「molecular ml」の検索結果

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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Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.

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3Dmol.js WebGL molecular visualization emitted as self-contained HTML. Render structures (PDB/SDF/XYZ/MOL2/cube) with stick, sphere, cartoon, line, and surface styles; animate trajectories with a frame-delay (interval, ms) control; and animate vibrational normal modes via vibrate() from per-atom dx/dy/dz displacements or from precomputed frames. Output standalone HTML that loads 3Dmol from a CDN, with optional play/pause and speed controls. Use for transition-state imaginary-mode animations, MD or reaction-path playback, docking poses, and orbital/density isosurfaces. For static 2D chemical structure drawings use rdkit-chemdraw-cdxml; for 2D statistical plots use matplotlib or plotly.

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Molecular featurization hub (100+ featurizers) for ML. SMILES to fingerprints (ECFP, MACCS, MAP4), descriptors (RDKit 2D, Mordred), pretrained embeddings (ChemBERTa, GIN, Graphormer), pharmacophores. Scikit-learn compatible with parallelization/caching. For QSAR, virtual screening, similarity, and molecular DL.

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Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For ready-made ADMET numbers without training a model use admet-prediction; for benchmark datasets and task-aware splits use pytdc.

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Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.

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Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs (GIN, GAT, SchNet), 40+ datasets, for PyTorch-based ML on molecules, proteins, and biomedical graphs.

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Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.

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Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or double-ML medDML. Use when testing whether a molecular phenotype (expression, methylation, protein) mediates a treatment-outcome relationship, decomposing exposure-mediator interaction via VanderWeele 4-way, screening high-dimensional EWAS mediators, or running MR-based mediation when sequential ignorability is implausible.

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PyTorch-based ML platform for drug discovery: graph molecular representation learning, property prediction (ADMET, activity), retrosynthesis, drug-target interaction (DTI), and pretraining on large molecular datasets. Provides GNN layers (GraphConv, GAT, MPNN), pretrained models, and benchmark datasets.

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AiZynthFinder retrosynthetic route planning (CASP) from AstraZeneca Molecular AI. Monte Carlo tree search guided by a template-based neural expansion policy recursively disconnects a target SMILES until precursors are found in a purchasable stock. Covers config.yml (v4 format), aizynthcli batch screening, the AiZynthFinder/AiZynthExpander Python API, one-step disconnections, custom stocks via smiles2stock, scorers, Retro*/breadth-first/DFPN search alternatives, and reading output.json.gz / trees.json. Use for synthesis route planning, synthesizability screening, and building-block/precursor search. For reaction barriers use neb-irc-activation-energy; for 2D reaction scheme drawing use rdkit-chemdraw-cdxml.

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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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Evaluate and review GO-CAM (Gene Ontology Causal Activity Model) activities / annotons — molecular-function typing, has-input, causal relations, complexes, evidence — and check their consistency with gene annotation reviews. Use when reviewing cached GO-CAMs under gocams/, filling a GoCamReview YAML (gocams/<id>/<id>-review.yaml), or grounding a module in GO-CAM models.

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Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or double-ML medDML. Use when testing whether a molecular phenotype (expression, methylation, protein) mediates a treatment-outcome relationship, decomposing exposure-mediator interaction via VanderWeele 4-way, screening high-dimensional EWAS mediators, or running MR-based mediation when sequential ignorability is implausible.

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Expert-level computational biology covering molecular dynamics simulation, protein structure prediction, systems biology, network analysis, and machine learning in biology.

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AiZynthFinder retrosynthetic route planning (CASP) from AstraZeneca Molecular AI. Monte Carlo tree search guided by a template-based neural expansion policy recursively disconnects a target SMILES until precursors are found in a purchasable stock. Covers config.yml (v4 format), aizynthcli batch screening, the AiZynthFinder/AiZynthExpander Python API, one-step disconnections, custom stocks via smiles2stock, scorers, Retro*/breadth-first/DFPN search alternatives, and reading output.json.gz / trees.json. Use for synthesis route planning, synthesizability screening, and building-block/precursor search. For reaction barriers use neb-irc-activation-energy; for 2D reaction scheme drawing use rdkit-chemdraw-cdxml.

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Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.

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Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.

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Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or double-ML medDML. Use when testing whether a molecular phenotype (expression, methylation, protein) mediates a treatment-outcome relationship, decomposing exposure-mediator interaction via VanderWeele 4-way, screening high-dimensional EWAS mediators, or running MR-based mediation when sequential ignorability is implausible.

日本語の概要は準備中です。原文の説明を表示しています。

Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.

日本語の概要は準備中です。原文の説明を表示しています。

Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or double-ML medDML. Use when testing whether a molecular phenotype (expression, methylation, protein) mediates a treatment-outcome relationship, decomposing exposure-mediator interaction via VanderWeele 4-way, screening high-dimensional EWAS mediators, or running MR-based mediation when sequential ignorability is implausible.

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Provides Therapeutics Data Commons workflows through PyTDC for registry discovery, dataset access, task-aware splits, evaluator metrics, benchmark groups, and bounded molecular-oracle scoring. Use when working with TDC therapeutic ML datasets or benchmarks.

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Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML. Covers ECFP/MACCS fingerprints, RDKit descriptors, pharmacophores, pretrained embeddings, configuration persistence, and molecule-to-label alignment.

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Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked labels, graph models and explicit pretrained encoder transfer. Used for ADMET, toxicity, solubility and chemistry ML when DeepChem data/model contracts and scientific validation are needed.

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