additional box tools

src/multiego/ensemble.py

@@ -516,7 +516,7 @@ def init_meGO_ensemble(args):
         ) = initialize_topology(topology, custom_dict, args)
         # check that the molecules defined have a reference
         unique_temp_molecule_names = temp_topology_dataframe["molecule_name"].unique()
-        #check_molecule_names(unique_ref_molecule_names, unique_temp_molecule_names)
+        # check_molecule_names(unique_ref_molecule_names, unique_temp_molecule_names)
 
         train_topology_dataframe = pd.concat(
             [train_topology_dataframe, temp_topology_dataframe],
@@ -591,7 +591,7 @@ def init_meGO_ensemble(args):
         ) = initialize_topology(topology, custom_dict, args)
         # check that the molecules defined have a reference
         unique_temp_molecule_names = temp_topology_dataframe["molecule_name"].unique()
-        #check_molecule_names(unique_ref_molecule_names, unique_temp_molecule_names)
+        # check_molecule_names(unique_ref_molecule_names, unique_temp_molecule_names)
         check_topology_dataframe = pd.concat(
             [check_topology_dataframe, temp_topology_dataframe],
             axis=0,

tools/box_concentration/get_box.py

@@ -1,13 +1,64 @@
 import argparse
+import numpy as np
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description="TODO!")
-    parser.add_argument("--n_mol", type=int, required=True, help="Number of molecules to simulate.")
-    parser.add_argument("--conc", type=float, required=True, help="Concentration in Molar")
+    parser = argparse.ArgumentParser(
+        description="Calculate number of moles, concentration, box size or volume based on provided parameters."
+    )
+    parser.add_argument(
+        "--n_mol",
+        type=int,
+        required=False,
+        help="Number of molecules, to be combined with --conc or one from (--volume, --sphere_r, --cubic_side)",
+    )
+    parser.add_argument(
+        "--conc",
+        type=float,
+        required=False,
+        help="Concentration in Molar, to be combined with --n_mol or one from (--volume, --sphere_r, --cubic_side)",
+    )
+    parser.add_argument("--volume", type=float, required=False, help="Volume in nm^3, to be combined with --n_mol or --conc")
+    parser.add_argument("--sphere_r", type=float, required=False, help="Radius of a sphere in nm")
+    parser.add_argument("--cubic_side", type=float, required=False, help="Side of a cube in nm")
 
     args = parser.parse_args()
 
+    # Print help if no arguments are provided
+    if not any(vars(args).values()):
+        parser.print_help()
+        exit(0)
+
     n_mol = args.n_mol
     conc = args.conc
-    box = 10**8 * (n_mol / (conc * 6.022 * 10**23)) ** (1 / 3)
-    print("cubic box of side: %.5f nm" % box)
+    volume = args.volume
+    sphere_r = args.sphere_r
+    cubic_side = args.cubic_side
+
+    if n_mol is not None and n_mol > 0 and conc is not None and conc > 0:
+        box = 10**8 * (n_mol / (conc * 6.022 * 10**23)) ** (1 / 3)
+        print("cubic box of side: %.5f nm" % box)
+        exit()
+
+    if sphere_r is not None and sphere_r > 0:
+        volume = (4 / 3) * np.pi * sphere_r**3
+
+    if cubic_side is not None and cubic_side > 0:
+        volume = cubic_side**3
+
+    if n_mol is not None and n_mol > 0 and volume is not None and volume > 0:
+        conc = 10**24 * (n_mol / (volume * 6.022 * 10**23))
+        print("concentration is: %.12f M" % conc)
+        exit()
+
+    if conc is not None and conc > 0 and volume is not None and volume > 0:
+        n_mol = int(round((volume * conc * 6.022 * 10**23) / 10**24))
+        print("n_mol is: %i" % n_mol)
+        exit()
+
+    if sphere_r is not None and sphere_r > 0:
+        volume = (4 / 3) * np.pi * sphere_r**3
+        side = volume ** (1 / 3)
+        print("volume is %.6f nm^3 and cubic side would be %.6f nm" % (volume, side))
+        exit()
+
+    parser.print_help()