ChemistryAtlas Apps

Chemistry bench apps

ChemistryAtlas includes 178 chemistry-first apps for compound identity, bench calculations, spectroscopy confirmation, solvent lookup, and safety triage.

Open interactive app catalog

Chemistry-first launch catalog

The public app catalog starts with daily chemistry workflows and also includes specialized advanced tools for energy, polymers, computation, and molecular systems.

Draw, Identity, and Visualization

Compound Card

Resolve names, formulas, SMILES, and InChI into formula, MW, exact mass, identifiers, drug-like descriptors, percent composition, and PubChem context.

AvailableOpen app

Wetcher

Draw molecules and reactions with the EPAM Ketcher editor, then export SMILES or molfile text into ChemistryAtlas tools.

AvailableOpen app

WeNGL

High-performance browser visualization for proteins, nucleic acids, complexes, and molecular structure files using NGL Viewer.

AvailableOpen app

WyMOL

Hybrid molecular figure app: preview structures in the browser, then generate PyMOL scripts and publication-style render outputs on the backend.

AvailableOpen app

ChimeraXWeb

Run ChimeraX-backed structure superposition, RMSD, contacts, H-bonds, clashes, surface/pocket inspection, density-map fitting, figure rendering, and command scripts from the web.

AvailableOpen app

VMDWeb

Analyze molecular-dynamics trajectories and VMD atom selections from the web with NGL preview and backend VMD Tcl workflows.

AvailableOpen app

JSMolView

Visualize molecules, crystals, and Jmol scripts with a JSmol/Jmol-compatible browser viewer.

AvailableOpen app

3DXView

Render small molecules, crystals, PDB files, SDF/MOL blocks, and XYZ coordinates with 3Dmol.js.

AvailableOpen app

MacroVis

Explore proteins, nucleic acids, complexes, CIF/mmCIF structures, PDB IDs, and AlphaFold entries using Mol*.

AvailableOpen app

WESTA

View crystal and molecular structures in a web-native VESTA-style structure viewer.

AvailableOpen app

Periodic Table

Explore elemental properties, periodic trends, filters, electron information, and selected element sets for chemistry workflows.

AvailableOpen app

Bench Calculators

Reaction Stoichiometry Calculator

Scale a reaction to a limiting reagent and generate equivalents, mmol, mass, optional volume, theoretical yield, percent yield, and a printable weigh-out sheet.

AvailableOpen app

Solution Prep Suite

Create molarity, dilution, serial dilution, buffer, and unit/concentration worksheets for common bench preparation tasks.

AvailableOpen app

Polymer Calculator

Calculate DP, Mn/Mw, monomer feed, copolymer composition, and Fox-equation Tg estimates for polymer planning.

AvailableOpen app

Spectra & Analysis

QM Input Generator

Generate RDKit 3D geometries, Gaussian/ORCA/Psi4/xTB input files, command manifests, and geometry-opt workflow scripts.

AvailableOpen app

NMR Data Processor

Process JCAMP-style text or peak lists into normalized integrals, coupling/assignment hints, and predicted-vs-observed context.

AvailableOpen app

Safety & Solvents

Waste Disposal Classifier

Classify common research waste streams into halogenated, nonhalogenated, aqueous acid/base, oxidizer, heavy-metal, and solid waste routes.

AvailableOpen app

Discovery + Design

Retrosynthesis Planner

Detect common retrosynthetic disconnections such as esters, amides, aryl halides, and boronic-acid coupling handles.

AvailableOpen app

Reference + Methods

Prediction + Cheminformatics

QSAR / ML Model Builder

Train a small Random Forest QSAR model from smiles,target CSV data and predict new molecules from RDKit descriptors.

AvailableOpen app

Workflow + Community

Pipeline Builder

Chain chemistry tools into reusable workflow definitions with JSON and table exports.

AvailableOpen app

Chemistry Problem Solvers

AI Synthesis

Route Scorer

Score candidate routes by step count, complexity, green metrics, safety flags, PMI, cost hints, and confidence.

AvailableOpen app

ASKCOS Sidecar Connector

Check ASKCOS sidecar availability and package requests for retrosynthesis, forward prediction, context, and impurity models.

AvailableOpen app

Generative Molecular Design Pro

R-Group Optimization Pro

Enumerate and rank substituent replacements using RDKit descriptors, synthesis filters, and optional ChemProp predictions.

AvailableOpen app

AI Spectra + Virtual Screening

AI MS/MS Predictor

Predict MS/MS fragments using ms-pred/ICEBERG sidecar when available or deterministic exact-mass losses locally.

AvailableOpen app

Docking-to-Design Loop

Convert docking hits into next design ideas with R-group/scaffold suggestions and active-learning priorities.

AvailableOpen app

Formula and Structure Checks

Energy Above Hull Calculator

Calculate energy above the Materials Project convex hull from formula energy, CIF energy, or an approximate MACE-predicted energy diagnostic.

AvailableOpen app

Properties and Prediction

2D Materials

Predict whether candidate compounds are likely two-dimensional materials.

AvailableOpen app

Band Gap

Predict band gap values from composition or structure input.

AvailableOpen app

Dielectric Constant

Predict scalar dielectric constants for capacitor, insulator, and functional dielectric screening.

AvailableOpen app

Inverse Design

Candidate Screening

Electrolyte and Energy Chemistry

Experimentalist Tools

XRD Analysis Studio

Simulate powder XRD patterns from structures and compare two structures with peak-shift summaries.

AvailableOpen app

QM and Computational Chemistry

Magnetism Assistant

Prepare magnetic DFT starting settings, MAGMOM hints, DFT+U notes, and SOC/noncollinear guidance.

AvailableOpen app

Phonon Post-processing

Parse phonopy/QE phonon outputs, flag imaginary modes, plot phonon band/DOS/thermal curves, and export mode data.

AvailableOpen app

Molecular Simulation

Utilities & Tools