semvec/pypi-packages huggingface dataset:
create-agent 0.0.3
CLI tool to generate LLM agent API projects
License: MIT
Requires Python: >=3.9

# create-agent

A CLI tool to quickly scaffold LLM agent API projects with an OpenAI-compatible interface.

## Features

- Create a new agent project with a single command
- Includes ready-to-use API endpoints compatible with OpenAI's chat completion API
- Built-in RAG (Retrieval Augmented Generation) capabilities using LangGraph
- Support for custom tool definitions
- Complete FastAPI application structure

## Installation

```bash
pip install create-agent
```

## Usage

Create a new agent project:

```bash
create-agent my-agent
```

This will create a new directory called `my-agent` with all the necessary files to run an agent API.

### Options

- `--template`: Specify a template to use (default: "default")
- `--output-dir`: Specify the output directory (default: current directory)

```bash
create-agent my-agent --output-dir projects
```

## Project Structure

The generated project follows a well-organized structure:

```
my-agent/
├── app/
│   ├── api/            # API definitions and models
│   ├── core/           # Core functionality
│   ├── rag/            # RAG implementation with LangGraph
│   ├── services/       # Business logic services
│   ├── utils/          # Utility functions
│   ├── config.py       # Application configuration
│   └── main.py         # FastAPI application
├── .env.example        # Environment variables template
├── .gitignore          # Git ignore file
├── README.md           # Project documentation
└── requirements.txt    # Dependencies
```

## Next Steps After Creating a Project

1. Navigate to your new project directory:

   ```bash
   cd my-agent
   ```

2. Create and activate a virtual environment:

   ```bash
   python -m venv venv
   source venv/bin/activate  # On Windows: venv\Scripts\activate
   ```

3. Install dependencies:

   ```bash
   pip install -r requirements.txt
   ```

4. Set up your environment variables:

   ```bash
   cp .env.example .env
   ```

5. Edit the `.env` file with your API keys and configuration

6. Run the application:
   ```bash
   uvicorn app.main:app --reload
   ```

## License

MIT
genice2-cage 2.5.2
A format plugin for GenIce2 to detect cages.
License: MIT
Requires Python: <4.0,>=3.10

![Logo](https://raw.githubusercontent.com/vitroid/GenIce/develop/logo/genice-v0.png)

# [genice2-cage](https://github.com/vitroid/genice-cage)

A format plugin for [GenIce2](https://github.com/vitroid/GenIce) to detect cages.

version 2.5

## Requirements

* python^3.10
* GenIce2^2.2.5.2
* graphstat^0.3.3
* yaplotlib^0.1.2
* numpy>=1.26.4
* networkx>=3.2.1
* cycless>=0.6.3


## Installation from PyPI

```shell
% pip install genice2-cage
```

## Usage
        
    A GenIce2 format plugin to detect cage-like topologies.

    Usage:
        % genice2 CS1 -r 2 2 2 -f cage[12,14-16:ring=-6]
        % genice2 CRN1 -f cage[sizes=3-10:json]
        % genice2 CRN1 -f cage[sizes=3-10:yaplot]
        % genice2 CS2 -w tip4p -f cage[gromacs:sizes=-16:ring=5,6]
        % analice2 traj.gro -O OW -H HW[12] -w tip4p -f cage[quad]
        % analice2 traj.gro -O OW -H HW[12] -w tip4p -f cage[quad:json]
        % genice2 FAU -r 2 2 2 -f cage[-26:maxring=12:json2]

    It may not work with a small structure. (In the example above, the unit cell of CS1 is extended to 2x2x2 so as to avoid detecting cell-spanning wierd cages.)

    Options:
        Cage sizes to be listed, separated by commas and ranged with hyphens. (e.g. -4,6,8-10,16-) (default is 3-16)
        ring=3,5-6 Specify the ring sizes that cages are built of (default is 3-8, maximum is 8).
        json       Output values in [JSON](https://www.json.org/) format.
        json2      Output values in [JSON](https://www.json.org/) format (Assess cage locations based on HB network topology by labeling them).
        yaplot     Visualize cages with [Yaplot](https://github.com/vitroid/Yaplot/). Cages are drawn in different layers according to the number of faces, and faces are colored according to the number of vertices.
        gromacs    Output individual cages in Gromacs format. (EXPERIMENTAL)
        quad       Quadcage order parameter to identify the Frank-Kasper-type crystal structures.[JMM2011] Cages sizes and maximum ring size are set appropriately automatically.
        python     Output cage types in python format convenient for GenIce lattice modules.
    * [JMM2011] Jacobson, L. C., Matsumoto, M. & Molinero, V. Order parameters for the multistep crystallization of clathrate hydrates. J. Chem. Phys. 135, 074501 (2011).[doi:10.1063/1.3613667](https://doi.org/10.1063/1.3613667)



## Test in place

```shell
% make test
```

## Algorithms

* M. Matsumoto, A. Baba, and I. Ohmine, Topological building blocks of hydrogen bond network in water, J. Chem. Phys. 127, 134504 (2007); [doi:10.1063/1.2772627](http://dx.doi.org/doi:10.1063/1.2772627)