Metadata-Version: 2.4
Name: ChemInformant
Version: 2.2.0
Summary: A robust and high-throughput Python client for the PubChem API, designed for automated data retrieval and analysis
Author-email: Zhiang He <ang@hezhiang.com>
License: MIT License
        
        Copyright (c) 2024 Ang <ang@hezhiang.com>
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Homepage, https://github.com/HzaCode/ChemInformant
Project-URL: Documentation, https://github.com/HzaCode/ChemInformant#readme
Project-URL: Issues, https://github.com/HzaCode/ChemInformant/issues
Keywords: chemistry,cheminformatics,pubchem,api,compound,drug,cache,pydantic,batch,smiles,sql
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: requests>=2.25.0
Requires-Dist: requests-cache>=1.2.0
Requires-Dist: pydantic>=2.0
Requires-Dist: pandas>=1.5.0
Requires-Dist: sqlalchemy>=1.4
Provides-Extra: plot
Requires-Dist: matplotlib>=3.1; extra == "plot"
Requires-Dist: Pillow>=10; extra == "plot"
Requires-Dist: seaborn>=0.12; extra == "plot"
Requires-Dist: scikit-learn>=1.1; extra == "plot"
Provides-Extra: all
Requires-Dist: ChemInformant[plot]; extra == "all"
Provides-Extra: dev
Requires-Dist: pytest>=7.0; extra == "dev"
Requires-Dist: pytest-mock>=3.5; extra == "dev"
Requires-Dist: pytest-cov>=2.12; extra == "dev"
Requires-Dist: black; extra == "dev"
Dynamic: license-file


# ChemInformant <img src="https://raw.githubusercontent.com/HzaCode/ChemInformant/main/images/logo.png" align="right" width="120px" />



[![Total Downloads](https://img.shields.io/pepy/dt/cheminformant?style=flat-square&color=306998&label=Downloads&logo=python)](https://pepy.tech/project/cheminformant)
[![Codacy Badge](https://app.codacy.com/project/badge/Grade/ba35e3e2f5224858bcaeb8f9c4ee2838)](https://app.codacy.com/gh/HzaCode/ChemInformant/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)


[![PyPI version](https://img.shields.io/pypi/v/ChemInformant.svg)](https://pypi.org/project/ChemInformant/)
[![Python Version](https://img.shields.io/badge/python-%3E%3D3.8-blue.svg)](https://pypi.org/project/ChemInformant/)
[![Build Status](https://img.shields.io/github/actions/workflow/status/HzaCode/ChemInformant/tests.yml?label=Build)](https://github.com/HzaCode/ChemInformant/actions/workflows/tests.yml) 
[![codecov](https://codecov.io/gh/HzaCode/ChemInformant/graph/badge.svg)](https://codecov.io/gh/HzaCode/ChemInformant)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![PyPI - License](https://img.shields.io/pypi/l/ChemInformant.svg)](https://github.com/HzaCode/ChemInformant/blob/main/LICENSE.md)
[![Docs](https://img.shields.io/badge/Docs-Read_Online-blue?style=flat-square&logo=book&logoColor=white)](https://hezhiang.com/ChemInformant)


**ChemInformant** is a robust data acquisition engine for the [PubChem](https.ncbi.nlm.nih.gov/pccompound/) database, engineered for the modern scientific workflow. It intelligently manages network requests, performs rigorous runtime data validation, and delivers analysis-ready results, providing a dependable foundation for any computational chemistry project in Python.

---

### Key Features

*   **Analysis-Ready Pandas Output:** The core API (`get_properties`) returns a clean Pandas DataFrame, eliminating data wrangling boilerplate and enabling immediate integration with the Python data science ecosystem.

*   **Automated Network Reliability:** Ensures your workflows run flawlessly with built-in persistent caching, smart rate-limiting, and automatic retries. It also transparently handles API pagination (`ListKey`) for large-scale queries, delivering complete result sets without any manual intervention.

*   **Flexible & Fault-Tolerant Input:** Natively accepts mixed lists of identifiers (names, CIDs, SMILES) and intelligently handles any invalid inputs by flagging them with a clear status in the output, ensuring a single bad entry never fails an entire batch operation.

*   **A Dual API for Simplicity and Power:** Offers a clear `get_<property>()` convenience layer for quick lookups, backed by a powerful `get_properties` engine for high-performance batch operations.

*   **Guaranteed Data Integrity:** Employs Pydantic v2 models for rigorous, runtime data validation when using the object-based API, preventing malformed or unexpected data from corrupting your analysis pipeline.

*   **Terminal-Ready CLI Tools:** Includes `chemfetch` and `chemdraw` for rapid data retrieval and 2D structure visualization directly from your terminal, perfect for quick lookups without writing a script.

*   **Modern and Actively Maintained:** Built on a contemporary tech stack for long-term consistency and compatibility, providing a reliable alternative to older or less frequently updated libraries.
  
---

### Installation

Install the library from PyPI:

```bash
pip install ChemInformant
```

To include plotting capabilities for use with the tutorial, install the `[plot]` extra:
```bash
pip install "ChemInformant[plot]"
```

---

### Quick Start

Retrieve multiple properties for multiple compounds, directly into a Pandas DataFrame, in a single function call:

```python
import ChemInformant as ci

# 1. Define your identifiers
identifiers = ["aspirin", "caffeine", 1983] # 1983 is paracetamol's CID

# 2. Specify the properties you need
properties = ["molecular_weight", "xlogp", "cas"]

# 3. Call the core function
df = ci.get_properties(identifiers, properties)

# 4. Save the results to an SQL database
ci.df_to_sql(df, "sqlite:///chem_data.db", "results", if_exists="replace")

# 5. Analyze your results!
print(df)


```

**Output:**

```
  input_identifier   cid status  molecular_weight  xlogp       cas
0          aspirin  2244     OK            180.16    1.2   50-78-2
1         caffeine  2519     OK            194.19   -0.1   58-08-2
2             1983  1983     OK            151.16    0.5  103-90-2
```

<details>
<summary><b>➡️ Click to see Convenience API Cheatsheet</b></summary>
<br>

| Function                   | Description                                   |
|----------------------------|-----------------------------------------------|
| `get_weight(id)`           | Molecular weight *(float)*                    |
| `get_formula(id)`          | Molecular formula *(str)*                     |
| `get_cas(id)`              | CAS Registry Number *(str)*                   |
| `get_iupac_name(id)`       | IUPAC name *(str)*                            |
| `get_canonical_smiles(id)` | Canonical SMILES with Canonical→Connectivity fallback *(str)* |
| `get_isomeric_smiles(id)`  | Isomeric SMILES *(str)*                       |
| `get_xlogp(id)`            | XLogP (calculated hydrophobicity) *(float)*   |
| `get_synonyms(id)`         | List of synonyms *(List[str])*                |
| `get_compound(id)`         | Full, validated **`Compound`** object (Pydantic v2 model) |


*All functions accept a **CID, name, or SMILES** and return `None`/`[]` on failure.*

</details>



ChemInformant also includes handy command-line tools for quick lookups directly from your terminal:

*   **`chemfetch`**: Fetches properties for one or more compounds.
    ```bash
    chemfetch aspirin --props "cas,molecular_weight,iupac_name"
    ```

*   **`chemdraw`**: Renders the 2D structure of a compound.
    ```bash
    chemdraw aspirin
    ```
---
### Documentation & Examples

For a deep dive, please see our detailed guides:

*   **➡️ Online Documentation:** The **[official documentation site](https://hezhiang.com/ChemInformant)** contains complete API references, guides, and usage examples. **This is the most comprehensive resource.**
*   **➡️ Interactive User Manual:** Our [**Jupyter Notebook Tutorial**](examples/ChemInformant_User_Manual_v1.0.ipynb) provides a complete, end-to-end walkthrough. This is the best place to start for a hands-on experience.
*   **➡️ Performance Benchmarks:** You can review and run our [**Benchmark Script**](./benchmark.py) to see the performance advantages of batching and caching.

---

### Why ChemInformant?

ChemInformant's core mission is to serve as a high-performance data backbone for the Python cheminformatics ecosystem. By delivering clean, validated, and analysis-ready Pandas DataFrames, it enables researchers to effortlessly pipe PubChem data into powerful toolkits like RDKit, Scikit-learn, or custom machine learning models, transforming multi-step data acquisition and wrangling tasks into single, elegant lines of code.

A detailed comparison with other existing tools is provided in our [JOSS paper](https://github.com/HzaCode/ChemInformant/blob/main/paper/paper.md).

### Contributing

Contributions are welcome! For guidelines on how to get started, please read our [contributing guide](https://github.com/HzaCode/ChemInformant/blob/main/CONTRIBUTING.md). You can [open an issue](https://github.com/HzaCode/ChemInformant/issues) to report bugs or suggest features, or [submit a pull request](https://github.com/HzaCode/ChemInformant/pulls) to contribute code.
### License

This project is licensed under the MIT License - see the [LICENSE](LICENSE.md) file for details.
### Citation

If you use **ChemInformant** in your research, please cite **the software** 
> **Software**: He, Z. *ChemInformant* (v2.1.1) [Software]. GitHub, https://github.com/HzaCode/ChemInformant.  
