Algorithms for Single Particle Reconstruction
Project description
[](https://dev.azure.com/vineetbansal0645/Aspire-Python/_build/latest?definitionId=3&branchName=master) [](https://travis-ci.org/ComputationalCryoEM/ASPIRE-Python) [](https://ci.appveyor.com/project/vineetbansal/aspire-python/branch/master) [](https://coveralls.io/github/ComputationalCryoEM/ASPIRE-Python?branch=master) [](https://aspire.readthedocs.io/en/latest/?badge=latest)
# ASPIRE - Algorithms for Single Particle Reconstruction
This is the Python version to supersede the [Matlab ASPIRE](https://github.com/PrincetonUniversity/aspire).
ASPIRE is an open-source software package for processing single-particle cryo-EM data to determine three-dimensional structures of biological macromolecules. The package includes advanced algorithms based on rigorous mathematics and recent developments in statistics and machine learning. It provides unique and improved solutions to important computational challenges of the cryo-EM processing pipeline, including 3-D ab-initio modeling, 2-D class averaging, automatic particle picking, and 3-D heterogeneity analysis.
## Installation Instructions
For end-users
ASPIRE is a pip-installable package that works on Linux/Mac/Windows, and requires Python 3.6. The simplest option is to use Anaconda 64-bit for your platform with a minimum of Python 3.6 and pip, and then use pip to install aspire in that environment.
` conda create -n aspire_env python=3.6 pip conda activate aspire_env pip install aspire `
The final step above should install any dependent packages from pip automatically.
Note that this step installs the base aspire package for you to work with, but not the unit tests/scripts/documentation. If you need to install ASPIRE for development purposes, read on.
For developers
After cloning this repo, the simplest option is to use Anaconda 64-bit for your platform, and use the provided environment.yml file to build a Conda environment to run ASPIRE.
` cd /path/to/git/clone/folder conda env create -f environment.yml conda activate aspire `
### Make sure everything works
Once ASPIRE is installed, make sure the unit tests run correctly on your platform by doing: ` cd /path/to/git/clone/folder python setup.py test `
Tests currently take around 2 minutes to run. If some tests fail, you may realize that python setup.py test produces too much information. You may want to re-run tests using: ` cd /path/to/git/clone/folder PYTHONPATH=./src pytest tests ` This provides a cleaner output to analyze.
### Install
If the tests pass, install the ASPIRE package for the currently active Conda environment: ` cd /path/to/git/clone/folder python setup.py install `
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