cleaned rc and updated regtests

carlocamilloni · Dec 7, 2024 · ae27191 · ae27191
1 parent 32239b4
commit ae27191
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Showing 28 changed files with 193,568 additions and 223,631 deletions.
diff --git a/multiego.py b/multiego.py
@@ -233,14 +233,6 @@ def main():
         elapsed_time = et - st
         st = et
         print("- Done in:", elapsed_time, "seconds")
-    else:
-        print("- Generate the LJ dataset")
-        meGO_LJ = ensemble.generate_OO_LJ(meGO_ensembles)
-        meGO_LJ_14 = pairs14
-        et = time.time()
-        elapsed_time = et - st
-        st = et
-        print("- Done in:", elapsed_time, "seconds")
 
     print("- Finalize pairs and exclusions")
     meGO_LJ_14 = ensemble.make_pairs_exclusion_topology(meGO_ensembles, meGO_LJ_14, args)

diff --git a/src/multiego/arguments.py b/src/multiego/arguments.py
@@ -5,9 +5,8 @@
     },
     "--egos": {
         "type": str,
-        "choices": ["rc", "mg", "production"],
-        "help": "rc: creates a force-field for random coil simulations. "
-        "mg: creates a force-field for molten globule simulations."
+        "choices": ["mg", "production"],
+        "help": "mg: creates a force-field for molten globule simulations."
         "production: creates a force-field combining random coil simulations and training simulations.",
     },
     "--reference": {
@@ -120,12 +119,6 @@
         "type": str,
         "help": "Explicit name for the output directory stored in outputs/system",
     },
-    "--regtest": {
-        "type": bool,
-        "default": False,
-        "action": "store_true",
-        "help": "Use old rules for regtests check.",
-    },
     "--config": {
         "default": "",
         "type": str,

diff --git a/src/multiego/ensemble.py b/src/multiego/ensemble.py
@@ -1200,32 +1200,23 @@ def generate_LJ(meGO_ensemble, train_dataset, parameters):
     # now we can remove contacts with default c6/c12 becasue these
     # are uninformative and predefined. This also allow to replace them with contact learned
     # by either intra/inter training. We cannot remove 1-4 interactions.
-    if not parameters.regtest:
-        meGO_LJ = meGO_LJ.loc[
-            ~(
-                (meGO_LJ["epsilon"] > 0)
-                & (meGO_LJ["mg_epsilon"] > 0)
-                & ((abs(meGO_LJ["epsilon"] - meGO_LJ["mg_epsilon"]) / meGO_LJ["mg_epsilon"]) < parameters.relative_c12d)
-                & ((abs(meGO_LJ["sigma"] - meGO_LJ["mg_sigma"]) / meGO_LJ["mg_sigma"]) < parameters.relative_c12d)
-                & (meGO_LJ["1-4"] == "1>4")
-            )
-        ]
-        meGO_LJ = meGO_LJ.loc[
-            ~(
-                (meGO_LJ["epsilon"] < 0)
-                & (meGO_LJ["mg_epsilon"] < 0)
-                & ((abs(meGO_LJ["epsilon"] - meGO_LJ["mg_epsilon"]) / abs(meGO_LJ["mg_epsilon"])) < parameters.relative_c12d)
-                & (meGO_LJ["1-4"] == "1>4")
-            )
-        ]
-    else:
-        meGO_LJ = meGO_LJ.loc[
-            ~(
-                (meGO_LJ["epsilon"] < 0)
-                & ((abs(-meGO_LJ["epsilon"] - meGO_LJ["rep"]) / meGO_LJ["rep"]) < parameters.relative_c12d)
-                & (meGO_LJ["1-4"] == "1>4")
-            )
-        ]
+    meGO_LJ = meGO_LJ.loc[
+        ~(
+            (meGO_LJ["epsilon"] > 0)
+            & (meGO_LJ["mg_epsilon"] > 0)
+            & ((abs(meGO_LJ["epsilon"] - meGO_LJ["mg_epsilon"]) / meGO_LJ["mg_epsilon"]) < parameters.relative_c12d)
+            & ((abs(meGO_LJ["sigma"] - meGO_LJ["mg_sigma"]) / meGO_LJ["mg_sigma"]) < parameters.relative_c12d)
+            & (meGO_LJ["1-4"] == "1>4")
+        )
+    ]
+    meGO_LJ = meGO_LJ.loc[
+        ~(
+            (meGO_LJ["epsilon"] < 0)
+            & (meGO_LJ["mg_epsilon"] < 0)
+            & ((abs(meGO_LJ["epsilon"] - meGO_LJ["mg_epsilon"]) / abs(meGO_LJ["mg_epsilon"])) < parameters.relative_c12d)
+            & (meGO_LJ["1-4"] == "1>4")
+        )
+    ]
 
     # transfer rule for inter/intra contacts:
     # 1) only attractive contacts can be transferd

diff --git a/src/multiego/io.py b/src/multiego/io.py
@@ -359,10 +359,7 @@ def write_nonbonded(topology_dataframe, meGO_LJ, parameters, output_folder):
         file.write("  1             1               no              1.0     1.0\n\n")
 
         file.write("[ atomtypes ]\n")
-        if parameters.egos == "rc":
-            atomtypes = topology_dataframe[["sb_type", "atomic_number", "mass", "charge", "ptype", "rc_c6", "rc_c12"]].copy()
-            atomtypes.rename(columns={"rc_c6": "c6", "rc_c12": "c12"}, inplace=True)
-        elif parameters.egos == "mg":
+        if parameters.egos == "mg":
             atomtypes = topology_dataframe[["sb_type", "atomic_number", "mass", "charge", "ptype", "mg_c6", "mg_c12"]].copy()
             atomtypes.rename(columns={"mg_c6": "c6", "mg_c12": "c12"}, inplace=True)
         else:
@@ -728,7 +725,7 @@ def get_name(parameters):
     name : str
         The name of the output directory
     """
-    if parameters.egos == "rc":
+    if parameters.egos == "mg":
         name = f"{parameters.system}_{parameters.egos}"
     else:
         name = f"{parameters.system}_{parameters.egos}_epsis_intra{ '-'.join(np.array(parameters.multi_epsilon, dtype=str)) }_{parameters.inter_epsilon}"
@@ -795,7 +792,7 @@ def check_files_existence(args):
             ndx_files = glob.glob(f"{ensemble}/*.ndx")
             ndx_files += glob.glob(f"{ensemble}/*.ndx.gz")
             ndx_files += glob.glob(f"{ensemble}/*.h5")
-            if not ndx_files and not args.egos == "rc":
+            if not ndx_files and not args.egos == "mg":
                 raise FileNotFoundError(
                     f"contact matrix input file(s) (e.g., intramat_1_1.ndx, etc.) were not found in {ensemble}/"
                 )

diff --git a/test/test_cases.txt b/test/test_cases.txt
@@ -1,8 +1,8 @@
---system gpref --egos rc --no_header --regtest --explicit_name case
---system gpref --egos production --epsilon 0.235 --train md_ensemble --single_molecule --no_header --regtest --explicit_name case
---config TEST_ROOT/test_inputs/abetaref/config.yml --regtest --explicit_name case # --system abetaref --egos production
---config TEST_ROOT/test_inputs/ttrref/config.yml --regtest --explicit_name case # --system ttrref --egos production
---config TEST_ROOT/test_inputs/lyso-bnz_ref/config_1.yml --regtest --explicit_name case # --system lyso-bnz_ref --egos production
---config TEST_ROOT/test_inputs/lyso-bnz_ref/config_2.yml --regtest --explicit_name case # --system lyso-bnz_ref --egos production
---system het_trim --egos rc --no_header --regtest --explicit_name case
---system het_trim --egos production --epsilon 0.3 --train train --no_header --regtest --explicit_name case
+--system gpref --egos mg --no_header --explicit_name case
+--system gpref --egos production --epsilon 0.235 --train md_ensemble --single_molecule --no_header --explicit_name case
+--config TEST_ROOT/test_inputs/abetaref/config.yml --explicit_name case # --system abetaref --egos production
+--config TEST_ROOT/test_inputs/ttrref/config.yml --explicit_name case # --system ttrref --egos production
+--config TEST_ROOT/test_inputs/lyso-bnz_ref/config_1.yml --explicit_name case # --system lyso-bnz_ref --egos production
+--config TEST_ROOT/test_inputs/lyso-bnz_ref/config_2.yml --explicit_name case # --system lyso-bnz_ref --egos production
+--system het_trim --egos mg --no_header --explicit_name case
+--system het_trim --egos production --epsilon 0.3 --train train --no_header --explicit_name case
diff --git a/test/test_inputs/abetaref/config.yml b/test/test_inputs/abetaref/config.yml
@@ -1,7 +1,7 @@
 ---
 - system: abetaref
 - egos: production 
-- epsilon: 0.33 
+- epsilon: 0.24 
 - train: native_MD 
 - reference: ref
 - single_molecule
@@ -16,4 +16,4 @@
   - TYR CE1 CE2
   - VAL CG1 CG2
   - ALA O1 O2
-- no_header
+- no_header