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Chemistry

Molecular modeling and reactions.

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computational-chemistry
18.1K

qutip

Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.

K-Dense-AI
K-Dense-AI
research
open
computational-chemistry
18.1K

rdkit

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.

K-Dense-AI
K-Dense-AI
research
open
computational-chemistry
18.1K

rowan

Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, docking and analogue docking, protein-ligand cofolding, MSA generation, molecular dynamics, permeability, descriptor workflows, and related small-molecule or protein modeling tasks. Ideal for programmatic batch screening, multi-step chemistry pipelines, and workflows that would otherwise require maintaining local HPC/GPU infrastructure.

K-Dense-AI
K-Dense-AI
research
open
computational-chemistry
18.1K

stable-baselines3

Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and well-documented algorithm implementations. Best for single-agent RL with Gymnasium environments. For high-performance parallel training, multi-agent systems, or custom vectorized environments, use pufferlib instead.

K-Dense-AI
K-Dense-AI
research
open
computational-chemistry
17.6K

pyhealth

Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).

davila7
davila7
research
open
computational-chemistry
17.6K

fda-consultant-specialist

Senior FDA consultant and specialist for medical device companies including HIPAA compliance and requirement management. Provides FDA pathway expertise, QSR compliance, cybersecurity guidance, and regulatory submission support. Use for FDA submission planning, QSR compliance assessments, HIPAA evaluations, and FDA regulatory strategy development.

davila7
davila7
research
open
computational-chemistry
17.6K

pymatgen

Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.

davila7
davila7
research
open
computational-chemistry
17.6K

cobrapy

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

davila7
davila7
research
open
computational-chemistry
17.6K

fda-database

Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.

davila7
davila7
research
open
computational-chemistry
17.6K

datamol

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.

davila7
davila7
research
open
computational-chemistry
17.6K

medchem

Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

davila7
davila7
research
open
computational-chemistry
17.6K

qiskit

Comprehensive quantum computing toolkit for building, optimizing, and executing quantum circuits. Use when working with quantum algorithms, simulations, or quantum hardware including (1) Building quantum circuits with gates and measurements, (2) Running quantum algorithms (VQE, QAOA, Grover), (3) Transpiling/optimizing circuits for hardware, (4) Executing on IBM Quantum or other providers, (5) Quantum chemistry and materials science, (6) Quantum machine learning, (7) Visualizing circuits and results, or (8) Any quantum computing development task.

davila7
davila7
research
open
computational-chemistry
17.6K

clinical-reports

Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.

davila7
davila7
research
open
computational-chemistry
17.6K

clinicaltrials-database

Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.

davila7
davila7
research
open
computational-chemistry
12.1K

simplify

Reduce formula complexity using Z3 tactic chains. Supports configurable tactic pipelines for boolean, arithmetic, and bitvector simplification.

Z3Prover
Z3Prover
research
open
computational-chemistry
11.3K

promptinjection

Test LLM applications for prompt injection vulnerabilities — jailbreak attempts, system prompt extraction, context manipulation, guardrail bypass techniques, direct injection, indirect injection, multi-stage attacks, and reconnaissance. USE WHEN prompt injection, jailbreak, LLM security, AI security assessment, pentest AI application, test chatbot, guardrail bypass, direct injection, indirect injection, RAG poisoning, multi-stage attack, complete assessment, reconnaissance.

danielmiessler
danielmiessler
research
open
computational-chemistry
10.9K

chemistry-rdkit

Computational chemistry with RDKit for molecular analysis, descriptors, fingerprints, and substructure search. Use when working with SMILES, drug discovery, or cheminformatics tasks.

aiming-lab
aiming-lab
research
open
computational-chemistry
10.9K

cv-detection

Best practices for object detection tasks. Use when working on COCO, VOC, or detection architectures like YOLO and DETR.

aiming-lab
aiming-lab
research
open
computational-chemistry
10.4K

fda-consultant-specialist

FDA regulatory consultant for medical device companies. Provides 510(k)/PMA/De Novo pathway guidance, QSR (21 CFR 820) compliance, HIPAA assessments, and device cybersecurity. Use when user mentions FDA submission, 510(k), PMA, De Novo, QSR, premarket, predicate device, substantial equivalence, HIPAA medical device, or FDA cybersecurity.

alirezarezvani
alirezarezvani
research
open
computational-chemistry
9.8K

prioritize-assumptions

Prioritize assumptions using an Impact × Risk matrix and suggest experiments for each. Use when triaging a list of assumptions, deciding what to test first, or applying the assumption prioritization canvas.

phuryn
phuryn
research
open
computational-chemistry
7.8K

review-delta

Review only changes since last commit using impact analysis. Token-efficient delta review with automatic blast-radius detection.

tirth8205
tirth8205
research
open
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