def test_initialize_systems(caplog):
caplog.set_level(logging.DEBUG)
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/test-toluene-methane-rsfe.yaml",
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
s1 = SystemStructure(configuration, "structure1")
assert int(s1.offset["waterbox"]) == 0
assert int(s1.offset["vacuum"]) == 0
s2 = SystemStructure(configuration, "structure2")
assert int(s2.offset["waterbox"]) == 0
assert int(s2.offset["vacuum"]) == 0
assert "vacuum" in s1.envs and "vacuum" in s2.envs
assert "waterbox" in s1.envs and "waterbox" in s2.envs
configuration = load_config_yaml(
config=
f"{get_testsystems_dir()}/config/test-2oj9-tautomer-pair-rsfe.yaml",
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
s1 = SystemStructure(configuration, "structure1")
assert int(s1.offset["waterbox"]) == 0
assert int(s1.offset["vacuum"]) == 0
s2 = SystemStructure(configuration, "structure2")
assert int(s2.offset["waterbox"]) == 0
assert int(s2.offset["vacuum"]) == 0
def test_generate_alchemical_path_for_methanol_common_core():
from transformato_testsystems.testsystems import perform_generic_mutation
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/test-methanol-methane-rsfe.yaml",
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
s1 = SystemStructure(configuration, "structure1")
s2 = SystemStructure(configuration, "structure2")
s1_to_s2 = ProposeMutationRoute(s1, s2)
s1_to_s2.calculate_common_core()
mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1()
i = IntermediateStateFactory(
system=s1,
configuration=configuration,
)
perform_mutations(
configuration=configuration,
i=i,
mutation_list=mutation_list,
nr_of_mutation_steps_charge=3,
)
assert len(i.output_files) == 11
def test_rbfe_mutate_2oj9():
from transformato import (ProposeMutationRoute, SystemStructure,
load_config_yaml)
from ..mutate import mutate_pure_tautomers
conf = f"{get_testsystems_dir()}/config/test-2oj9-tautomer-pair-rbfe.yaml"
configuration = load_config_yaml(
config=conf,
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
s1 = SystemStructure(configuration, "structure1")
s2 = SystemStructure(configuration, "structure2")
s1_to_s2 = ProposeMutationRoute(s1, s2)
s1_to_s2.calculate_common_core()
return (
mutate_pure_tautomers(
s1_to_s2,
s1,
s2,
configuration,
nr_of_bonded_windows=4,
),
configuration,
s1_to_s2,
)
def test_lonepairs_in_common_core():
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/tyk2-ejm_45_ejm_42.yaml",
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
s1 = SystemStructure(configuration, "structure1")
s2 = SystemStructure(configuration, "structure2")
s1_to_s2 = ProposeMutationRoute(s1, s2)
s1_to_s2.propose_common_core()
s1_to_s2.finish_common_core()
mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1()
i = IntermediateStateFactory(
system=s1,
configuration=configuration,
)
# check for ligand 1
cc_region = s1_to_s2.get_common_core_idx_mol1()
assert (39 in cc_region and 40 in cc_region) == True
perform_mutations(configuration=configuration,
i=i,
mutation_list=mutation_list)
# check for ligand 2
cc_region2 = s1_to_s2.get_common_core_idx_mol2()
assert (35 in cc_region2 and 36 in cc_region2) == True
def test_setup_system_for_methane_common_core_with_HMR():
from transformato_testsystems.testsystems import perform_generic_mutation
configuration = load_config_yaml(
config=
f"{get_testsystems_dir()}/config/test-toluene-methane-rsfe-HMR.yaml",
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
output_files = perform_generic_mutation(configuration=configuration)
assert len(output_files) == 3
# set up openMM system
base = f"{get_test_output_dir()}/toluene-methane-rsfe/methane/intst3/"
import sys
# sys.path is a list of absolute path strings
sys.path.append(base)
system, psf = generate_openMM_system_using_cgui_scripts(base)
# enumearte and iterate over all constraints in the system
for cons_idx in range(system.getNumConstraints()):
idx1, idx2, value = system.getConstraintParameters(cons_idx)
print(
f"{psf.atom_list[idx1]}: {system.getParticleMass(idx1)}; {psf.atom_list[idx2]}: {system.getParticleMass(idx2)}"
)
print(value)
print("Finsihed.")
assert system.getNumConstraints() == 2557
def test_lonepairs_in_dummy_region():
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/jnk1-17124-18631.yaml",
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
s1 = SystemStructure(configuration, "structure1")
s2 = SystemStructure(configuration, "structure2")
s1_to_s2 = ProposeMutationRoute(s1, s2)
s1_to_s2.propose_common_core()
s1_to_s2.finish_common_core()
mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1()
i = IntermediateStateFactory(
system=s1,
configuration=configuration,
)
assert s1_to_s2.dummy_region_cc1.connected_dummy_regions == [
[46, 22],
[45, 44, 43, 26, 25],
]
perform_mutations(configuration=configuration,
i=i,
mutation_list=mutation_list)
mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol2()
assert s1_to_s2.dummy_region_cc2.connected_dummy_regions == [[39], [40]]
def test_run_1a0q_1a07_rsfe_with_openMM(caplog):
import logging
# Test that TF can handel multiple dummy regions
caplog.set_level(logging.DEBUG)
import warnings
from transformato import (
load_config_yaml,
SystemStructure,
IntermediateStateFactory,
ProposeMutationRoute,
)
from transformato.mutate import perform_mutations
warnings.filterwarnings("ignore", module="parmed")
workdir = get_test_output_dir()
conf = f"{get_testsystems_dir()}/config/test-1a0q-1a07-rsfe.yaml"
configuration = load_config_yaml(
config=conf, input_dir="data/test_systems_mutation", output_dir=workdir
)
s1 = SystemStructure(configuration, "structure1")
s2 = SystemStructure(configuration, "structure2")
s1_to_s2 = ProposeMutationRoute(s1, s2)
s1_to_s2.propose_common_core()
s1_to_s2.finish_common_core()
# generate the mutation list for the original
mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1()
print(mutation_list.keys())
i = IntermediateStateFactory(
system=s1,
configuration=configuration,
)
perform_mutations(configuration=configuration, i=i, mutation_list=mutation_list)
run_simulation(i.output_files, engine="openMM")
def test_generate_alchemical_path_for_toluene_commmon_core():
from transformato_testsystems.testsystems import \
mutate_toluene_to_methane_cc
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/test-toluene-methane-rsfe.yaml",
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
output_files = mutate_toluene_to_methane_cc(configuration=configuration)
assert len(output_files) == 16
with open(
f"{get_test_output_dir()}/toluene-methane-rsfe/toluene/intst1/openmm_run.py",
"r",
) as f:
i = 0
for line in f.readlines():
if "# Set platform" in line and i == 0:
i += 1
elif i == 1:
assert "CPU" in line
print(line)
i += 1
def test_change_platform():
from transformato.constants import (
change_platform_to_test_platform,
test_platform_openMM,
test_platform_CHARMM,
)
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/test-toluene-methane-rsfe.yaml",
input_dir=".",
output_dir=get_test_output_dir(),
)
change_platform_to_test_platform(configuration, engine="openMM")
print(configuration["simulation"]["GPU"])
print(test_platform_openMM)
if test_platform_openMM.upper() == "CPU":
assert configuration["simulation"]["GPU"] == False
else:
assert configuration["simulation"]["GPU"] == True
change_platform_to_test_platform(configuration, engine="CHARMM")
print(configuration["simulation"]["GPU"])
print(test_platform_openMM)
if test_platform_CHARMM.upper() == "CPU":
assert configuration["simulation"]["GPU"] == False
else:
assert configuration["simulation"]["GPU"] == True
def test_generate_alchemical_path_for_7_CPI_to_common_core():
from transformato_testsystems.testsystems import mutate_7_CPI_to_2_CPI_cc
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/test-7-CPI-2-CPI-rsfe.yaml",
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
output_files = mutate_7_CPI_to_2_CPI_cc(configuration=configuration)
assert len(output_files) == 13
def test_generate_alchemical_path_acetylaceton_methyl_common_core():
from transformato_testsystems.testsystems import \
mutate_acetylaceton_methyl_common_core
conf = f"{get_testsystems_dir()}/config/test-acetylacetone-tautomer-rsfe.yaml"
configuration = load_config_yaml(
config=conf,
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
) # NOTE: for preprocessing input_dir is the output dir
mutate_acetylaceton_methyl_common_core(configuration=configuration)
def test_generate_alchemical_path_for_acetylacetone_tautomer_pair(caplog):
caplog.set_level(logging.WARNING)
from .test_mutation import setup_acetylacetone_tautomer_pair
conf = f"{get_testsystems_dir()}/config/test-acetylacetone-tautomer-rsfe.yaml"
configuration = load_config_yaml(
config=conf, input_dir=get_testsystems_dir(), output_dir=get_test_output_dir()
)
(output_files_t1, output_files_t2), _, _ = setup_acetylacetone_tautomer_pair(
configuration=configuration, nr_of_bonded_windows=8
)
def test_generate_alchemical_path_for_neopentane_common_core():
from transformato_testsystems.testsystems import \
mutate_neopentane_to_methane_cc
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/test-neopentane-methane-rsfe.yaml",
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
output_files = mutate_neopentane_to_methane_cc(configuration=configuration)
assert len(output_files) == 16
def test_run_methane_to_methane_cc_with_openMM():
from transformato.testsystems import mutate_methane_to_methane_cc
workdir = get_test_output_dir()
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/test-toluene-methane-rsfe.yaml",
input_dir="data/",
output_dir=workdir,
)
change_platform_to_test_platform(configuration=configuration, engine="openMM")
output_files = mutate_methane_to_methane_cc(configuration=configuration)
run_simulation(output_files)
def test_setup_system_for_methane_common_core():
from transformato_testsystems.testsystems import perform_generic_mutation
print(get_testsystems_dir())
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/test-toluene-methane-rsfe.yaml",
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
print(configuration)
output_files = perform_generic_mutation(configuration=configuration)
assert len(output_files) == 3
def test_io_psf_files():
from openmm.app import CharmmPsfFile
from transformato_testsystems.testsystems import mutate_toluene_to_methane_cc
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/test-toluene-methane-rsfe.yaml",
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
output_files = mutate_toluene_to_methane_cc(configuration=configuration)
output_path = output_files[0]
print(output_path)
CharmmPsfFile(f"{output_path}/lig_in_waterbox.psf")
CharmmPsfFile(f"{output_path}/lig_in_waterbox_corr.psf")
def test_run_methane_to_methane_common_core_with_CHARMM():
from transformato.testsystems import mutate_methane_to_methane_cc
workdir = get_test_output_dir()
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/test-toluene-methane-rsfe.yaml",
input_dir="data/",
output_dir=workdir,
)
change_platform_to_test_platform(configuration=configuration, engine="CHARMM")
output_files = mutate_methane_to_methane_cc(configuration=configuration)
run_simulation(output_files, engine="CHARMM")
f = "/".join(output_files[0].split("/")[:-3])
print(f)
shutil.rmtree(f)
def test_run_1a0q_1a07_rsfe_with_openMM(caplog):
# Test that TF can handel multiple dummy regions
caplog.set_level(logging.DEBUG)
conf = f"{get_testsystems_dir()}/config/test-1a0q-1a07-rsfe.yaml"
configuration = load_config_yaml(
config=conf, input_dir=get_testsystems_dir(), output_dir=get_test_output_dir()
)
s1 = SystemStructure(configuration, "structure1")
s2 = SystemStructure(configuration, "structure2")
s1_to_s2 = ProposeMutationRoute(s1, s2)
s1_to_s2.propose_common_core()
s1_to_s2.finish_common_core()
# generate the mutation list for the original
mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1()
print(mutation_list.keys())
i = IntermediateStateFactory(
system=s1,
configuration=configuration,
)
perform_mutations(configuration=configuration, i=i, mutation_list=mutation_list)
run_simulation(i.output_files, engine="openMM")
# Analysis with mda
ddG_openMM_mda, dddG_mda, f_openMM_mda = postprocessing(
configuration,
name="1a0q",
engine="openMM",
analyze_traj_with="mda",
num_proc=4,
max_snapshots=50,
)
print(f"Free energy difference using mda: {ddG_openMM_mda} +- {dddG_mda} [kT")
# Analysis with mdtraj
ddG_openMM_mtraj, dddG_mtraj, f_openMM_mtraj = postprocessing(
configuration,
name="1a0q",
engine="openMM",
max_snapshots=50,
)
print(
f"Free energy difference using mdtraj: {ddG_openMM_mtraj} +- {dddG_mtraj} [kT"
)
assert np.isclose(ddG_openMM_mda, ddG_openMM_mda, rtol=0.2)
assert np.isclose(dddG_mda, dddG_mda, rtol=0.2)
def test_run_2OJ9_tautomer_pair_with_openMM(caplog):
caplog.set_level(logging.WARNING)
from .test_mutation import setup_2OJ9_tautomer_pair_rbfe
workdir = get_test_output_dir()
conf = f"{get_testsystems_dir()}/config/test-2oj9-tautomer-pair-rsfe.yaml"
configuration = load_config_yaml(
config=conf, input_dir="data/", output_dir=workdir
) # NOTE: for preprocessing input_dir is the output dir
change_platform_to_test_platform(configuration=configuration, engine="openMM")
(output_files_t1, output_files_t2), _, _ = setup_2OJ9_tautomer_pair_rbfe(
configuration=configuration
)
run_simulation(output_files_t1)
run_simulation(output_files_t2)
def test_run_acetylacetone_tautomer_pair(caplog):
caplog.set_level(logging.WARNING)
from .test_mutation import setup_acetylacetone_tautomer_pair
workdir = get_test_output_dir()
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/test-acetylacetone-tautomer-rsfe.yaml",
input_dir="data/",
output_dir=workdir,
)
change_platform_to_test_platform(configuration=configuration, engine="openMM")
(output_files_t1, output_files_t2), _, _ = setup_acetylacetone_tautomer_pair(
configuration=configuration
)
run_simulation(output_files_t1)
run_simulation(output_files_t2)
def test_run_acetylacetone_tautomer_pair_only_in_vacuum(caplog):
caplog.set_level(logging.WARNING)
from .test_mutation import setup_acetylacetone_tautomer_pair
workdir = get_test_output_dir()
conf = f"{get_testsystems_dir()}/config/test-acetylacetone-tautomer-rsfe.yaml"
configuration = load_config_yaml(
config=conf, input_dir="data/", output_dir=workdir
) # NOTE: for preprocessing input_dir is the output dir
change_platform_to_test_platform(configuration=configuration, engine="openMM")
(output_files_t1, output_files_t2), _, _ = setup_acetylacetone_tautomer_pair(
configuration=configuration, nr_of_bonded_windows=16
)
run_simulation(output_files_t1, only_vacuum=True)
run_simulation(output_files_t2, only_vacuum=True)
def test_run_28_1h1q_rbfe_with_openMM():
# Generating output for a run of the CDK2 Ligand System
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/test-28_1h1q_rbfe.yaml",
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
s1 = SystemStructure(configuration, "structure1")
s2 = SystemStructure(configuration, "structure2")
s1_to_s2 = ProposeMutationRoute(s1, s2)
s1_to_s2.propose_common_core()
s1_to_s2.finish_common_core()
mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1()
print(mutation_list.keys())
i = IntermediateStateFactory(
system=s1,
configuration=configuration,
)
perform_mutations(
configuration=configuration,
i=i,
mutation_list=mutation_list,
nr_of_mutation_steps_charge=2,
nr_of_mutation_steps_cc=2,
)
run_simulation(i.output_files, engine="charmm")
from transformato.utils import postprocessing
ddG_openMM, dddG, f_openMM = postprocessing(
configuration,
name="cdk2-28",
engine="openMM",
max_snapshots=50,
num_proc=4,
analyze_traj_with="mda",
)
print(f"Free energy difference: {ddG_openMM} +- {dddG} [kT")
def test_generate_alchemical_path_for_1a0q_1a07(caplog):
# Test that TF can handel multiple dummy regions
caplog.set_level(logging.INFO)
conf = f"{get_testsystems_dir()}/config/test-1a0q-1a07-rsfe.yaml"
configuration = load_config_yaml(
config=conf, input_dir=get_testsystems_dir(), output_dir=get_test_output_dir()
)
s1 = SystemStructure(configuration, "structure1")
s2 = SystemStructure(configuration, "structure2")
s1_to_s2 = ProposeMutationRoute(s1, s2)
s1_to_s2.propose_common_core()
s1_to_s2.finish_common_core()
# generate the mutation list for the original
mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1()
print(mutation_list.keys())
i = IntermediateStateFactory(
system=s1,
configuration=configuration,
)
perform_mutations(configuration=configuration, i=i, mutation_list=mutation_list)
assert i.current_step == 24
def test_run_28_1h1q_rbfe_production_with_CHARMM():
# Generating output for a run of the CDK2 Ligand System
from transformato import (
IntermediateStateFactory,
ProposeMutationRoute,
SystemStructure,
load_config_yaml,
)
from transformato.mutate import perform_mutations
configuration = load_config_yaml(
config=f"{get_testsystems_dir()}/config/test-28_1h1q_rbfe.yaml",
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
)
s1 = SystemStructure(configuration, "structure1")
s2 = SystemStructure(configuration, "structure2")
s1_to_s2 = ProposeMutationRoute(s1, s2)
s1_to_s2.propose_common_core()
s1_to_s2.finish_common_core()
mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1()
print(mutation_list.keys())
i = IntermediateStateFactory(
system=s1,
configuration=configuration,
)
perform_mutations(
configuration=configuration,
i=i,
mutation_list=mutation_list,
nr_of_mutation_steps_charge=1,
nr_of_mutation_steps_cc=1,
)
def test_reading_of_coords():
env = "vacuum"
output_files_t1, _ = get_output_files_2oj9_tautomer_pair()
conf = f"{get_testsystems_dir()}/config/test-2oj9-tautomer-pair-rsfe.yaml"
configuration = load_config_yaml(
config=conf, input_dir=get_testsystems_dir(), output_dir=get_test_output_dir()
) # NOTE: for preprocessing input_dir is the output dir
b = output_files_t1[0]
print(b)
traj_load = md.load_dcd(
f"{b}/lig_in_{env}.dcd",
f"{b}/lig_in_{env}.psf",
)
print(traj_load.xyz[0])
traj_open = md.open(f"{b}/lig_in_{env}.dcd")
xyz, unitcell_lengths, _ = traj_open.read()
xyz = xyz / 10
print(xyz[0])
assert np.allclose(xyz[0], traj_load.xyz[0])
def test_run_28_1h1q_rsfe_analysis_with_CHARMM():
# Running the analysis, first the productions script needs to be finisehd
# Change output dir
# Check transformato/bin/charmm_eval_energy.sh for the correct name of the charmm
# executable!
from transformato import load_config_yaml
from transformato.utils import postprocessing
from transformato.utils import postprocessing
configuration = load_config_yaml(
input_dir=get_testsystems_dir(),
output_dir=get_test_output_dir(),
config=f"{get_testsystems_dir()}/config/test-28_1h1q_rbfe.yaml",
)
ddG_openMM, dddG, f_openMM = postprocessing(
configuration,
name="cdk2-28",
engine="CHARMM",
max_snapshots=10,
num_proc=1,
analyze_traj_with="mdtraj",
)
print(f"Free energy difference: {ddG_openMM} +- {dddG} [kT")
