def test_solvation_potassium_control(clean_files):
""" Test there is no potassium by default. A negative control. """
waters = np.random.randint(1000, 10000)
logger.debug("Trying {} waters with potassium...".format(waters))
sys = TLeap()
sys.template_file = os.path.join(
os.path.dirname(__file__), "../data/cb6-but/tleap_solvate.in"
)
sys.output_path = "tmp"
sys.loadpdb_file = os.path.join(
os.path.dirname(__file__), "../data/cb6-but/cb6-but.pdb"
)
sys.target_waters = waters
sys.output_prefix = "solvate"
sys.counter_cation = "K+"
sys.build()
potassium = sp.check_output(
["grep -oh 'K+' ./tmp/solvate.prmtop | wc -w"], shell=True
)
assert int(potassium) == 0
def test_solvation_spatial_size(clean_files):
""" Test that we can solvate CB6-BUT with an buffer size in Angstroms. """
random_int = np.random.randint(10, 20)
random_size = random_int * np.random.random_sample(1) + random_int
logger.debug("Trying buffer size of {} A...".format(random_size[0]))
sys = TLeap()
sys.template_file = os.path.join(
os.path.dirname(__file__), "../data/cb6-but/tleap_solvate.in"
)
sys.output_path = "tmp"
sys.loadpdb_file = os.path.join(
os.path.dirname(__file__), "../data/cb6-but/cb6-but.pdb"
)
sys.buffer_value = float(random_size[0])
sys.output_prefix = "solvate"
sys.pbc_type = PBCBox.cubic
sys.build()
grepped_waters = sp.check_output(
["grep -oh 'WAT' ./tmp/solvate.prmtop | wc -w"], shell=True
)
assert int(grepped_waters) == sys.target_waters
def test_multiple_pdb_files(clean_files):
"""
Test that multiple `loadpdb` lines are carried through.
Reference: https://github.com/slochower/pAPRika/issues/141
"""
temporary_directory = os.path.join(os.path.dirname(__file__), "tmp")
sys = TLeap()
cb6_frcmod = os.path.abspath(
os.path.join(os.path.dirname(__file__), "../data/cb6-but/cb6.frcmod")
)
cb6_mol2 = os.path.abspath(
os.path.join(os.path.dirname(__file__), "../data/cb6-but/cb6.mol2")
)
but_frcmod = os.path.abspath(
os.path.join(os.path.dirname(__file__), "../data/cb6-but/but.frcmod")
)
but_mol2 = os.path.abspath(
os.path.join(os.path.dirname(__file__), "../data/cb6-but/but.mol2")
)
sys.template_lines = [
"source leaprc.gaff",
f"loadamberparams {cb6_frcmod}",
f"CB6 = loadmol2 {cb6_mol2}",
f"loadamberparams {but_frcmod}",
f"BUT = loadmol2 {but_mol2}",
"a = loadpdb cb6-but-notcentered.pdb",
"b = loadpdb cb6-but-minimized.pdb",
"model = combine { a b }",
]
sys.output_path = temporary_directory
sys.output_prefix = "multi"
sys.pbc_type = None
sys.neutralize = False
sys.build(clean_files=False)
with open(f"{temporary_directory}/multi.tleap.in", "r") as f:
lines = f.read()
assert "a = loadpdb cb6-but-notcentered.pdb" in lines
assert "b = loadpdb cb6-but-minimized.pdb" in lines
assert "combine" in lines
assert "savepdb model multi.pdb" in lines
def test_solvation_simple(clean_files):
""" Test that we can solvate CB6-BUT using default settings. """
waters = np.random.randint(100, 10000)
logger.debug("Trying {} waters with default settings...".format(waters))
sys = TLeap()
sys.template_file = os.path.join(
os.path.dirname(__file__), "../data/cb6-but/tleap_solvate.in"
)
sys.output_path = "tmp"
sys.target_waters = waters
sys.output_prefix = "solvate"
sys.build()
grepped_waters = sp.check_output(
["grep -oh 'WAT' ./tmp/solvate.prmtop | wc -w"], shell=True
)
assert int(grepped_waters) == waters
def test_alignment_workflow(clean_files):
""" Test that we can solvate CB6-BUT after alignment. """
cb6 = pmd.load_file(
os.path.join(
os.path.dirname(__file__), "../data/cb6-but/cb6-but-notcentered.pdb"
)
)
zalign(cb6, ":CB6", ":BUT", save=True, filename="./tmp/tmp.pdb")
waters = np.random.randint(1000, 10000)
sys = TLeap()
sys.template_file = os.path.join(
os.path.dirname(__file__), "../data/cb6-but/tleap_solvate.in"
)
sys.output_path = "tmp"
sys.loadpdb_file = "tmp.pdb"
sys.target_waters = waters
sys.output_prefix = "solvate"
sys.build()
logger.debug("Trying {} waters after alignment...".format(waters))
grepped_waters = sp.check_output(
["grep -oh 'WAT' ./tmp/solvate.prmtop | wc -w"], shell=True
)
assert int(grepped_waters) == waters
def test_add_dummy(clean_files):
""" Test that dummy atoms get added correctly """
temporary_directory = os.path.join(os.path.dirname(__file__), "tmp")
host_guest = pmd.load_file(
os.path.join(
os.path.dirname(__file__), "../data/cb6-but/cb6-but-notcentered.pdb"
),
structure=True,
)
host_guest = zalign(host_guest, ":BUT@C", ":BUT@C3", save=False)
host_guest = add_dummy(host_guest, residue_name="DM1", z=-11.000, y=2.000, x=-1.500)
host_guest.write_pdb(
os.path.join(temporary_directory, "cb6-but-dum.pdb"), renumber=False
)
with open(os.path.join(temporary_directory, "cb6-but-dum.pdb"), "r") as f:
lines = f.readlines()
test_line1 = lines[123].rstrip()
test_line2 = lines[124].rstrip()
ref_line1 = "TER 123 BUT 2"
ref_line2 = (
"HETATM 123 DUM DM1 3 -1.500 2.000 -11.000 0.00 0.00 PB"
)
assert ref_line1 == test_line1
assert ref_line2 == test_line2
write_dummy_frcmod(path=temporary_directory)
write_dummy_mol2(path=temporary_directory, filename="dm1.mol2", residue_name="DM1")
sys = TLeap()
cb6_frcmod = os.path.abspath(
os.path.join(os.path.dirname(__file__), "../data/cb6-but/cb6.frcmod")
)
cb6_mol2 = os.path.abspath(
os.path.join(os.path.dirname(__file__), "../data/cb6-but/cb6.mol2")
)
but_frcmod = os.path.abspath(
os.path.join(os.path.dirname(__file__), "../data/cb6-but/but.frcmod")
)
but_mol2 = os.path.abspath(
os.path.join(os.path.dirname(__file__), "../data/cb6-but/but.mol2")
)
sys.template_lines = [
"source leaprc.gaff",
f"loadamberparams {cb6_frcmod}",
f"CB6 = loadmol2 {cb6_mol2}",
f"loadamberparams {but_frcmod}",
f"BUT = loadmol2 {but_mol2}",
"loadamberparams dummy.frcmod",
"DM1 = loadmol2 dm1.mol2",
"model = loadpdb cb6-but-dum.pdb",
]
sys.output_path = temporary_directory
sys.output_prefix = "cb6-but-dum"
sys.pbc_type = None
sys.neutralize = False
sys.build()
with open(
os.path.join(os.path.dirname(__file__), "../data/cb6-but/REF_cb6-but-dum.rst7"),
"r",
) as f:
contents = f.read()
reference = [float(i) for i in contents.split()[2:]]
with open(os.path.join(temporary_directory, "cb6-but-dum.rst7"), "r") as f:
contents = f.read()
new = [float(i) for i in contents.split()[2:]]
assert np.allclose(reference, new)
def test_solvation_water_model(water_model, clean_files):
""" Test that we can solvate CB6-BUT with a truncated octahedron. """
waters = np.random.randint(1000, 10000)
logger.debug("Trying {} waters in a truncated octahedron...".format(waters))
sys = TLeap()
sys.output_path = "tmp"
sys.loadpdb_file = os.path.join(
os.path.dirname(__file__), "../data/cb6-but/cb6-but.pdb"
)
sys.target_waters = waters
sys.output_prefix = "solvate"
sys.pbc_type = PBCBox.cubic
sys.set_water_model(water_model)
sys.template_lines = [
"source leaprc.protein.ff14SB",
"source leaprc.gaff",
"loadamberparams ../paprika/data/cb6-but/cb6.frcmod",
"CB6 = loadmol2 ../paprika/data/cb6-but/cb6.mol2",
"loadamberparams ../paprika/data/cb6-but/but.frcmod",
"BUT = loadmol2 ../paprika/data/cb6-but/but.mol2",
"model = loadpdb ../paprika/data/cb6-but/cb6-but.pdb",
]
sys.build()
grepped_waters = sp.check_output(
["grep -oh 'WAT' ./tmp/solvate.prmtop | wc -w"], shell=True
)
assert int(grepped_waters) == waters
def test_ion_solvation(clean_files):
""" Test that tleap module is solvating an ion properly."""
temporary_directory = os.path.join(os.path.dirname(__file__), "tmp")
ions = ["Na+", "Cl-"]
for ion in ions:
# Write PDB file
with open(os.path.join(temporary_directory, "ion.pdb"), "w") as f:
f.writelines(
"CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 1\n"
)
f.writelines(
f"ATOM 1 {ion:3s} {ion:3s} 1 0.000 0.000 0.000 1.00 0.00\n"
)
f.writelines("END")
# Write MOL2 file
with open(os.path.join(temporary_directory, "ion.mol2"), "w") as f:
charge = 1.0 if "+" in ion else -1.0
gaff_type = ion.split("+" if "+" in ion else "-")[0].lower()
f.writelines("@<TRIPOS>MOLECULE\n")
f.writelines(f"{ion}\n")
f.writelines("1 0 1 0 0\n")
f.writelines("SMALL\n")
f.writelines("No Charge or Current Charge\n\n\n")
f.writelines("@<TRIPOS>ATOM\n")
f.writelines(
f" 1 {ion:3s} 0.0000 0.0000 0.0000 {gaff_type} 1 {ion} {charge:.6f}\n"
)
f.writelines("@<TRIPOS>BOND\n")
f.writelines("@<TRIPOS>SUBSTRUCTURE\n")
f.writelines(
f" 1 {ion:3s} 1 TEMP 0 **** **** 0 ROOT"
)
# Run tleap
ion_sys = TLeap()
ion_sys.output_path = temporary_directory
ion_sys.target_waters = 1000
ion_sys.pbc_type = PBCBox.cubic
ion_sys.neutralize = False
ion_sys.template_lines = [
"source leaprc.gaff",
"source leaprc.water.tip3p",
f"{ion} = loadmol2 ion.mol2",
"model = loadpdb ion.pdb",
]
ion_sys.build()
# Make sure Amber files are generated
assert (
is_file_and_not_empty(os.path.join(temporary_directory, "build.prmtop"))
is True
)
assert (
is_file_and_not_empty(os.path.join(temporary_directory, "build.rst7"))
is True
)
# Check number of atoms in files
structure = pmd.load_file(
os.path.join(temporary_directory, "build.prmtop"),
os.path.join(temporary_directory, "build.rst7"),
)
assert len(structure.atoms) == 3001
def test_conversions(clean_files):
""" Test that conversion methods work in Tleap module. """
temporary_directory = os.path.join(os.path.dirname(__file__), "tmp")
but_frcmod = os.path.abspath(
os.path.join(os.path.dirname(__file__), "../data/cb6-but/but.frcmod")
)
but_mol2 = os.path.abspath(
os.path.join(os.path.dirname(__file__), "../data/cb6-but/but.mol2")
)
sys = TLeap()
sys.template_lines = [
"source leaprc.gaff",
f"loadamberparams {but_frcmod}",
f"BUT = loadmol2 {but_mol2}",
f"model = loadmol2 {but_mol2}",
]
sys.output_path = temporary_directory
sys.output_prefix = "but"
sys.pbc_type = None
sys.neutralize = False
sys.build()
from paprika.build.system.utils import ConversionToolkit
from paprika.utils import is_file_and_not_empty
# Gromacs ParmEd test
sys.convert_to_gromacs(overwrite=True)
top_file = os.path.join(sys.output_path, sys.output_prefix + ".top")
gro_file = os.path.join(sys.output_path, sys.output_prefix + ".gro")
assert is_file_and_not_empty(top_file) is True
assert is_file_and_not_empty(gro_file) is True
# Gromacs InterMol test
sys.convert_to_gromacs(toolkit=ConversionToolkit.InterMol)
assert is_file_and_not_empty(top_file) is True
assert is_file_and_not_empty(gro_file) is True
top_file = os.path.join(sys.output_path, sys.output_prefix + "_from_amber.top")
gro_file = os.path.join(sys.output_path, sys.output_prefix + "_from_amber.gro")
assert is_file_and_not_empty(top_file) is True
assert is_file_and_not_empty(gro_file) is True
# CHARMM ParmEd test
sys.convert_to_charmm()
psf_file = os.path.join(sys.output_path, sys.output_prefix + ".psf")
crd_file = os.path.join(sys.output_path, sys.output_prefix + ".crd")
assert is_file_and_not_empty(psf_file) is True
assert is_file_and_not_empty(crd_file) is True
# CHARMM Intermol test
sys.convert_to_charmm(toolkit=ConversionToolkit.InterMol)
rtf_file = os.path.join(sys.output_path, sys.output_prefix + ".rtf")
prm_file = os.path.join(sys.output_path, sys.output_prefix + ".prm")
assert is_file_and_not_empty(psf_file) is True
assert is_file_and_not_empty(crd_file) is True
assert is_file_and_not_empty(rtf_file) is True
assert is_file_and_not_empty(prm_file) is True
# LAMMPS test
sys.convert_to_lammps()
input_file = os.path.join(sys.output_path, sys.output_prefix + ".input")
lmp_file = os.path.join(sys.output_path, sys.output_prefix + ".lmp")
assert is_file_and_not_empty(input_file) is True
assert is_file_and_not_empty(lmp_file) is True
# DESMOND test
sys.convert_to_desmond()
cms_file = os.path.join(sys.output_path, sys.output_prefix + ".cms")
assert is_file_and_not_empty(cms_file) is True
def test_hydrogen_mass_repartitioning(clean_files):
""" Test that hydrogen mass is repartitioned. """
temporary_directory = os.path.join(os.path.dirname(__file__), "tmp")
sys = TLeap()
but_frcmod = os.path.abspath(
os.path.join(os.path.dirname(__file__), "../data/cb6-but/but.frcmod")
)
but_mol2 = os.path.abspath(
os.path.join(os.path.dirname(__file__), "../data/cb6-but/but.mol2")
)
sys.template_lines = [
"source leaprc.gaff",
f"loadamberparams {but_frcmod}",
f"BUT = loadmol2 {but_mol2}",
f"model = loadmol2 {but_mol2}",
]
sys.output_path = temporary_directory
sys.output_prefix = "but"
sys.pbc_type = None
sys.neutralize = False
sys.build()
but = pmd.load_file(
os.path.join(temporary_directory, sys.output_prefix + ".prmtop")
)
assert np.allclose(but["@H="].atoms[0].mass, 1.008)
sys.repartition_hydrogen_mass()
but = pmd.load_file(
os.path.join(temporary_directory, sys.output_prefix + ".prmtop")
)
assert np.allclose(but["@H="].atoms[0].mass, 3.024)
def test_solvation_by_M_and_m(clean_files):
""" Test that we can solvate CB6-BUT through molarity and molality. """
logger.debug("Trying 10 A buffer with 150 mM NaCl...")
sys = TLeap()
sys.template_file = os.path.join(
os.path.dirname(__file__), "../data/cb6-but/tleap_solvate.in"
)
sys.output_path = "tmp"
sys.loadpdb_file = os.path.join(
os.path.dirname(__file__), "../data/cb6-but/cb6-but.pdb"
)
sys.buffer_value = 10.0
sys.output_prefix = "solvate"
sys.neutralize = False
sys.pbc_type = PBCBox.rectangular
sys.add_ions = ["NA", "0.150M", "CL", "0.150M", "K", "0.100m", "BR", "0.100m"]
sys.build(clean_files=False)
# Molarity Check
obs_num_na = sp.check_output(
["grep -A 99 RESIDUE_LABEL ./tmp/solvate.prmtop | " + "grep -oh 'NA ' | wc -w"],
shell=True,
)
obs_num_cl = sp.check_output(
["grep -A 99 RESIDUE_LABEL ./tmp/solvate.prmtop | " + "grep -oh 'CL ' | wc -w"],
shell=True,
)
volume = sys.get_volume()
volume_in_liters = volume * ANGSTROM_CUBED_TO_LITERS
calc_num_na = np.ceil((6.022 * 10 ** 23) * 0.150 * volume_in_liters)
calc_num_cl = np.ceil((6.022 * 10 ** 23) * 0.150 * volume_in_liters)
assert int(obs_num_na) == int(calc_num_na)
assert int(obs_num_cl) == int(calc_num_cl)
# Molality Check
obs_num_k = sp.check_output(
["grep -A 99 RESIDUE_LABEL ./tmp/solvate.prmtop | " + "grep -oh 'K ' | wc -w"],
shell=True,
)
obs_num_br = sp.check_output(
["grep -A 99 RESIDUE_LABEL ./tmp/solvate.prmtop | " + "grep -oh 'BR ' | wc -w"],
shell=True,
)
calc_num_waters = sys.count_residues()["WAT"]
calc_num_k = np.ceil(0.100 * calc_num_waters * 0.018)
calc_num_br = np.ceil(0.100 * calc_num_waters * 0.018)
assert int(obs_num_k) == int(calc_num_k)
assert int(obs_num_br) == int(calc_num_br)
def test_solvation_with_additional_ions(clean_files):
""" Test that we can solvate CB6-BUT with additional ions. """
waters = np.random.randint(1000, 10000)
cations = ["LI", "Na+", "K+", "RB", "CS"]
anions = ["F", "Cl-", "BR", "IOD"]
n_cations = np.random.randint(1, 10)
n_anions = np.random.randint(1, 10)
random_cation = random.choice(cations)
random_anion = random.choice(anions)
logger.debug("Trying {} waters with additional ions...".format(waters))
sys = TLeap()
sys.template_file = os.path.join(
os.path.dirname(__file__), "../data/cb6-but/tleap_solvate.in"
)
sys.output_path = "tmp"
sys.loadpdb_file = os.path.join(
os.path.dirname(__file__), "../data/cb6-but/cb6-but.pdb"
)
sys.target_waters = waters
sys.output_prefix = "solvate"
sys.neutralize = False
sys.add_ions = [random_cation, n_cations, random_anion, n_anions]
sys.build()
# These should come in the RESIDUE_LABEL region of the prmtop and be before all the water.
cation_number = sp.check_output(
[
"grep -A 99 RESIDUE_LABEL ./tmp/solvate.prmtop | "
+ "grep -oh '{} ' | wc -w".format(random_cation)
],
shell=True,
)
anion_number = sp.check_output(
[
"grep -A 99 RESIDUE_LABEL ./tmp/solvate.prmtop | "
+ "grep -oh '{} ' | wc -w".format(random_anion)
],
shell=True,
)
logger.debug("Expecting...")
logger.debug("cation = {}\tn_cations={}".format(random_cation, n_cations))
logger.debug("anion = {}\t n_anions={}".format(random_anion, n_anions))
logger.debug("Found...")
logger.debug(" n_cations={}".format(cation_number))
logger.debug(" n_anions={}".format(anion_number))
assert int(cation_number) == n_cations and int(anion_number) == n_anions
def test_solvation_bind3p(clean_files):
logger.debug("Solvating with 500 Bind3P waters in a truncated octahedron...")
sys = TLeap()
sys.output_path = "tmp"
sys.loadpdb_file = os.path.join(
os.path.dirname(__file__), "../data/cb6-but/cb6-but.pdb"
)
sys.target_waters = 2000
sys.output_prefix = "solvate"
sys.pbc_type = PBCBox.cubic
sys.set_water_model("tip3p", model_type="bind3p")
sys.template_lines = [
"source leaprc.gaff",
"loadamberparams ../paprika/data/cb6-but/cb6.frcmod",
"CB6 = loadmol2 ../paprika/data/cb6-but/cb6.mol2",
"BUT = loadmol2 ../paprika/data/cb6-but/but.mol2",
"model = loadpdb ../paprika/data/cb6-but/cb6-but.pdb",
]
sys.build()
prmtop = os.path.join("./tmp/solvate.prmtop")
inpcrd = os.path.join("./tmp/solvate.rst7")
structure = pmd.load_file(prmtop, inpcrd, structure=True)
water_index = [
atom.index
for atom in structure.topology.atoms()
if atom.residue.name == "WAT" and atom.residue.index == 10
]
system = structure.createSystem()
nonbonded = [
force for force in system.getForces() if isinstance(force, NonbondedForce)
][0]
oxygen = nonbonded.getParticleParameters(water_index[0])
assert (
pytest.approx(oxygen[1].value_in_unit(unit.angstrom) - 3.1319, abs=1e-3) == 0.0
)
assert (
pytest.approx(
oxygen[2].value_in_unit(unit.kilocalorie_per_mole) - 0.1818, abs=1e-3
)
== 0.0
)