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_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_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")