Searching Structure Databases

CatGo integrates with three online databases for finding crystal structures and molecules: OPTIMADE, Materials Project, and PubChem.

OPTIMADE Search

OPTIMADE is a standardized API for querying crystal structure databases. CatGo supports searching across multiple providers.

Opening the Search

Click the OPTIMADE button in the toolbar (or the database icon) to open the search modal.

Searching by Formula

1. Type a chemical formula in the Formula field (e.g., NaCl, Fe2O3, SrTiO3)
2. Click Search or press Enter
3. Results show structure ID, formula, number of sites, and crystal system

Formulas are automatically normalized to OPTIMADE format (alphabetically sorted elements).

Searching by Elements

1. Enter element symbols in the Elements field (e.g., Fe, O)
2. Toggle Elements only to find structures containing only those elements
3. Set optional filters:
   • Nelements — Exact number of elements (or min/max range)
   • Nsites — Min/max number of atomic sites

Using the Periodic Table

Click any element in the embedded periodic table to instantly search for structures containing that element.

Choosing a Provider

Use the Database dropdown to select a provider:

• Materials Project — Large database of computed materials
• AFLOW — Automatic flow for materials discovery
• COD — Crystallography Open Database (experimental structures)
• And more OPTIMADE-compliant databases

Materials Project Enrichment

If you configure a Materials Project API key, search results from MP are enriched with computed properties:

• Band gap (eV)
• Energy above hull (eV/atom) — stability metric
• Crystal system and space group
• Formation energy

To add your API key:

1. Click Add API key in the search modal
2. Enter your key from materialsproject.org
3. The key is stored locally in your browser (localStorage)

Importing a Structure

Click Import on any result to load it into the 3D viewer. For OPTIMADE results, a preview modal may appear first showing the structure before confirming the import.

PubChem Search

PubChem provides molecular compound data. Use this for organic molecules, drugs, and small molecules.

PubChem Search Details

Click the PubChem button in the toolbar to open the search modal.

Searching

• By name — Type a compound name (e.g., benzene, aspirin, caffeine)
• By formula — Type a molecular formula (e.g., C6H6, H2O)
• By element — Click elements in the periodic table

CatGo auto-detects whether you entered a name or formula.

Results

Results show:

• PubChem Compound ID (CID)
• Molecular formula
• Compound name
• Molecular weight
• Composition pie chart

Importing

Click Import to load the molecule's 3D structure. PubChem compounds are loaded as molecules (no periodic lattice). The 3D coordinates come from PubChem's computed conformer data.

Key Differences

Feature	OPTIMADE	PubChem
Structure type	Crystals (periodic)	Molecules (non-periodic)
Lattice	Yes	No
Periodic boundaries	pbc = [true, true, true]	pbc = [false, false, false]
Search parameters	Formula, elements, nsites	Name, formula, elements
Authentication	Optional (MP API key)	None
Requires server	Yes (backend proxy for CORS)	Yes (backend proxy for CORS)

Server Requirement

Both database search features route through the Python backend to handle CORS restrictions. Make sure the server is running:

cd server
python main.py

Tips

• Start broad, then filter — Search by elements first, then narrow down by formula or site count.
• Use MP API key — The enriched properties (band gap, stability) make it much easier to find useful structures.
• Export after import — Once imported, use the Export pane to save structures in your preferred format (CIF, POSCAR, etc.).
• Combine with tools — Import a bulk crystal from OPTIMADE, then use the slab cutter to create a surface.