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chembl-structure-pipeline

library1.2.4pypypi✓ verified 82d ago

A Python toolkit for standardizing and processing chemical structures in the ChEMBL database. Current version 1.2.4. It applies curation rules (e.g., standardization, salt stripping, charge neutralization) commonly used in ChEMBL. Release cadence is irregular, typically a few updates per year.

data database

pip install chembl-structure-pipeline

package ↗homepage ↗

INSTALL

IMPORT

SIG · CHEMBL-STRUCTURE-P

chembl-structure-pipeline

datapythonv1.2.4

Install

6.0s avg

Import

—

Disk

255MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.2.4 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.910 runs

build_error

glibc

py 3.10–3.910 runs

installs and imports cleanly · install 6.0s · import 0.000s · 251MB

255MB installed

● package 255MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

standardize_mol

✓ from chembl_structure_pipeline import standardize_mol

✗ from chembl_structure_pipeline import ChEMBLStructurePipeline

standardizer

✓ from chembl_structure_pipeline import standardizer

get_parent_mol

✓ from chembl_structure_pipeline import get_parent_mol

Basic usage: create pipeline, standardize a molblock, and strip salts.

from chembl_structure_pipeline import ChEMBLStructurePipeline # Create pipeline instance pipeline = ChEMBLStructurePipeline() # A sample molblock (MOL format) molblock = ''' ChemDraw03312216322D 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 4 0 0 0 M V30 BEGIN ATOM M V30 1 C -1.2990 0.0000 0.0000 0 M V30 2 C 0.0000 1.2990 0.0000 0 M V30 3 C 1.2990 0.0000 0.0000 0 M V30 4 C 0.0000 -1.2990 0.0000 0 M V30 5 C 0.0000 0.0000 0.0000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 3 4 M V30 4 1 4 1 M V30 END BOND M V30 END CTAB M END ''' # Standardize the molecule standardized = pipeline.standardize(molblock) print(standardized) # Get parent (salt stripped) parent = pipeline.get_parent(molblock) print(parent)

Debug

Known issues

gotchaThe pipeline expects molblock (V3000 or V2000) strings, not SMILES. Failing to convert SMILES to molblock will cause silent failures or errors.

fix

Use RDKit to convert SMILES to molblock before calling pipeline methods.

affects: all

deprecatedThe function `standardize_molblock` (imported directly) is deprecated in favor of `ChEMBLStructurePipeline.standardize`.

fix

Use the class-based pipeline or the module-level function if still present (but prefer new API).

affects: >=1.1.0

gotchaThe pipeline may remove stereochemistry information during standardization. This is by design but can be surprising for chiral molecules.

fix

Review ChEMBL curation rules; if stereochemistry must be preserved, check options in pipeline constructor.

affects: all

Upgrade

Version history

1.2.4latest on PyPI · released Nov 24, 2025

Audit

Dependencies

rdkitoptionalRequired for molecule operations; the package works best with RDKit backend.

indigooptionalAlternative backend; used if RDKit is not available.

Agent activity

9 hits · last 30 days

node

OpenAI (training)

Resources

packagehttps://pypi.org/project/chembl-structure-pipeline/ ↗

homepagehttps://www.ebi.ac.uk/chembl/ ↗