Add support for modification dictionary and JSON output

README.md

@@ -101,7 +101,10 @@ stream file for the perturbable molecule, or AMBER or GROMACS files for the two
 The format can be specified using the the `--output-format` option. If you require input
 for a free-energy perturbation simulation, e.g. a hybrid GROMACS toplogy file, the you can
 use the stream file with [BioSimSpace](https://biosimspace.openbiosim.org) to generate the
-required input files.
+required input files. Additionally, the program will output a JSON file summarising the
+modifications that were made.
+
+```bash
 
 > [!NOTE]
 > When a stream file is used as input, the `--mapping` option is ignored. and

src/ghostly/_cli.py

@@ -35,6 +35,7 @@ def run():
     from loguru import logger
 
     import argparse
+    import json
     import os
     import sys
 
@@ -268,7 +269,7 @@ def run():
     try:
         if args.system is None:
             system = merged.toSystem()._sire_object
-        system = modify(
+        system, modifications = modify(
             system,
             k_hard.value(),
             k_soft.value(),
@@ -307,3 +308,11 @@ def run():
             sys.exit(1)
     else:
         sr.stream.save(system, f"{args.output_prefix}.bss")
+
+    # Try to save the modifications to JSON.
+    try:
+        with open(f"{args.output_prefix}_modifications.json", "w") as f:
+            json.dump(modifications, f, indent=4)
+    except Exception as e:
+        logger.error(f"An error occurred while saving the modifications to JSON: {e}")
+        sys.exit(1)