feat/docs/cases: Covalent Bond Input

[YaoYinYing]

This is one of the separated PRs from #321 .

Full PR roadmap

id	purpose	# commits	Affected
1	Hydra-Omegaconf and Pip module	6	Code, Config, Doc
2	BFD supports and MSA parallelism fixes	5	Code, Config, Case
3	Small molecule inputs and covalent bonds	4	Code, Case, Doc

Changelog

Added

• Support for SDF file inputs for small molecules and additional file formats.
• Expanded set of demo cases.
• PTM Inputs (phosphorylations, isopeptides, metal bindings, disulfide bridges, glycosylations, etc.)

Fixed

• Implemented automatic binary search within the PATH if not explicitly specified.
• Resolved an issue with dummy assertions of ref_atom_name_chars and problematic atoms that caused errors.
• Addressed the None-value in TemplateAtomMaskAllZerosError to prevent incorrect warning triggers.

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[alephreish]

@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: leave_atom_flag is currently ignored, so the user has to modify ccd_preprocessed_etkdg.pkl.gz to remove the atoms that leave upon formation of the corresponding covalent bond.

[YaoYinYing]

@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.

[alephreish]

@YaoYinYing I've seen the main branch in your fork. I personally like the current interface of helixfold - it's flexible enough, although switching to your new interface would not be a big deal. I have the feeling that this small PR does have a chance of being merged into PaddlePaddle/PaddleHelix:dev since patch-hydra diverged too much by now.