Update README.md

tools/make_mat/README.md

@@ -7,22 +7,22 @@ Usage:
 python make_mat.py --histo <histogram_directory> --target_top <target_topology> --mego_top <mego_topology> [--inter] [--out <output_path>] [--out_name <output_name>] [--proc <num_processes>] [--cutoff <max_cutoff>]
 ```
 Parameters:
-```
-    --histo: Path to the directory containing the histograms.
-            Histogram files should contain the prefix "intra_" for intramolecular contact descriptions and "inter_" for intermolecular.
+
+`--histo`: Path to the directory containing the histograms.
+         Histogram files should contain the prefix "intra_" for intramolecular contact descriptions and "inter_" for intermolecular.
 
-    --target_top: Path to the topology file of the system on which the histograms were calculated.
+`--target_top`: Path to the topology file of the system on which the histograms were calculated.
 
-    --mego_top: Path to the standard multi-eGO topology of the system generated by pdb2gmx.
+`--mego_top`: Path to the standard multi-eGO topology of the system generated by pdb2gmx.
 
-    --inter: Flag to indicate that the calculation is adapted to intermolecular histograms. If not provided, intramolecular calculations are assumed.
+`--inter`: Flag to indicate that the calculation is adapted to intermolecular histograms. If not provided, intramolecular calculations are assumed.
 
-    --out: Optional parameter to set the output path. Default is the current directory.
+-`-out`: Optional parameter to set the output path. Default is the current directory.
 
-    --out_name: Optional parameter to set the output name of files. It will be added to the default one.
+`--out_name`: Optional parameter to set the output name of files. It will be added to the default one.
                 Example: intermat_<out_name>_mi_mj.ndx or intramat_<out_name>_mi_mj.ndx
 
-    --proc: Optional parameter to set the number of processes to perform the calculation. Default is 1.
+`--proc`: Optional parameter to set the number of processes to perform the calculation. Default is 1.
 
-    --cutoff: The maximum cutoff used for the accumulation of the histograms.
-```
+`--cutoff`: The maximum cutoff used for the accumulation of the histograms.
+