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feat/docs/cases: Covalent Bond Input #329
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drop: buildin logger fix: template try-except bugs fix: output logs refactor: deduplicate code fix: hetatm input raise from smiles fix: hetatm input raise and dialognoses docs&cases: covalent bonds feat: covalent bond fix: covalent bond add: use_3d opt for ligand
This reverts commit 561a0af.
|
@YaoYinYing I had to bring back a couple of imports in order to make it work: diff --git a/apps/protein_folding/helixfold3/infer_scripts/feature_processing_aa.py b/apps/protein_folding/helixfold3/infer_scripts/feature_processing_aa.py
index 603e8da..c994b0d 100644
--- a/apps/protein_folding/helixfold3/infer_scripts/feature_processing_aa.py
+++ b/apps/protein_folding/helixfold3/infer_scripts/feature_processing_aa.py
@@ -19,6 +19,7 @@ import os
from pathlib import Path
import pickle
from typing import List, Mapping, Optional, Tuple
+import time
import numpy as np
import logging
@@ -28,7 +29,7 @@ from helixfold.data import pipeline_multimer
from helixfold.data import pipeline_rna_multimer
from helixfold.data import pipeline_conf_bonds, pipeline_token_feature, pipeline_hybrid
from helixfold.data import label_utils
-
+from concurrent.futures import ProcessPoolExecutor, as_completed
from helixfold.data.tools import utils
from .preprocess import Entity, digit2alphabet
diff --git a/apps/protein_folding/helixfold3/inference.py b/apps/protein_folding/helixfold3/inference.py
index 429809b..9edc0a1 100644
--- a/apps/protein_folding/helixfold3/inference.py
+++ b/apps/protein_folding/helixfold3/inference.py
@@ -24,6 +24,7 @@ import pickle
import pathlib
import shutil
import numpy as np
+import logging
from helixfold.common import all_atom_pdb_save
from helixfold.data.pipeline_conf_bonds import load_ccd_dict
from helixfold.model import config, utils
@@ -116,7 +117,7 @@ def resolve_bin_path(cfg_path: str, default_binary_name: str)-> str:
raise FileNotFoundError(f"Could not find a proper binary path for {default_binary_name}: {cfg_path}.")
-def get_msa_templates_pipeline(cfg: DictConfig) -> Dict:
+def get_msa_templates_pipeline(cfg) -> Dict:
use_precomputed_msas = True # Assuming this is a constant or should be set globally
template_searcher = hmmsearch.Hmmsearch(
diff --git a/apps/protein_folding/helixfold3/utils/model.py b/apps/protein_folding/helixfold3/utils/model.py
index 4a5b2d6..2ba6337 100644
--- a/apps/protein_folding/helixfold3/utils/model.py
+++ b/apps/protein_folding/helixfold3/utils/model.py
@@ -17,6 +17,7 @@
import numpy as np
import paddle
import paddle.nn as nn
+import logging
import io
from helixfold.model import modules_all_atom Also a side note: |
@alephreish Hi Andrey, this PR is a cherry-pick(which means there exists some poteintal bugs) from one branch that has been definitely out-of-dated. If you are looking for a full-featured branch for you project, please consider this fork. |
@YaoYinYing I've seen the main branch in your fork. I personally like the current interface of |
This is one of the separated PRs from #321 .
Full PR roadmap
Changelog
Added
Fixed
ref_atom_name_chars
and problematic atoms that caused errors.None-value
inTemplateAtomMaskAllZerosError
to prevent incorrect warning triggers.