remove unused calls

cbc-univie · Oct 26, 2021 · fbfa10e · fbfa10e
1 parent 58e0d72
commit fbfa10e
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diff --git a/transformato/mutate.py b/transformato/mutate.py
@@ -1777,121 +1777,3 @@ def mutate_pure_tautomers(
     )
 
     return (i_tautomer1.output_files, i_tautomer2.output_files)
-
-
-def mutate_systems(
-    config: str,
-    nr_of_bonded_windows: int = 4,
-    input_dir: str = "../data/",
-    output_dir: str = ".",
-    connected_dummy_regions_cc1: list = [],
-    connected_dummy_regions_cc2: list = [],
-    el_nr_of_states: int = 5,
-):
-
-    from transformato import (
-        IntermediateStateFactory,
-        ProposeMutationRoute,
-        SystemStructure,
-        load_config_yaml,
-    )
-
-    configuration = load_config_yaml(
-        config=config, input_dir=input_dir, output_dir=output_dir
-    )
-    s1 = SystemStructure(configuration, "structure1")
-    s2 = SystemStructure(configuration, "structure2")
-    s1_to_s2 = ProposeMutationRoute(s1, s2)
-
-    # setup mutation route
-    if connected_dummy_regions_cc1:
-        s1_to_s2.propose_common_core()
-        s1_to_s2.finish_common_core(
-            connected_dummy_regions_cc1=connected_dummy_regions_cc1
-        )
-    elif connected_dummy_regions_cc2:
-        s1_to_s2.propose_common_core()
-        s1_to_s2.finish_common_core(
-            connected_dummy_regions_cc2=connected_dummy_regions_cc2
-        )
-    elif connected_dummy_regions_cc2 and connected_dummy_regions_cc1:
-        s1_to_s2.propose_common_core()
-        s1_to_s2.finish_common_core(
-            connected_dummy_regions_cc1=connected_dummy_regions_cc1,
-            connected_dummy_regions_cc2=connected_dummy_regions_cc2,
-        )
-    else:
-        raise RuntimeError()
-
-    # setup mutation and StateFactory
-    mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1()
-
-    # system 1
-    i = IntermediateStateFactory(
-        system=s1,
-        configuration=configuration,
-    )
-
-    # write out states
-    # start with charge
-    intst = 1
-    charges = mutation_list["charge"]
-    output_files_t1 = []
-    for lambda_value in np.linspace(1, 0, el_nr_of_states):
-        # turn off charges
-        o, intst = i.write_state(
-            mutation_conf=charges,
-            lambda_value_electrostatic=lambda_value,
-            intst_nr=intst,
-        )
-        output_files_t1.append(o)
-
-    # turn off the lj of the hydrogen
-    lj = mutation_list["lj"]
-    o, intst = i.write_state(
-        mutation_conf=lj,
-        lambda_value_vdw=0.0,
-        intst_nr=intst,
-    )
-    output_files_t1.append(o)
-
-    # transform common core
-    for lambda_value in np.linspace(1, 0, nr_of_bonded_windows + 1)[1:]:
-        # turn off charges
-        o, intst = i.write_state(
-            mutation_conf=mutation_list["transform"],
-            common_core_transformation=lambda_value,
-            intst_nr=intst,
-        )
-        output_files_t1.append(o)
-
-    # setup other tautomer
-    mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol2()
-    i = IntermediateStateFactory(
-        system=system2,
-        configuration=configuration,
-    )
-    # write out states
-    # start with charge
-    intst = 1
-    output_files_t2 = []
-    charges = mutation_list["charge"]
-    for lambda_value in np.linspace(1, 0, 2):
-        # turn off charges
-        o, intst = i.write_state(
-            mutation_conf=charges,
-            lambda_value_electrostatic=lambda_value,
-            intst_nr=intst,
-        )
-        output_files_t2.append(o)
-
-    # turn off the lj of the hydrogen
-    lj = mutation_list["lj"]
-    o, intst = i.write_state(
-        mutation_conf=lj,
-        lambda_value_vdw=0.0,
-        intst_nr=intst,
-    )
-    output_files_t2.append(o)
-
-    return (output_files_t1, output_files_t2)
diff --git a/transformato/state.py b/transformato/state.py
@@ -60,12 +60,6 @@ def write_state(
         common_core_transformation : float, optional
             [description], by default 1.0
 
-        Returns
-        -------
-        [type]
-            [description]
-        intst_nr : int
-            automatically incremented intst nr
         """
 
         logger.debug("#########################################")

diff --git a/transformato/tests/test_mutation.py b/transformato/tests/test_mutation.py
@@ -939,7 +939,6 @@ def test_vdw_mutation_for_hydrogens_system2():
             i.write_state(
                 mutation_conf=hydrogen_lj_mutations,
                 lambda_value_vdw=lambda_value,
-                intst_nr=0,
             )
             print("Set epsilon/rmin for selected atoms")