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Process molecular datasets in Python through a simpler interface to RDKit, a chemistry toolkit. Convert and standardize structures, calculate molecular properties, compare and cluster compounds, generate 3D conformations, and visualize results for drug discovery workflows.

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• Load and standardize molecular datasets
• Calculate molecular properties and similarities
• Cluster compounds and select diverse subsets

Read, analyze, modify, and visualize molecular structures with RDKit in Python. Calculate molecular properties, search for similar structures or specific structural patterns, apply reaction rules, and generate 2D or 3D coordinates with detailed control over processing.

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• Calculating properties for a collection of molecules
• Searching for molecules with similar structures
• Filtering molecules by specific structural patterns

Read, write, and edit ChemDraw CDX/CDXML files with RDKit's rdkit.Chem.rdChemDraw plus direct XML editing, always paired with a rendered PNG. Parse molecules and reactions from .cdxml/.cdx, write structures with good 2D depiction, and hand-build or modify the parts RDKit cannot write: reaction arrows, plus signs, schemes/steps, and text/labels. Use for reaction schemes, synthesis routes, mechanisms, retrosynthesis, or SI figures. Critical: RDKit writes structures only — round-tripping a reaction through a Mol silently drops arrows and text; this skill shows the XML layer that preserves them. For pure molecular analysis (descriptors, fingerprints, SMARTS) use rdkit-cheminformatics; for multi-format 3D conversion use openbabel.

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Cheminformatics toolkit for fine-grained molecular control. Parse and write SMILES, SDF, MOL and InChI; compute descriptors (MW, LogP, TPSA, QED, Bertz); build fingerprints (Morgan/ECFP, RDKit, MACCS, atom pair, torsion) and score Tanimoto, Dice or cosine similarity; run SMARTS substructure search and reaction SMARTS; generate 2D depictions and ETKDG 3D conformers; extract Murcko scaffolds and canonical hashes; control sanitization and stereochemistry directly. Also trigger on rdkit, Chem.MolFromSmiles, rdFingerprintGenerator, SDMolSupplier, SMARTS query, ETKDG, or FilterCatalog. For standard workflows with a simpler interface use the datamol skill, which wraps RDKit; use rdkit for advanced control, custom sanitization, and specialized algorithms.

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Pythonic wrapper around RDKit with a simplified interface and sensible defaults. Preferred for standard drug discovery work — SMILES/SELFIES/InChI conversion, molecule standardization and sanitization, descriptors, ECFP and other fingerprints, Tanimoto distance matrices, Butina clustering and diverse subset picking, Bemis-Murcko scaffolds and scaffold splits, BRICS/RECAP fragmentation, 3D conformer generation, SDF/CSV/Excel and cloud I/O, and parallel processing via n_jobs. Returns native rdkit.Chem.Mol objects, so it composes with RDKit throughout. Also trigger on datamol, `import datamol as dm`, dm.to_mol, dm.standardize_mol, dm.cluster_mols, or dm.pick_diverse. For advanced control or custom parameters, use the rdkit skill directly.

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Turn small-molecule structures into numerical features for similarity searches and models that predict activity or properties. Using Molfeat, the skill covers representation choices, invalid inputs, alignment with experimental labels, and saving feature-generation settings for reuse.

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• Prepare molecular features for activity or property prediction
• Choose molecular representations for similarity searches
• Keep experimental labels aligned after rejecting invalid molecules

Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.

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Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

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Pythonic RDKit wrapper with sensible defaults for drug discovery. SMILES parsing, standardization, descriptors, fingerprints, similarity, clustering, diversity selection, scaffold analysis, BRICS/RECAP fragmentation, 3D conformers, and visualization. Returns native rdkit.Chem.Mol. Prefer datamol for standard workflows; use RDKit directly for advanced control.

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Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.

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Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

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Screen compound libraries for drug discovery using drug-likeness guidelines, structural alerts that flag patterns for review, and molecular complexity measures. Combine criteria to shortlist candidates and retain filtering results with reasons for further assessment.

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• Screen compound libraries with drug-likeness rules
• Flag PAINS and other structures for review
• Combine property, structure, and complexity filters

Use when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers, clustering, and molecular searches.

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Standardizes molecular structures using the ChEMBL structure pipeline for normalization and parent selection plus RDKit rdMolStandardize for explicit custom steps such as tautomer canonicalization, salt/solvent stripping, charge handling, stereochemistry handling, mixture selection, and isotope normalization. Explicitly compares ChEMBL, canSARchem, RDKit, and PubChem standardization choices. Use when preparing libraries for QSAR training, joining datasets across sources, deduplicating compound collections, or building canonical compound registries.

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Cheminformatics toolkit for molecular analysis and virtual screening: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints (Morgan/ECFP, MACCS), Tanimoto similarity, SMARTS substructure filtering, Lipinski drug-likeness, reaction enumeration, 2D/3D coordinates. For simpler API use datamol; use RDKit for fine-grained sanitization, custom fingerprints, or SMARTS/reaction control.

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Medicinal chemistry filters for compound triage. Drug-likeness rules (Lipinski Ro5, Veber, Oprea, CNS, leadlike, REOS, Golden Triangle, Ro3), structural alerts (PAINS, NIBR, Lilly Demerits), chemical group detectors, complexity metrics, and filter composition query language. Built on RDKit/datamol. For hit-to-lead filtering, library design, ADMET pre-screening. For molecular I/O use rdkit-cheminformatics or datamol.

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Molecular featurization hub with one consistent interface over 100+ featurizers. Fingerprints (ECFP/Morgan, MACCS, atom pair, topological torsion, Avalon, RDKit, ERG), RDKit and Mordred descriptor sets, pharmacophore and 3D shape descriptors, scaffold keys, and pretrained embeddings (ChemBERTa, ChemGPT, MolT5, GIN, Graphormer) through a common transformer API with caching and parallelism. Use this skill to convert SMILES into model-ready feature matrices for QSAR, virtual screening, and molecular ML, and to choose between featurizer families. Also trigger on molfeat, MoleculeTransformer, FPVecTransformer, PretrainedHFTransformer, molfeat model store, or featurizer selection.

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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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Build and troubleshoot TorchDrug 0.2.1 workflows for molecular property prediction, molecule generation, protein modeling, and knowledge graph reasoning. Connect datasets, models, training tasks, and evaluation while checking version compatibility and common implementation errors.

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• Training and evaluating molecular property prediction models
• Building molecule generation workflows
• Learning representations of protein sequences and structures

Build molecular property prediction workflows with DeepChem for solubility, toxicity, and related chemistry tasks. Prepare molecular representations, choose compatible models, handle missing labels, and evaluate predictions using data splits designed for the intended scientific question.

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• Predicting solubility from molecular structures
• Comparing graph models on MoleculeNet datasets
• Checking data splits for information leakage

Core cheminformatics toolkit for SMILES/SDF/InChI parsing, descriptors (MW, LogP, TPSA), fingerprints, ECFP/Morgan fingerprints, substructure search, 2D/3D generation, similarity, reactions, and datamol-style molecule standardization when no separate wrapper skill is routed.

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Run predictions with a finetuned KERMT checkpoint on a SMILES-only CSV. The skill validates that the input ckpt has task FFN heads (refuses pretrain ckpts with a redirect to kermt-finetune), validates the CSV, prepares the data (clean + rdkit_2d features), then launches main.py predict inside the kermt container (blocking, minutes-scale).

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