.0
rest1.pull["fc"] = rest1.attach["fc_final"]
rest1.pull["num_windows"] = 4
rest1.pull["target_initial"] = rest1.attach["target"]
rest1.pull["target_final"] = 6.0
rest1.release["target"] = rest1.pull["target_final"]
rest1.release["num_windows"] = rest1.attach["num_windows"]
rest1.release["fc_initial"] = rest1.attach["fc_initial"]
rest1.release["fc_final"] = rest1.attach["fc_final"]
rest1.initialize()
assert rest1.index1 == [13, 31, 49, 67, 85, 103]
assert rest1.index2 == [119]
assert rest1.index3 is None
assert rest1.index4 is None
assert np.allclose(rest1.phase["attach"]["force_constants"],
np.array([0.0, 1.0, 2.0, 3.0]))
assert np.allclose(rest1.phase["attach"]["targets"],
np.array([3.0, 3.0, 3.0, 3.0]))
assert np.allclose(rest1.phase["pull"]["force_constants"],
np.array([3.0, 3.0, 3.0, 3.0]))
assert np.allclose(rest1.phase["pull"]["targets"],
np.array([3.0, 4.0, 5.0, 6.0]))
assert np.allclose(rest1.phase["release"]["force_constants"],
np.array([0.0, 1.0, 2.0, 3.0]))
assert np.allclose(rest1.phase["release"]["targets"],
np.array([6.0, 6.0, 6.0, 6.0]))
window_list = create_window_list([rest1])
assert window_list == [
"a000",
"a001",
"a002",
"a003",
"p000",
"p001",
"p002",
"p003",
"r000",
"r001",
"r002",
"r003",
]
# Method 1a
logger.info("### Testing restraint 2, Method 1a")
rest2 = DAT_restraint()
rest2.amber_index = True
rest2.continuous_apr = False
rest2.auto_apr = False
rest2.topology = os.path.join(os.path.dirname(__file__),
"../data/cb6-but/cb6-but-notcentered.pdb")
rest2.mask1 = ":CB6@O,O2,O4,O6,O8,O10"
rest2.mask2 = ":BUT@C3"
rest2.mask3 = ":BUT@C"
rest2.attach["target"] = 180.0
rest2.attach["num_windows"] = 4
rest2.attach["fc_final"] = 75.0
rest2.pull["fc"] = rest2.attach["fc_final"]
rest2.pull["num_windows"] = 4
rest2.pull["target_final"] = 180.0
rest2.release["target"] = rest2.pull["target_final"]
rest2.release["num_windows"] = rest2.attach["num_windows"]
rest2.release["fc_final"] = rest2.attach["fc_final"]
rest2.initialize()
assert rest2.index1 == [13, 31, 49, 67, 85, 103]
assert rest2.index2 == [119]
assert rest2.index3 == [109]
assert rest2.index4 is None
assert np.allclose(rest2.phase["attach"]["force_constants"],
np.array([0.0, 25.0, 50.0, 75.0]))
assert np.allclose(rest2.phase["attach"]["targets"],
np.array([180.0, 180.0, 180.0, 180.0]))
assert np.allclose(rest2.phase["pull"]["force_constants"],
np.array([75.0, 75.0, 75.0, 75.0]))
assert np.allclose(rest2.phase["pull"]["targets"],
np.array([0.0, 60.0, 120.0, 180.0]))
assert np.allclose(rest2.phase["release"]["force_constants"],
np.array([0.0, 25.0, 50.0, 75.0]))
assert np.allclose(rest2.phase["release"]["targets"],
np.array([180.0, 180.0, 180.0, 180.0]))
window_list = create_window_list([rest2])
assert window_list == [
"a000",
"a001",
"a002",
"a003",
"p000",
"p001",
"p002",
"p003",
"r000",
"r001",
"r002",
"r003",
]
# Method 2 (Note auto_apr = True)
logger.info("### Testing restraint 3, Method 2")
rest3 = DAT_restraint()
rest3.amber_index = True
rest3.continuous_apr = False
rest3.auto_apr = True
rest3.topology = os.path.join(os.path.dirname(__file__),
"../data/cb6-but/cb6-but-notcentered.pdb")
rest3.mask1 = ":CB6@O2"
rest3.mask2 = ":CB6@O"
rest3.mask3 = ":BUT@C3"
rest3.mask4 = ":BUT@C"
rest3.attach["target"] = 90.0
rest3.attach["fc_increment"] = 25.0
rest3.attach["fc_initial"] = 0.0
rest3.attach["fc_final"] = 75.0
rest3.pull["target_increment"] = 1.0
rest3.pull["target_final"] = 93.0
rest3.release["fc_final"] = 75.0
rest3.initialize()
assert rest3.index1 == [31]
assert rest3.index2 == [13]
assert rest3.index3 == [119]
assert rest3.index4 == [109]
assert np.allclose(rest3.phase["attach"]["force_constants"],
np.array([0.0, 25.0, 50.0, 75.0]))
assert np.allclose(rest3.phase["attach"]["targets"],
np.array([90.0, 90.0, 90.0, 90.0]))
assert np.allclose(rest3.phase["pull"]["force_constants"],
np.array([75.0, 75.0, 75.0, 75.0]))
assert np.allclose(rest3.phase["pull"]["targets"],
np.array([90.0, 91.0, 92.0, 93.0]))
assert np.allclose(rest3.phase["release"]["force_constants"],
np.array([0.0, 25.0, 50.0, 75.0]))
assert np.allclose(rest3.phase["release"]["targets"],
np.array([93.0, 93.0, 93.0, 93.0]))
window_list = create_window_list([rest3])
assert window_list == [
"a000",
"a001",
"a002",
"a003",
"p000",
"p001",
"p002",
"p003",
"r000",
"r001",
"r002",
"r003",
]
# Method 2a
logger.info("### Testing restraint 4, Method 2a")
rest4 = DAT_restraint()
rest4.amber_index = True
rest4.continuous_apr = False
rest4.auto_apr = False
rest4.topology = os.path.join(os.path.dirname(__file__),
"../data/cb6-but/cb6-but-notcentered.pdb")
rest4.mask1 = ":CB6@O2"
rest4.mask2 = ":CB6@O"
rest4.mask3 = ":BUT@C3"
rest4.mask4 = ":BUT@C"
rest4.attach["target"] = 0.0
rest4.attach["fc_increment"] = 25.0
rest4.attach["fc_final"] = 75.0
rest4.pull["fc"] = 75.0
rest4.pull["target_increment"] = 1.0
rest4.pull["target_final"] = 3.0
rest4.release["target"] = 3.0
rest4.release["fc_increment"] = 25.0
rest4.release["fc_final"] = 75.0
rest4.initialize()
assert rest4.index1 == [31]
assert rest4.index2 == [13]
assert rest4.index3 == [119]
assert rest4.index4 == [109]
assert np.allclose(rest4.phase["attach"]["force_constants"],
np.array([0.0, 25.0, 50.0, 75.0]))
assert np.allclose(rest4.phase["attach"]["targets"],
np.array([0.0, 0.0, 0.0, 0.0]))
assert np.allclose(rest4.phase["pull"]["force_constants"],
np.array([75.0, 75.0, 75.0, 75.0]))
assert np.allclose(rest4.phase["pull"]["targets"],
np.array([0.0, 1.0, 2.0, 3.0]))
assert np.allclose(rest4.phase["release"]["force_constants"],
np.array([0.0, 25.0, 50.0, 75.0]))
assert np.allclose(rest4.phase["release"]["targets"],
np.array([3.0, 3.0, 3.0, 3.0]))
window_list = create_window_list([rest4])
assert window_list == [
"a000",
"a001",
"a002",
"a003",
"p000",
"p001",
"p002",
"p003",
"r000",
"r001",
"r002",
"r003",
]
# Method 3
logger.info("### Testing restraint 5, Method 3")
rest5 = DAT_restraint()
rest5.amber_index = True
rest5.continuous_apr = False
rest5.auto_apr = False
rest5.topology = os.path.join(os.path.dirname(__file__),
"../data/cb6-but/cb6-but-notcentered.pdb")
rest5.mask1 = ":CB6@O,O2,O4,O6,O8,O10"
rest5.mask2 = ":BUT@C*"
rest5.attach["target"] = 0.0
rest5.attach["fraction_list"] = [0.0, 0.2, 0.5, 1.0]
rest5.attach["fc_final"] = 5.0
rest5.pull["fc"] = rest5.attach["fc_final"]
rest5.pull["fraction_list"] = [0.0, 0.5, 1.0]
rest5.pull["target_final"] = 1.0
rest5.release["target"] = rest5.pull["target_final"]
rest5.release["fraction_list"] = [0.0, 0.3, 0.6, 1.0]
rest5.release["fc_final"] = rest5.attach["fc_final"]
rest5.initialize()
assert rest5.index1 == [13, 31, 49, 67, 85, 103]
assert rest5.index2 == [109, 113, 115, 119]
assert rest5.index3 is None
assert rest5.index4 is None
assert np.allclose(rest5.phase["attach"]["force_constants"],
np.array([0.0, 1.0, 2.5, 5.0]))
assert np.allclose(rest5.phase["attach"]["targets"],
np.array([0.0, 0.0, 0.0, 0.0]))
assert np.allclose(rest5.phase["pull"]["force_constants"],
np.array([5.0, 5.0, 5.0]))
assert np.allclose(rest5.phase["pull"]["targets"],
np.array([0.0, 0.5, 1.0]))
assert np.allclose(rest5.phase["release"]["force_constants"],
np.array([0.0, 1.5, 3.0, 5.0]))
assert np.allclose(rest5.phase["release"]["targets"],
np.array([1.0, 1.0, 1.0, 1.0]))
window_list = create_window_list([rest5])
assert window_list == [
"a000",
"a001",
"a002",
"a003",
"p000",
"p001",
"p002",
"r000",
"r001",
"r002",
"r003",
]
# Method 4
logger.info("### Testing restraint 6, Method 4")
rest6 = DAT_restraint()
rest6.amber_index = True
rest6.continuous_apr = False
rest6.auto_apr = False
rest6.topology = os.path.join(os.path.dirname(__file__),
"../data/cb6-but/cb6-but-notcentered.pdb")
rest6.mask1 = ":CB6@O,O2,O4,O6,O8,O10"
rest6.mask2 = ":BUT@C*"
rest6.attach["target"] = 0.0
rest6.attach["fraction_increment"] = 0.25
rest6.attach["fc_final"] = 5.0
rest6.pull["fc"] = rest6.attach["fc_final"]
rest6.pull["fraction_increment"] = 0.5
rest6.pull["target_final"] = 1.0
rest6.release["target"] = rest6.pull["target_final"]
rest6.release["fraction_increment"] = 0.33
rest6.release["fc_final"] = rest6.attach["fc_final"]
rest6.initialize()
assert rest6.index1 == [13, 31, 49, 67, 85, 103]
assert rest6.index2 == [109, 113, 115, 119]
assert rest6.index3 is None
assert rest6.index4 is None
assert np.allclose(rest6.phase["attach"]["force_constants"],
np.array([0.0, 1.25, 2.5, 3.75, 5.0]))
assert np.allclose(rest6.phase["attach"]["targets"],
np.array([0.0, 0.0, 0.0, 0.0, 0.0]))
assert np.allclose(rest6.phase["pull"]["force_constants"],
np.array([5.0, 5.0, 5.0]))
assert np.allclose(rest6.phase["pull"]["targets"],
np.array([0.0, 0.5, 1.0]))
### Note, the 6.6 in the following test is wrong ... needs to get fixed.
assert np.allclose(rest6.phase["release"]["force_constants"],
np.array([0.0, 1.65, 3.3, 4.95, 6.6]))
assert np.allclose(rest6.phase["release"]["targets"],
np.array([1.0, 1.0, 1.0, 1.0, 1.0]))
window_list = create_window_list([rest6])
assert window_list == [
"a000",
"a001",
"a002",
"a003",
"a004",
"p000",
"p001",
"p002",
"r000",
"r001",
"r002",
"r003",
"r004",
]
# Method 5 (Note continuous_apr = True)
logger.info("### Testing restraint 7, Method 5")
rest7 = DAT_restraint()
rest7.amber_index = True
rest7.continuous_apr = True
rest7.auto_apr = False
rest7.topology = os.path.join(os.path.dirname(__file__),
"../data/cb6-but/cb6-but-notcentered.pdb")
rest7.mask1 = ":1@O,O1,:BUT@H1"
rest7.mask2 = ":CB6@N"
rest7.attach["target"] = 0.0
rest7.attach["fc_list"] = [0.0, 0.5, 1.0, 2.0]
rest7.pull["fc"] = 2.0
rest7.pull["target_list"] = [0.0, 0.5, 1.0, 1.5]
rest7.release["target"] = 1.5
rest7.release["fc_list"] = [0.0, 0.66, 1.2, 2.0]
rest7.initialize()
assert rest7.index1 == [13, 14, 111]
assert rest7.index2 == [3]
assert rest7.index3 is None
assert rest7.index4 is None
assert np.allclose(rest7.phase["attach"]["force_constants"],
np.array([0.0, 0.5, 1.0, 2.0]))
assert np.allclose(rest7.phase["attach"]["targets"],
np.array([0.0, 0.0, 0.0, 0.0]))
assert np.allclose(rest7.phase["pull"]["force_constants"],
np.array([2.0, 2.0, 2.0, 2.0]))
assert np.allclose(rest7.phase["pull"]["targets"],
np.array([0.0, 0.5, 1.0, 1.5]))
assert np.allclose(rest7.phase["release"]["force_constants"],
np.array([0.0, 0.66, 1.2, 2.0]))
assert np.allclose(rest7.phase["release"]["targets"],
np.array([1.5, 1.5, 1.5, 1.5]))
window_list = create_window_list([rest7])
assert window_list == [
"a000",
"a001",
"a002",
"p000",
"p001",
"p002",
"p003",
"r001",
"r002",
"r003",
]
# Just Attach
logger.info("### Testing restraint 8, just attach")
rest8 = DAT_restraint()
rest8.amber_index = True
rest8.continuous_apr = False
rest8.auto_apr = False
rest8.topology = os.path.join(os.path.dirname(__file__),
"../data/cb6-but/cb6-but-notcentered.pdb")
rest8.mask1 = ":CB6@O"
rest8.mask2 = ":BUT@C3"
rest8.attach["target"] = 0.0
rest8.attach["num_windows"] = 4
rest8.attach["fc_initial"] = 0.0
rest8.attach["fc_final"] = 3.0
rest8.initialize()
assert rest8.index1 == [13]
assert rest8.index2 == [119]
assert rest8.index3 is None
assert rest8.index4 is None
assert np.allclose(rest8.phase["attach"]["force_constants"],
np.array([0.0, 1.0, 2.0, 3.0]))
assert np.allclose(rest8.phase["attach"]["targets"],
np.array([0.0, 0.0, 0.0, 0.0]))
assert rest8.phase["pull"]["force_constants"] is None
assert rest8.phase["pull"]["targets"] is None
assert rest8.phase["release"]["force_constants"] is None
assert rest8.phase["release"]["targets"] is None
window_list = create_window_list([rest8])
assert window_list == ["a000", "a001", "a002", "a003"]
# Just Pull
logger.info("### Testing restraint 9, just pull")
rest9 = DAT_restraint()
rest9.amber_index = True
rest9.continuous_apr = False
rest9.auto_apr = False
rest9.topology = os.path.join(os.path.dirname(__file__),
"../data/cb6-but/cb6-but-notcentered.pdb")
rest9.mask1 = ":CB6@O"
rest9.mask2 = ":BUT@C3"
rest9.pull["fc"] = 3.0
rest9.pull["num_windows"] = 4
rest9.pull["target_initial"] = 0.0
rest9.pull["target_final"] = 3.0
rest9.initialize()
assert rest9.index1 == [13]
assert rest9.index2 == [119]
assert rest9.index3 is None
assert rest9.index4 is None
assert rest9.phase["attach"]["force_constants"] is None
assert rest9.phase["attach"]["targets"] is None
assert np.allclose(rest9.phase["pull"]["force_constants"],
np.array([3.0, 3.0, 3.0, 3.0]))
assert np.allclose(rest9.phase["pull"]["targets"],
np.array([0.0, 1.0, 2.0, 3.0]))
assert rest9.phase["release"]["force_constants"] is None
assert rest9.phase["release"]["targets"] is None
window_list = create_window_list([rest9])
assert window_list == ["p000", "p001", "p002", "p003"]
# Just Release
logger.info("### Testing restraint 10, just release")
rest10 = DAT_restraint()
rest10.amber_index = True
rest10.continuous_apr = False
rest10.auto_apr = False
rest10.topology = os.path.join(os.path.dirname(__file__),
"../data/cb6-but/cb6-but-notcentered.pdb")
rest10.mask1 = ":CB6@O"
rest10.mask2 = ":BUT@C3"
rest10.release["target"] = 0.0
rest10.release["num_windows"] = 3
rest10.release["fc_initial"] = 0.0
rest10.release["fc_final"] = 2.0
rest10.initialize()
assert rest10.index1 == [13]
assert rest10.index2 == [119]
assert rest10.index3 is None
assert rest10.index4 is None
assert rest10.phase["attach"]["force_constants"] is None
assert rest10.phase["attach"]["targets"] is None
assert rest10.phase["pull"]["force_constants"] is None
assert rest10.phase["pull"]["targets"] is None
assert np.allclose(rest10.phase["release"]["force_constants"],
np.array([0.0, 1.0, 2.0]))
assert np.allclose(rest10.phase["release"]["targets"],
np.array([0.0, 0.0, 0.0]))
window_list = create_window_list([rest10])
assert window_list == ["r000", "r001", "r002"]
# Test inconsistent continuous_apr:
with pytest.raises(Exception):
window_list = create_window_list([rest7, rest8])
# Test inconsistent windows:
with pytest.raises(Exception):
window_list = create_window_list([rest1, rest10])