Minor fixes

abcfold/abcfold.py

@@ -1,6 +1,7 @@
 import configparser
 import json
 import os
+import re
 import shutil
 import socketserver
 import sys
@@ -156,11 +157,12 @@ def run(args, config, defaults, config_file):
             )
 
             if af3_success:
+                pattern = re.compile(f"^{name}.*", re.IGNORECASE)
                 af3_out_dir = list(
                     [
                         dir_
-                        for dir_ in args.output_dir.glob(f"*{name.lower()}*")
-                        if dir_.is_dir()
+                        for dir_ in args.output_dir.glob("*")
+                        if dir_.is_dir() and pattern.match(dir_.name)
                     ]
                 )[0]
                 ao = AlphafoldOutput(af3_out_dir, input_params, name)

abcfold/alphafold3/run_alphafold3.py

@@ -109,6 +109,7 @@ def generate_af3_cmd(
         --json_path=/root/af_input/{input_json.name} \
         --model_dir=/root/models \
         --output_dir=/root/af_output \
+        --db_dir=/root/public_databases \
         --num_diffusion_samples {number_of_models}\
         --num_recycles {num_recycles}
     """

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "abcfold"
-version = "1.0.8"
+version = "1.0.9"
 description = "Input processing tools for AlphaFold3, Boltz and Chai-1"
 readme = "README.md"
 license = { text = "BSD License" }