Installation

MacSyFinder works with models for macromolecular systems that are not shipped with it, you have to install them separately. See the macsydata section below. We also provide container so you can use macsyfinder directly.

MacSyFinder dependencies

Python version >=3.10 is required to run MacSyFinder: https://docs.python.org/3.10/index.html

MacSyFinder has one program dependency:

The hmmsearch program should be installed (e.g., in the PATH) in order to use MacSyFinder. Otherwise, the paths to this executable must be specified in the command-line: see the command-line options.

MacSyFinder also relies on some Python library dependencies:

  • colorlog

  • colorama

  • pyyaml

  • packaging

  • networkx

  • pandas

  • GitPython

  • sphinx

  • sphinx_rtd_theme

  • sphinx-autodoc-typehints

  • sphinxcontrib-svg2pdfconverter

  • coverage

  • build

  • ruff

  • pre-commit

These dependencies will be automatically retrieved and installed when using pip for installation (see below).

MacSyFinder Installation procedure

Installation steps:

Make sure every required dependency/software is present.

By default MacSyFinder will try to use hmmsearch in your PATH. If hmmsearch is not in the PATH, you have to set the absolute path to hmmsearch in a configuration file or in the command-line upon execution. If the tools are not in the path, some test will be skipped and a warning will be raised.

installation in a virtualenv
# create a new virtaulenv
python3 -m venv macsyfinder
# activate it
cd macsyfinder
source bin/activate
# clone/install the project in editable mode
git clone
cd macsyfinder
python3 -m pip install -e .[dev]
# install tools to ensure coding style
pre-commit install

To exit the virtualenv just execute the deactivate command.

source macsyfinder/bin/activate

Then run macsyfinder or macsydata.

Note

from 2.1.4 version, MacSyFinder has adopted ruff as linter and pre-commit to ensure the coding style. please read CONTRIBUTING.md guide lines.