RosettaPy 0.1.0rc107.post1

Searching for Rosetta Binaries.

RosettaFinder

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

CI Status

Release

Python version supported

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 RosettaPy directly from PyPI:

pip install RosettaPy -U

This allows you to use RosettaPy without cloning the repository.

Usage

Command-Line Shortcut

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

Using the whichrosetta Command

After installing RosettaPy, 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 RosettaPy in your Python scripts.

from RosettaPy 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:

1. The path specified in the ROSETTA_BIN environment variable.
2. ROSETTA3/bin
3. ROSETTA/main/source/bin/
4. 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 RosettaPy 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

1. Clone the repository (if not already done):

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

2. Navigate to the project directory:

   cd RosettaPy
   

3. 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