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PubChemCrawler.jl

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Utilities to programmatically query the PubChem database

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- - ci.yml
  - CompatHelper.yml
  - Documenter.yml
  - TagBot.yml
- - index.md
- make.jl
- Project.toml
- PubChemCrawler.jl
- pugxml.jl
- query.jl
- utils.jl
- - aspirin_cid_from_name.bson
  - aspirin_cid_from_smiles.bson
  - aspirin_cids.bson
  - aspirin_smiles_from_cid.bson
  - asprin_sdf_3d.bson
  - CAS_as_json.bson
  - CAS_as_txt.bson
  - cGMP_cid.bson
  - estriol_cid.bson
  - estriol_substructure.bson
  - estriol_substructure_formulas.bson
  - estriol_synonyms_from_cid.bson
  - estriol_synonyms_from_name.bson
  - estriol_synonyms_from_smiles.bson
  - ethanol_pug.bson
  - smarts.bson
  - smarts_pug.bson
  - sodium_acetate_parent.bson
- runtests.jl
.git-blame-ignore-revs
.gitignore
.JuliaFormatter.toml
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
Project.toml
README.md

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PubChemCrawler.jl makes it easy to query the [PubChem database](https://pubchem.ncbi.nlm.nih.gov/) from Julia. This package provides a simple interface to search for chemical compounds, retrieve their properties, and perform substructure searches.

## Features

- **Compound Lookup**: Search for compounds by name, SMILES, or CAS number
- **Property Retrieval**: Get molecular formulas, weights, and other properties
- **Substructure Search**: Find compounds containing specific molecular substructures
- **Synonym Retrieval**: Access chemical names and synonyms
- **Multiple Output Formats**: CSV, JSON, TXT, SDF, and more

## Installation

Install PubChemCrawler.jl using Julia's package manager:

```julia
using Pkg
Pkg.add("PubChemCrawler")
```

Or in the Julia REPL, press `]` to enter package mode and run:

```
add PubChemCrawler
```

## Quick Start

```julia
using PubChemCrawler

# Get compound ID for a chemical by name
cid = get_cid(name="aspirin")

# Get compound ID using SMILES notation
cid = get_cid(smiles="CC(=O)OC1=CC=CC=C1C(=O)O")

# Get all compound IDs for a CAS number
cids = get_cids(cas_number="50-78-2")
```

## Usage Examples

For detailed usage examples including:
- Finding compound IDs
- Retrieving compound properties
- Substructure searching
- Getting synonyms
- Parsing chemical formulas

See the [Getting Started guide](https://juliahealth.org/PubChemCrawler.jl/stable/#Getting-started).

## Documentation

For detailed documentation, including all available functions and options, visit the [official documentation](https://JuliaHealth.github.io/PubChemCrawler.jl/stable).

## Contributing

We welcome contributions! Please see our [Contributing Guidelines](CONTRIBUTING.md) for details on how to:

- Report issues
- Submit pull requests
- Follow code style guidelines (Blue style)

## License

This package is licensed under the MIT License. See [LICENSE](LICENSE) for details.