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RDKit · By GPTomics
Skills
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape)… | GPTomics/ | 1.2k | 2 repos | ~4.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 2 | Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and reaction templates, with explicit handling of atom mapping, RDChiral template extraction, product… | GPTomics/ | 1.2k | 2 repos | ~4.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 3 | Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape +… | GPTomics/ | 1.2k | 2 repos | ~3.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 4 | Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and… | GPTomics/ | 1.2k | 2 repos | ~4.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 5 | Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware… | GPTomics/ | 1.2k | 2 repos | ~5.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 6 | Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain… | GPTomics/ | 1.2k | 2 repos | ~5.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 7 | Predicts absorption, distribution, metabolism, excretion and toxicity for drug candidates with ADMETlab 3.0, ADMET-AI, DeepChem and chemprop, plus druglikeness filters. | GPTomics/ | 1.2k | 1 repo | ~5k | Automated safety check: Pass | MIT | 1 mo ago |
| 8 | Designs covalent inhibitors and warheads targeting cysteine, lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide… | GPTomics/ | 1.2k | 1 repo | ~4.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 9 | Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, and BinaryCIF) using RDKit and Open Babel with rigorous handling of aromaticity perception… | GPTomics/ | 1.2k | 1 repo | ~3.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 10 | Standardizes molecular structures using the ChEMBL structure pipeline for normalization and parent selection plus RDKit rdMolStandardize for explicit custom steps such as tautomer canonicalization… | GPTomics/ | 1.2k | 1 repo | ~4.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 11 | Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al. | GPTomics/ | 1.2k | 1 repo | ~4.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 12 | Validates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy quantification, geometric checks (planarity, vdW overlap, bond/angle distortion), and… | GPTomics/ | 1.2k | 1 repo | ~4k | Automated safety check: Pass | MIT | 1 mo ago |
