From 4c17b321c17fb7b2f181ed43b445c150f268dd42 Mon Sep 17 00:00:00 2001 From: hlasimpk Date: Tue, 23 Sep 2025 13:06:21 +0100 Subject: [PATCH 1/3] Fixed missing flag in singularity code, fixed changes to out_dir naming in AF3, and updating pypi toml --- abcfold/abcfold.py | 5 +++-- abcfold/alphafold3/run_alphafold3.py | 1 + pyproject.toml | 2 +- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/abcfold/abcfold.py b/abcfold/abcfold.py index c32fb05..c07baed 100644 --- a/abcfold/abcfold.py +++ b/abcfold/abcfold.py @@ -158,8 +158,9 @@ def run(args, config, defaults, config_file): if af3_success: af3_out_dir = list( [ - dir_ - for dir_ in args.output_dir.glob(f"*{name.lower()}*") + dir_ + for n in (name.lower(), name.upper()) + for dir_ in args.output_dir.glob(f"{n}*") if dir_.is_dir() ] )[0] diff --git a/abcfold/alphafold3/run_alphafold3.py b/abcfold/alphafold3/run_alphafold3.py index 61f44a6..4af2334 100644 --- a/abcfold/alphafold3/run_alphafold3.py +++ b/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} """ diff --git a/pyproject.toml b/pyproject.toml index 7a3ff14..d7ace81 100644 --- a/pyproject.toml +++ b/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" } From c73dcc3cdfaa0e6bac4f3fbc819cf988a9d2a335 Mon Sep 17 00:00:00 2001 From: hlasimpk Date: Tue, 23 Sep 2025 14:16:32 +0100 Subject: [PATCH 2/3] fix whitespace error --- abcfold/abcfold.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/abcfold/abcfold.py b/abcfold/abcfold.py index c07baed..1ac22b5 100644 --- a/abcfold/abcfold.py +++ b/abcfold/abcfold.py @@ -158,9 +158,9 @@ def run(args, config, defaults, config_file): if af3_success: af3_out_dir = list( [ - dir_ - for n in (name.lower(), name.upper()) - for dir_ in args.output_dir.glob(f"{n}*") + dir_ + for n in (name.lower(), name.upper()) + for dir_ in args.output_dir.glob(f"{n}*") if dir_.is_dir() ] )[0] From 45eba54c87ac2acb1dec3251ae2bd6a49931e2e5 Mon Sep 17 00:00:00 2001 From: hlasimpk Date: Tue, 23 Sep 2025 16:25:22 +0100 Subject: [PATCH 3/3] Changed to re expression to catch edge cases --- abcfold/abcfold.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/abcfold/abcfold.py b/abcfold/abcfold.py index 1ac22b5..7bd9e96 100644 --- a/abcfold/abcfold.py +++ b/abcfold/abcfold.py @@ -1,6 +1,7 @@ import configparser import json import os +import re import shutil import socketserver import sys @@ -156,12 +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 n in (name.lower(), name.upper()) - for dir_ in args.output_dir.glob(f"{n}*") - 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)