Accepts ChemrytIQ handoff, URL fallback, cached input, MOL block, SELFIES, SMILES, InChI, name, or internal ID.
Prerequisite: Load The Molecule From ChemrytIQ
Before opening ChemrytIQ-AEM, search the molecule in ChemrytIQ by SMILES, InChI, molecule name, or CAS number. Confirm the correct molecule on the ChemrytIQ page, then open the required Chemryt app from that same molecule context so the selected structure is loaded into the app automatically.
What It Does
ChemrytIQ-AEM resolves molecule input from ChemrytIQ, SMILES, SELFIES, InChI, names, MOL blocks, or cached local input, then prepares a 3D structure for visual cleanup and handoff to other ChemrytIQ workflows.
Initializes coordinates, runs geometry cleanup, tracks energy, and previews structures with 3Dmol.js.
Supports dihedral adjustment, conformer ensembles, ESP surface generation, structural validation, and comparative alignment.
Quick Tutorial
- Start from a ChemrytIQ molecule or paste a molecular identifier into the AEM input source.
- Run initialization and confirm that the 2D preview, resolved name, SMILES, and 3D viewer look correct.
- Run optimization or streaming optimization to clean the geometry and review the energy trace.
- Use validation alerts to inspect atom, bond, stereochemistry, or coordinate issues before continuing.
- Open dihedral, conformer, ESP surface, or comparative alignment tools when the geometry needs deeper review.
- Return the minimized MOL block or selected structure state to ChemrytIQ when another module needs the prepared geometry.
Main Areas
| Area | What to review | When to use it |
|---|---|---|
| Engine status | Runtime capability, backend status, active alerts, and issue tracker. | Use before trusting a generated geometry. |
| 3D molecule | Viewer, minimized structure, energy trace, conformer selector, and lifecycle table. | Use to inspect the prepared molecule. |
| Visual tools | Dihedral controls, rotamer scan, ESP surface, comparative alignment, and output actions. | Use for detailed geometry review and handoff. |
ML Model / Computation Used
| Model or method | What it predicts | Implementation details |
|---|---|---|
| Approximate energy minimization workflow | 3D cleanup, conformer/dihedral review, ESP surface, and alignment support. | No deployed trained ML artifact was found for AEM. The module is documented as geometry preparation, visualization, and computational chemistry workflow support. |
Good Practice
Use AEM geometry as preparation and visualization support. Confirm important conformations, charges, protonation states, and alignment decisions with validated computational chemistry or experimental evidence.
Reference Used
This Tutorial page mirrors the ChemrytIQ reference module: ChemrytIQ-AEM.