draft autosolve by redrodeo03 · Pull Request #183 · deepforestsci/DeepRetro

redrodeo03 · 2026-03-27T16:55:07Z

Description

Fix #(issue)

we still need
cache.py
parse.py
rec_prithvi.py
prithvi.py
llm.py
from src/

Type of change

Please check the option that is related to your PR.

Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Breaking change (fix or feature that would cause existing functionality to not work as expected)
- In this case, we recommend to discuss your modification on GitHub issues before creating the PR
Documentations (modification for documents)

Checklist

I have performed a self-review of my own code
I have commented my code, particularly in hard-to-understand areas
I have made corresponding changes to the documentation
I have added tests that prove my fix is effective or that my feature works
New unit tests pass locally with my changes
I have checked my code and corrected any misspellings

rbharath · 2026-04-01T19:10:16Z

@@ -0,0 +1,204 @@
+"""Batch and single-molecule retrosynthesis runners.


Move this to algorithms

rbharath · 2026-04-01T19:13:38Z

+    smiles: str,
+    *,
+    llm: str = "anthropic/claude-3-7-sonnet-20250219:adv",
+    az_model: str = "Pistachio_100+",


Separate PR we need aizynthfinder

rbharath · 2026-04-01T19:15:06Z

+
+    Returns
+    -------
+    dict[str, Any]


More details on output format please

rbharath · 2026-04-01T19:18:51Z

+    from src.utils.job_context import logger as context_logger
+    from src.utils.parse import format_output
+
+    def _run(smiles, **kwargs):


Don't do this...

Make it a public function; avoid "private" functions

rbharath · 2026-04-01T19:20:10Z

+    )
+
+    stability_flag = str(stability_check)
+    semaphore = asyncio.Semaphore(max_concurrent)


You need to document this thoroughly

rbharath · 2026-04-01T19:20:54Z

+        hallucination_mode, hallucination_classifier,
+    )
+
+    stability_flag = str(stability_check)


What is this? Document

rbharath · 2026-04-01T19:21:10Z

+    semaphore = asyncio.Semaphore(max_concurrent)
+    loop = asyncio.get_running_loop()
+
+    async def _process(smi: str) -> dict[str, Any]:


shreyasvinaya · 2026-04-07T17:11:43Z

+def get_pipeline():
+    """Lazy-import the retrosynthesis pipeline and return a runner callable.
+
+    Imports are deferred so that ``import deepretro.algorithms.autosolve``


how heavy is the aizynthfinder import?

also i'm not sure if the LLM libraries are heavy, they cause issues if they are not installed

shreyasvinaya

some simple fixes like usage examples, type annotations have to be added, rst docs to be added

some feedback on autosolve

shreyasvinaya · 2026-04-07T17:11:55Z

+    from deepretro.migration.job_context import logger as context_logger
+    from deepretro.migration.parse import format_output
+
+    def run_retrosynthesis(smiles, **kwargs):


usage example, type annotations

shreyasvinaya · 2026-04-07T17:14:29Z

+def autosolve(
+    smiles: str,
+    *,
+    llm: str = "anthropic/claude-3-7-sonnet-20250219:adv",


switch this to opus 4.6 as default

shreyasvinaya · 2026-04-07T17:14:48Z

+    az_model: str = "Pistachio_100+",
+    stability_check: bool = True,
+    hallucination_mode: str = "heuristic",
+    hallucination_classifier: Any = None,


avoid using any for typechecks

shreyasvinaya · 2026-04-07T17:16:11Z

+    )
+
+
+async def autosolve_async(


do we need a async autosolve?
@rbharath do we want to handle this at a function level or do we want to do this at a script level?
i'm not sure how well async functions work on jupyter notebooks

shreyasvinaya · 2026-04-07T17:16:31Z

+async def autosolve_async(
+    smiles_list: list[str],
+    *,
+    llm: str = "anthropic/claude-3-7-sonnet-20250219:adv",


switch default model to opus 4.6

shreyasvinaya · 2026-04-07T17:17:55Z

@@ -6,22 +6,34 @@
 """


you can skip changes to this file, it is being fixed in #193

shreyasvinaya · 2026-04-07T17:20:10Z

+    Examples
+    --------
+    >>> from deepretro.algorithms.autosolve import autosolve  # doctest: +SKIP
+    >>> result = autosolve("c1ccccc1")                        # doctest: +SKIP


you might want to move the different ways of calling autosove to rst docs

shreyasvinaya · 2026-04-07T17:22:05Z

+    ...     hallucination_classifier="model_out/",
+    ... )                                                      # doctest: +SKIP
+    """
+    run_retrosynthesis = get_pipeline()


do we need to initialize the pipeline and then call it like a class?
can it not be called directly?

ARY2260

left few comments, concerned about type mixing

ARY2260 · 2026-04-13T16:55:03Z

+4. Recurse on each reactant until all leaves are purchasable.
+5. Flatten the tree into a step-by-step synthesis plan.
+
+Examples


please keep examples is main autosolve function docstring itself

ARY2260 · 2026-04-13T16:57:43Z

+        ``{"steps": [...], "dependencies": {...}}``.
+        When *return_image* is ``True``, also contains ``"image"``.
+    """
+    import os


please keep imports outside the function in general

ARY2260 · 2026-04-13T16:59:31Z

+
+        if isinstance(classifier, (str, Path)):
+            clf = HallucinationClassifier()
+            clf.load(str(classifier))


Why is not a deepchem style model with restore to reload the model?

we do use restore, there is a thin wrapper on top to accommodate for threshold which we calculate separately

ARY2260 · 2026-04-13T17:01:20Z

+    from deepretro.utils.parse import format_output
+
+    hallucination_check, hallucination_checker_fn = resolve_hallucination(
+        hallucination_mode, hallucination_classifier,


hallucination_classifier type is quite mixed, I think its a path as well as callable? Why is this variation needed?

Fixed, resolve_hallucination now returns a single callable (or None) instead of a (str, callable) tuple. The hallucination_classifier parameter accepts either a path to a saved model or a pre-loaded instance; resolve_hallucination normalises both into one ready-to-use checker function. The type variation is handled internally, not leaked to the caller.

ARY2260 · 2026-04-13T17:08:17Z

+    depth: int = 0,
+    max_depth: int = 50,
+) -> tuple[dict, bool]:
+    """Recursively solve a molecule via AZ, falling back to LLM.


Please add a detailed doctring explaining how the rec run works and add example.

ARY2260 · 2026-04-13T17:09:26Z

+    Returns a nested mol/reaction tree and a *solved* flag.
+    """
+    from rdkit import Chem
+    from deepretro.algorithms.llm import llm_pipeline


please avoid internal imports, dependencies issues might creep in.

understood, added

ARY2260 · 2026-04-13T17:11:24Z

+    return result_dict, solved
+
+
+def unsolved_leaf(smiles: str) -> dict:


if there are a more of such retrosynthesis tree utils, please add them in utils file or something

ARY2260 · 2026-04-13T17:13:08Z

+        if isinstance(pathway, list):
+            all_solved = True
+            for smi in pathway:
+                res, stat = rec_run(molecule=smi, **recurse_kw)


there is logic type mixing for molecule ie, smi or pathway, why this mixing is required?

there was a case in which either a list (multiple reactants) or a single element was passed, hence the mixing. We now perform a normalising step

ARY2260 · 2026-04-13T17:43:28Z

+
+
+def rec_run(
+    molecule: str,


an AutoSolver class would be a better design to avoid parameter shuffle.

ARY2260

refactor to AutoSolver class would be better.

rbharath · 2026-04-15T16:53:41Z

+
+
+class AutoSolver:
+    """Holds shared config"""


Expand docs significantly. This needs to be the core API object not just a config holder

rbharath · 2026-04-15T16:56:49Z

+    """Convert user-facing mode to a single checker callable (or None).
+
+    Returns None (skip checking), or a callable with signature
+    ``(product: str, pathways: list) -> (int, list)``.


Document arguments and add usage examples for every function

ARY2260 · 2026-04-20T14:49:06Z

@@ -0,0 +1,261 @@
+"""Synthesis pathway visualization.


Already pushed to a separate PR #195

ARY2260 · 2026-04-20T15:00:43Z

+}
+
+
+def mask_protecting_groups_multisymbol(smiles: str) -> str:


@shreyasvinaya can you please take this utility function in your PR and add a parameter for path of config if path is accessible to the module that will be using this function at runtime.

path can be none by default, which leads to a warning and then use the default dict PG_MAP

protecting group will be ported over after the main llm.py is merged, it needs a thorough refactor, will include this in that refactor

ARY2260 · 2026-04-20T15:02:12Z

+
+import joblib
+
+from deepretro import logging as job_context


part of new upcoming PR along with parse.py

ARY2260 · 2026-04-20T15:05:36Z

+import json
+from pathlib import Path
+from typing import Any, Dict
+


@redrodeo03 Please check if this function is needed any longer after refactor. If not, delete it from the PR.

@shreyasvinaya i dont think we've used langfuse in a while, are we ok to remove this?

ARY2260 · 2026-04-20T15:06:38Z

+    from aizynthfinder.aizynthfinder import AiZynthFinder
+
    finder = AiZynthFinder(configfile=config_filename)
    finder.stock.select("zinc")


Put a separate small PR, and update the rst docs.

this is already a part of #198

ARY2260 · 2026-04-20T15:44:23Z

+from typing import Any
+
+
+def build_ml_checker(clf: Any) -> Callable:


Next steps:

please remove hallucination_helper from models folder.

in algorithm create a folder named hallucination checks, that will have the base check class with a core method "check_hallucinations(react, product)", and subs classes from this base class for heuristicHallucinationChecker() and XBBoostHallucinationChecker()

redrodeo03 temporarily deployed to testing March 27, 2026 16:55 — with GitHub Actions Inactive

redrodeo03 temporarily deployed to testing March 27, 2026 17:03 — with GitHub Actions Inactive

redrodeo03 temporarily deployed to testing March 31, 2026 16:48 — with GitHub Actions Inactive

redrodeo03 temporarily deployed to testing April 1, 2026 16:23 — with GitHub Actions Inactive

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redrodeo03 marked this pull request as ready for review April 1, 2026 17:24

redrodeo03 temporarily deployed to testing April 1, 2026 18:21 — with GitHub Actions Inactive

redrodeo03 temporarily deployed to testing April 1, 2026 18:37 — with GitHub Actions Inactive

rbharath reviewed Apr 1, 2026

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redrodeo03 temporarily deployed to testing April 7, 2026 17:08 — with GitHub Actions Inactive

shreyasvinaya reviewed Apr 7, 2026

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ARY2260 reviewed Apr 13, 2026

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rbharath reviewed Apr 15, 2026

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redrodeo03 added 6 commits April 15, 2026 22:48

draft autosolve

643dec1

lazy import

e77097d

function updates

81462c4

import error

50d72c2

helpers file

669f299

test error fix

a952ae5

redrodeo03 added 11 commits April 15, 2026 22:53

remove main.py dependency

2f87d9b

examples

657ad28

self contained run

c23a30b

visualisation + autosolve cleanup

d16ef1b

cleanup

6c3bf57

refactor from migration folder

8122555

default model

04d0b3e

cleanup

66b243d

imports

679d0af

refaactor

9dba274

autosolver class

dd6f3c5

redrodeo03 force-pushed the autosolve branch from 14f7190 to dd6f3c5 Compare April 16, 2026 16:09

redrodeo03 temporarily deployed to testing April 16, 2026 16:09 — with GitHub Actions Inactive

lint fix + others

01a224e

redrodeo03 temporarily deployed to testing April 16, 2026 16:26 — with GitHub Actions Inactive

lint fix + others

e7f6be7

redrodeo03 temporarily deployed to testing April 16, 2026 16:34 — with GitHub Actions Inactive

remove old decorator

d3b5ab0

redrodeo03 temporarily deployed to testing April 16, 2026 16:51 — with GitHub Actions Inactive

patching error

30186c2

redrodeo03 temporarily deployed to testing April 16, 2026 16:58 — with GitHub Actions Inactive

ARY2260 reviewed Apr 20, 2026

View reviewed changes

		@@ -0,0 +1,204 @@
		"""Batch and single-molecule retrosynthesis runners.

		return result_dict, solved


		def unsolved_leaf(smiles: str) -> dict:

		}


		def mask_protecting_groups_multisymbol(smiles: str) -> str:

		from typing import Any


		def build_ml_checker(clf: Any) -> Callable:

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redrodeo03 commented Mar 27, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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redrodeo03 commented Mar 27, 2026 •

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