---
title: Inputs & Restraints
description: >-
  Prepare SMILES, PXRD patterns, and analysis parameters for XTalNet crystal
  structure prediction and polymorph screening.
---

You provide either a SMILES string (de novo prediction) or an experimental PXRD pattern plus the compound's formula (matching against candidates), then pick an analysis type. That choice is what most affects the result, since it sets how many candidate structures are generated and whether a full polymorph screen runs.

## Webapp input methods

The .bloom* webapp provides a comprehensive interface for XtalNet crystal structure prediction from a SMILES string or PXRD data.

## Analysis type selection

| Analysis Type | Description |
|---------------|-------------|
| **Crystal Structure Prediction** | Predict crystalline structures from a SMILES string, or match candidates against PXRD data |
| **Polymorph Screening** | Comprehensive polymorph analysis — 10-50 candidates, default 25 |

## PXRD data input

### Upload options

- **Upload PXRD File**: Upload `.csv`, `.txt`, or `.dat` files with angle,intensity pairs
- **Load Example**: Select from curated example datasets

### File format

PXRD files should contain angle (2θ) and intensity pairs:
- Comma, semicolon, or whitespace separated
- Lines starting with `#` or `//` are treated as comments
- Format: `angle,intensity` (e.g., `10.5,120`)

### Data preview

After upload, the tool shows:
- Filename and data point count
- First 10 data points preview
- Success/error status

## Compound information

Provide a SMILES string for de novo prediction, or PXRD data plus a formula for experimental matching — one of the two is required.

| Parameter | Required | Description |
|-----------|----------|-------------|
| **SMILES String** | Required for de novo CSP (or use PXRD data instead) | SMILES of the molecule, e.g. `"CC(=O)Oc1ccccc1C(=O)O"` |
| **Compound Formula** | Required when matching against PXRD data | Chemical formula (e.g., `C15H12N2O`) |
| **Compound Name** | No | Descriptive name for tracking |
| **Coformer SMILES** | No (polymorph mode only) | SMILES of a coformer for co-crystal prediction, e.g. nicotinamide, saccharin, fumaric acid |

## Webapp parameters

### Analysis parameters — Crystal Structure Prediction mode (`xtalnet_csp_predict`)

| Parameter | Range | Default | Description |
|-----------|-------|---------|-------------|
| **Analysis Level** | basic/standard/comprehensive | standard | Depth of analysis |
| **Number of Candidates** | 1-50 | 10 | Crystal structures to generate |
| **Sampling Temperature** | 0.1-2.0 | 1.0 | Randomness in generation |
| **Min Confidence Threshold** | 0-1 | 0.5 | Filter uncertain predictions |

### Analysis parameters — Polymorph Screening mode (`xtalnet_polymorph_predict`)

| Parameter | Range | Default | Description |
|-----------|-------|---------|-------------|
| **Search Depth** | quick/standard/thorough | standard | `thorough` for late-stage candidates, `quick` for early screening |
| **Number of Candidates** | 10-50 | 25 | Polymorph candidates to generate |
| **Sampling Temperature** | 0.1-2.0 | 1.0 | Randomness in structure generation |
| **Stability Ranking Temperature** | 100-500 K | 298 K | Temperature used to rank polymorph stability — use 310 K for body temperature |
| **Polymorph Similarity Threshold** | 0.5-0.99 | 0.85 | Similarity threshold for treating two candidates as distinct polymorphs |
| **Min Confidence Threshold** | 0-1 | 0.5 | Filter uncertain predictions |

### Crystal system preference (optional, both modes)

Select to constrain predictions:
- Cubic, Tetragonal, Orthorhombic
- Hexagonal, Trigonal
- Monoclinic, Triclinic

### Target application (both modes)

- Polymorph Screening
- Formulation Development
- Stability Assessment
- Materials Characterization

### Analysis options

| Option | CSP default | Polymorph default | Description |
|--------|-------------|--------------------|-------------|
| **Include Polymorph Analysis** | Enabled | -- (CSP mode only) | Add a polymorph screening pass on top of CSP |
| **Include Pharmaceutical Properties** | Disabled | Enabled | Assess drug formulation relevance |
| **Include Stability Ranking** | Enabled | Enabled | Rank candidates thermodynamically |
| **Include Metastable Forms** | -- (polymorph mode only) | Enabled | Include metastable, not just the most stable, forms |

## Advanced parameters (accordion)

Additional parameters typically left at defaults:
- Min Atoms per Unit Cell (default: 1)
- Max Atoms per Unit Cell (default: 400)
- Max Structure Energy (eV/atom)

## Submit buttons

- **CSP mode**: "Run Crystal Structure Prediction"
- **Polymorph mode**: "Run Polymorph Screening"
- **Disabled when**: No SMILES and no PXRD data, or PXRD data provided without a compound formula

## Read next