Installation

Installation#

MolR can be installed using pip or from source for development.

Requirements#

MolR requires Python 3.8 or later and the following dependencies:

  • NumPy ≥ 1.20.0

  • SciPy ≥ 1.7.0 (for KDTree spatial indexing)

  • pyparsing ≥ 3.0.0 (for selection language)

  • pdbreader ≥ 0.1.0 (for PDB file parsing)

  • mmcif ≥ 0.1.0 (for mmCIF file parsing)

Installing from PyPI#

The simplest way to install MolR is using pip:

pip install molr

This will install MolR and all its dependencies.

Installing from Source#

For development or to get the latest features, you can install from source:

git clone https://github.com/abhishektiwari/molr.git
cd molr
pip install -e .

Development Installation#

If you plan to contribute to MolR or run tests, install with development dependencies:

git clone https://github.com/abhishektiwari/molr.git
cd molr
pip install -r requirements-dev.txt

This installs additional tools for development:

  • pytest (for running tests)

  • black (for code formatting)

  • mypy (for type checking)

  • flake8 (for linting)

  • isort (for import sorting)

  • pytest-cov (for test coverage)

Virtual Environment Setup#

We recommend using a Python virtual environment for development:

Using pyenv (recommended):

pyenv virtualenv 3.10.0 molr
pyenv activate molr
pip install -r requirements-dev.txt

Using venv:

python -m venv molr-env
source molr-env/bin/activate  # On Windows: molr-env\\Scripts\\activate
pip install -r requirements-dev.txt

Verifying Installation#

To verify your installation, you can run:

import molr
print(molr.__version__)

# Test basic functionality
structure = molr.Structure(n_atoms=10)
print(f"Created structure with {structure.n_atoms} atoms")

Running Tests#

After development installation, you can run the test suite:

# Run all tests except slow ones
make test

# Run all tests including slow ones
make test-all

# Run with coverage report
make test-coverage

Building Documentation#

To build the documentation locally:

cd docs
make html

The documentation will be available at docs/build/html/index.html.

Troubleshooting#

Import Error: If you get import errors, ensure all dependencies are installed:

pip install -r requirements.txt

NumPy Version: MolR requires NumPy 1.20.0 or later. Check your version:

import numpy
print(numpy.__version__)

SciPy KDTree: If spatial queries are slow, ensure SciPy is properly installed:

from scipy.spatial import cKDTree
print("SciPy KDTree available")

For more help, please open an issue on the GitHub repository.

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