Update README and refactor and improve logging

rigdenlab · Jan 16, 2025 · 505901e · 505901e
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diff --git a/README.md b/README.md
@@ -58,7 +58,7 @@ abcfold <input_json>  <output_dir> -abc --model_params <model_params> --database
 
 ## Extra Features
 
-Below are scripts for adding MMseqs2 MSAs and custom templates to AlphaFold3 input JSON files.
+Below are scripts for adding MMseqs2 MSAs and custom templates to AlphaFold3 input JSON files but does not run any ABCFold.
 
 
 These scripts are designed to take in a prepared [AlphaFold3](https://github.com/google-deepmind/alphafold3/tree/main) JSON files, e.g.:

diff --git a/abcfold/abcfold.py b/abcfold/abcfold.py
@@ -85,7 +85,11 @@ def run(args, config, defaults, config_file):
         else:
             run_json = Path(args.input_json)
 
-        if not args.alphafold3 and not args.boltz1 and not args.chai1:  #
+        if not args.alphafold3 and not args.boltz1 and not args.chai1:
+            logger.info(
+                "Neither AlphaFold3, Boltz-1, or Chai-1 selected. Running AlphaFold3 \
+by default"
+            )
             args.alphafold3 = True
 
         if args.alphafold3: