code cleaning

Author: carlocamilloni

CITATION.cff

@@ -14,7 +14,7 @@ authors:
 - family-names: "Camilloni"
   given-names: "Carlo"
 title: "Multi-eGO"
-version: beta.1
+version: beta.4
 date-released: 2023-10-24
 url: "https://github.com/multi-ego/multi-ego"
 preferred-citation:

README.md

@@ -99,7 +99,7 @@ Create a folder in which you want to run the random coil simulation. Copy the ``
 python multiego.py --system $SYSTEM_NAME --egos rc
 ```
 ```multiego.py``` will then create an output directory in ```multi-eGO/outputs/${SYSTEM_NAME}_rc``` which provides the inputs for the random coil simulation.
-The contents of the output folder are ```ffnonbonded.itp``` and ```topol_GRETA.top```. The former is the non-bonded interaction file and needs to be copied into the ```multi-ego-basic.ff/``` folder. The latter needs to be placed in the simulation root directory. We provide ```mdps``` simulation setup files tested with various multi-*e*GO setups in the ```multi-eGO/mdps``` folder. The order in which the simulations are run is as follows:
+The contents of the output folder are ```ffnonbonded.itp``` and ```topol_mego.top```. The former is the non-bonded interaction file and needs to be copied into the ```multi-ego-basic.ff/``` folder. The latter needs to be placed in the simulation root directory. We provide ```mdps``` simulation setup files tested with various multi-*e*GO setups in the ```multi-eGO/mdps``` folder. The order in which the simulations are run is as follows:
 
 ```
     1. ff_em.mdp
@@ -138,7 +138,7 @@ To setup a multi-*e*GO production simulation, you need to run ```multiego.py```
 ```
 python multiego.py --system $SYSTEM_NAME --egos production --epsilon 0.3 --train md_ensemble
 ```
-Here one sets the energy scale ε to 0.3 kJ/mol and trains the model from the ```md_ensemble``` data. The output directory will be ```multi-eGO/outputs/${SYSTEM_NAME}_production_e0.3_0.3``` and will contain the inputs for the production simulation. Again, the contents of the output directory are ```ffnonbonded.itp``` and ```topol_GRETA.top``` and need to be copied to the ```multi-ego-basic.ff/``` folder and the simulation root directory. The ```mdps``` files are the same except for the last step which is now ```ff_aa.mdp```.
+Here one sets the energy scale ε to 0.3 kJ/mol and trains the model from the ```md_ensemble``` data. The output directory will be ```multi-eGO/outputs/${SYSTEM_NAME}_production_e0.3_0.3``` and will contain the inputs for the production simulation. Again, the contents of the output directory are ```ffnonbonded.itp``` and ```topol_mego.top``` and need to be copied to the ```multi-ego-basic.ff/``` folder and the simulation root directory. The ```mdps``` files are the same except for the last step which is now ```ff_aa.mdp```.
 
 Happy simulating :)
 

multiego.py

@@ -54,6 +54,11 @@ def meGO_parsing():
     args.root_dir = os.path.dirname(os.path.abspath(__file__))
     multi_flag = False
 
+    # Check if no arguments are provided
+    if len(sys.argv) == 1:
+        parser.print_help()
+        sys.exit(1)
+
     if args.config:
         config_yaml = io.read_config(args.config, args_dict)
         # check if yaml file is empty

src/multiego/io.py

@@ -649,7 +649,7 @@ def make_header(parameters):
     now = time.strftime("%d-%m-%Y %H:%M", time.localtime())
 
     header = f"""
-; Multi-eGO force field version beta.1
+; Multi-eGO force field version beta.4
 ; https://github.com/multi-ego/multi-eGO
 ; Please read and cite:
 ; Scalone, E. et al. PNAS 119, e2203181119 (2022) 10.1073/pnas.2203181119
@@ -698,7 +698,7 @@ def write_topology(
     output_folder,
 ):
     """
-    Writes the topology output content into GRETA_topol.top
+    Writes the topology output content into topol_mego.top
 
     Parameters
     ----------
@@ -721,7 +721,7 @@ def write_topology(
     if write_header:
         header = make_header(vars(parameters))
 
-    with open(f"{output_folder}/topol_GRETA.top", "w") as file:
+    with open(f"{output_folder}/topol_mego.top", "w") as file:
         header += """
 ; Include forcefield parameters
 #include "ffnonbonded.itp"