RosettaFinder

A Python utility for finding Rosetta binaries based on a specific naming convention.

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Overview

RosettaFinder is a Python module designed to locate Rosetta biomolecular modeling suite binaries that follow a specific naming pattern. It searches predefined directories and can handle custom search paths. The module includes:

An object-oriented RosettaFinder class to search for binaries.
A RosettaBinary dataclass to represent the binary and its attributes.
A command-line shortcut for quick access to Rosetta binaries.
Unit tests to ensure reliability and correctness.

Features

Flexible Binary Search: Finds Rosetta binaries based on their naming convention.
Platform Support: Supports Linux and macOS operating systems.
Customizable Search Paths: Allows specification of custom directories to search.
Structured Binary Representation: Uses a dataclass to encapsulate binary attributes.
Command-Line Shortcut: Provides a quick way to find binaries via the command line.
Available on PyPI: Installable via pip without the need to clone the repository.
Unit Tested: Includes tests for both classes to ensure functionality.

Naming Convention

The binaries are expected to follow this naming pattern:

rosetta_scripts[.mode].oscompilerrelease

Binary Name: rosetta_scripts (default) or specified.
Mode (optional): default, mpi, or static.
OS: linux or macos.
Compiler: gcc or clang.
Release: release or debug.

Examples of valid binary filenames:

rosetta_scripts.linuxgccrelease
rosetta_scripts.mpi.macosclangdebug
rosetta_scripts.static.linuxgccrelease

Installation

Ensure you have Python 3.6 or higher installed.

Install via PyPI

You can install rosetta_finder directly from PyPI:

pip install rosetta_finder -U

This allows you to use rosetta_finder without cloning the repository.

Usage

Command-Line Shortcut

rosetta_finder provides a command-line shortcut to quickly locate Rosetta binaries.

Using the `whichrosetta` Command

After installing rosetta_finder, you can use the whichrosetta command in your terminal.

whichrosetta <binary_name>

Example:

To find the relax binary:

relax_bin=$(whichrosetta relax)
echo $relax_bin

This command assigns the full path of the relax binary to the relax_bin variable and prints it.

Importing the Module

You can also use rosetta_finder in your Python scripts.

from rosetta_finder import RosettaFinder, RosettaBinary

Finding a Rosetta Binary in Python

# Initialize the finder (optional custom search path)
finder = RosettaFinder(search_path='/custom/path/to/rosetta/bin')

# Find the binary (default is 'rosetta_scripts')
rosetta_binary = finder.find_binary('rosetta_scripts')

# Access binary attributes
print(f"Binary Name: {rosetta_binary.binary_name}")
print(f"Mode: {rosetta_binary.mode}")
print(f"OS: {rosetta_binary.os}")
print(f"Compiler: {rosetta_binary.compiler}")
print(f"Release: {rosetta_binary.release}")
print(f"Full Path: {rosetta_binary.full_path}")

Example Output

Binary Name: rosetta_scripts
Mode: mpi
OS: linux
Compiler: gcc
Release: release
Full Path: /custom/path/to/rosetta/bin/rosetta_scripts.mpi.linuxgccrelease

Environment Variables

The RosettaFinder searches the following directories by default:

The path specified in the ROSETTA_BIN environment variable.
ROSETTA3/bin
ROSETTA/main/source/bin/
A custom search path provided during initialization.

Set the ROSETTA_BIN environment variable to include your custom binary directory:

export ROSETTA_BIN=/path/to/your/rosetta/bin

API Reference

`whichrosetta` Command

The whichrosetta command is installed as part of the rosetta_finder package and allows you to find the path to a Rosetta binary from the command line.

Usage:

whichrosetta <binary_name>

binary_name: The name of the Rosetta binary you want to locate (e.g., relax, rosetta_scripts).

Example:

relax_bin=$(whichrosetta relax)
echo $relax_bin

This command finds the relax binary and prints its full path.

`RosettaFinder` Class

Initialization
```
RosettaFinder(search_path=None)
```
- search_path (optional): A custom directory to include in the search paths.
Methods
- find_binary(binary_name='rosetta_scripts')
  
  Searches for the specified binary and returns a RosettaBinary instance.
  - binary_name (optional): Name of the binary to search for.
  - Raises:
    - FileNotFoundError: If the binary is not found.
    - EnvironmentError: If the OS is not Linux or macOS.

`RosettaBinary` Dataclass

Attributes
- dirname: Directory where the binary is located.
- binary_name: Base name of the binary.
- mode: Build mode (static, mpi, default, or None).
- os: Operating system (linux or macos).
- compiler: Compiler used (gcc or clang).
- release: Build type (release or debug).
Properties
- filename: Reconstructed filename based on the attributes.
- full_path: Full path to the binary executable.
Class Methods
- from_filename(dirname: str, filename: str)
  
  Creates an instance by parsing the filename.
  - Raises:
    - ValueError: If the filename does not match the expected pattern.

Running Tests

The project includes unit tests using Python's unittest framework.

Running Tests

Clone the repository (if not already done):

git clone https://github.com/yourusername/rosetta_finder.git
cd rosetta_finder

Navigate to the project directory:
```
cd rosetta_finder
```
Run the tests:
```
python -m unittest discover tests
```

Test Coverage

The tests cover:

Parsing valid and invalid filenames with RosettaBinary.
Finding binaries with RosettaFinder, including scenarios where binaries are found or not found.
OS compatibility checks.

Contributing

Contributions are welcome! Please submit a pull request or open an issue for bug reports and feature requests.

License

This project is licensed under the MIT License.

Acknowledgements

Rosetta Commons: The Rosetta software suite for the computational modeling and analysis of protein structures.

Contact

For questions or support, please contact:

Name: Yinying Yao
Email:yaoyy.hi(a)gmail.com

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