Merge pull request #123 from cbc-univie/moving_function

Another Cleanup
cbc-univie · Jan 18, 2024 · 96417e1 · 96417e1
2 parents 170802a + 9ff54d4
commit 96417e1
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Showing 3 changed files with 99 additions and 109 deletions.
diff --git a/transformato/mutate.py b/transformato/mutate.py
@@ -2240,75 +2240,3 @@ def _modify_type(atom, psf, atom_type_suffix: str):
                 new_type = f"{atom_type_suffix}{psf.mutations_to_default}"
 
             atom.type = new_type
-
-
-def mutate_pure_tautomers(
-    s1_to_s2: ProposeMutationRoute,
-    system1: SystemStructure,
-    system2: SystemStructure,
-    configuration,
-    single_state=False,
-    nr_of_bonded_windows: int = 4,
-):
-    from transformato import (
-        IntermediateStateFactory,
-    )
-
-    # setup mutation and StateFactory
-    mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1()
-    i_tautomer1 = IntermediateStateFactory(
-        system=system1,
-        configuration=configuration,
-    )
-
-    # write out states
-    # start with charge
-    charges = mutation_list["charge"]
-    for lambda_value in np.linspace(1, 0, 2):
-        # turn off charges
-        i_tautomer1.write_state(
-            mutation_conf=charges,
-            lambda_value_electrostatic=lambda_value,
-        )
-        if single_state:
-            return (i_tautomer1.output_files, [])
-
-    # turn off the lj of the hydrogen
-    lj = mutation_list["lj"]
-    i_tautomer1.write_state(
-        mutation_conf=lj,
-        lambda_value_vdw=0.0,
-    )
-
-    # transform common core
-    for lambda_value in np.linspace(1, 0, nr_of_bonded_windows + 1)[1:]:
-        # turn off charges
-        i_tautomer1.write_state(
-            mutation_conf=mutation_list["transform"],
-            common_core_transformation=lambda_value,
-        )
-
-    # setup other tautomer
-    mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol2()
-    i_tautomer2 = IntermediateStateFactory(
-        system=system2,
-        configuration=configuration,
-    )
-    # write out states
-    # start with charge
-    charges = mutation_list["charge"]
-    for lambda_value in np.linspace(1, 0, 2):
-        # turn off charges
-        i_tautomer2.write_state(
-            mutation_conf=charges,
-            lambda_value_electrostatic=lambda_value,
-        )
-
-    # turn off the lj of the hydrogen
-    lj = mutation_list["lj"]
-    i_tautomer2.write_state(
-        mutation_conf=lj,
-        lambda_value_vdw=0.0,
-    )
-
-    return (i_tautomer1.output_files, i_tautomer2.output_files)
diff --git a/transformato/tests/test_alchemical_path_generation.py b/transformato/tests/test_alchemical_path_generation.py
@@ -45,37 +45,6 @@ def test_generate_alchemical_path_acetylaceton_methyl_common_core():
     mutate_acetylaceton_methyl_common_core(configuration=configuration)
 
 
-@pytest.mark.rbfe
-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,
-    )
-
-
 @pytest.mark.rsfe
 def test_generate_alchemical_path_for_acetylacetone_tautomer_pair(caplog):
     caplog.set_level(logging.WARNING)

diff --git a/transformato/tests/test_mutation.py b/transformato/tests/test_mutation.py
@@ -26,6 +26,78 @@
 )
 
 
+def mutate_pure_tautomers(
+    s1_to_s2: ProposeMutationRoute,
+    system1: SystemStructure,
+    system2: SystemStructure,
+    configuration,
+    single_state=False,
+    nr_of_bonded_windows: int = 4,
+):
+    from transformato import (
+        IntermediateStateFactory,
+    )
+
+    # setup mutation and StateFactory
+    mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1()
+    i_tautomer1 = IntermediateStateFactory(
+        system=system1,
+        configuration=configuration,
+    )
+
+    # write out states
+    # start with charge
+    charges = mutation_list["charge"]
+    for lambda_value in np.linspace(1, 0, 2):
+        # turn off charges
+        i_tautomer1.write_state(
+            mutation_conf=charges,
+            lambda_value_electrostatic=lambda_value,
+        )
+        if single_state:
+            return (i_tautomer1.output_files, [])
+
+    # turn off the lj of the hydrogen
+    lj = mutation_list["lj"]
+    i_tautomer1.write_state(
+        mutation_conf=lj,
+        lambda_value_vdw=0.0,
+    )
+
+    # transform common core
+    for lambda_value in np.linspace(1, 0, nr_of_bonded_windows + 1)[1:]:
+        # turn off charges
+        i_tautomer1.write_state(
+            mutation_conf=mutation_list["transform"],
+            common_core_transformation=lambda_value,
+        )
+
+    # setup other tautomer
+    mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol2()
+    i_tautomer2 = IntermediateStateFactory(
+        system=system2,
+        configuration=configuration,
+    )
+    # write out states
+    # start with charge
+    charges = mutation_list["charge"]
+    for lambda_value in np.linspace(1, 0, 2):
+        # turn off charges
+        i_tautomer2.write_state(
+            mutation_conf=charges,
+            lambda_value_electrostatic=lambda_value,
+        )
+
+    # turn off the lj of the hydrogen
+    lj = mutation_list["lj"]
+    i_tautomer2.write_state(
+        mutation_conf=lj,
+        lambda_value_vdw=0.0,
+    )
+
+    return (i_tautomer1.output_files, i_tautomer2.output_files)
+
+
 def read_params(output_file_base):
     extlist = ["rtf", "prm", "str"]
     print(output_file_base)
@@ -97,8 +169,6 @@ def generate_system(output_file_base, env):
 def setup_acetylacetone_tautomer_pair(
     configuration: dict, single_state=False, nr_of_bonded_windows=4
 ):
-    from ..mutate import mutate_pure_tautomers
-
     s1 = SystemStructure(configuration, "structure1")
     s2 = SystemStructure(configuration, "structure2")
     s1_to_s2 = ProposeMutationRoute(s1, s2)
@@ -382,6 +452,33 @@ def test_mutation_with_multiple_dummy_regions(caplog):
     s1_to_s2.finish_common_core()
 
 
+@pytest.mark.rbfe
+def test_rbfe_mutate_2oj9():
+    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,
+    )
+
+
 @pytest.mark.rsfe
 @pytest.mark.skipif(
     os.getenv("CI") == "true",
@@ -1833,8 +1930,6 @@ def test_vdw_mutation_for_hydrogens_and_heavy_atoms():
 def setup_2OJ9_tautomer_pair_rsfe(
     configuration: dict, single_state=False, nr_of_bonded_windows: int = 4
 ):
-    from ..mutate import mutate_pure_tautomers
-
     s1 = SystemStructure(configuration, "structure1")
     s2 = SystemStructure(configuration, "structure2")
     s1_to_s2 = ProposeMutationRoute(s1, s2)
@@ -1856,8 +1951,6 @@ def setup_2OJ9_tautomer_pair_rsfe(
 def setup_2OJ9_tautomer_pair_rbfe(
     configuration: dict, single_state: bool = False, nr_of_bonded_windows: int = 4
 ):
-    from ..mutate import mutate_pure_tautomers
-
     s1 = SystemStructure(configuration, "structure1")
     s2 = SystemStructure(configuration, "structure2")
     s1_to_s2 = ProposeMutationRoute(s1, s2)