sblu 0.7.2

Library for munging data files from ClusPro/FTMap/etc.

Python library and associated scripts for munging data files from ClusPro/FTMap/etc.

Installation

From PyPI

Ensure you have pip, then run:

[sudo] pip install sblu

From source

First, install psfgen (see below) if you’re planning to use pdbprep functionality.

Clone the repository to your local machine:

git clone [e-mail]:bu-structure/sb-lab-utils.git

After cloning, you should be able to install using:

cd sb-lab-utils
[sudo] pip install -r requirements/development.txt
pytest
[sudo] python setup.py install

sudo is only needed if you are installing it globally. We recommend use of Anaconda (https://www.continuum.io).

Requirements

psfgen

Building PSF files requires psfgen utility from NAMD package.

Download recent precompiled version of NAMD (2.12 Linux-x86_64-multicore) from http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1501 (registration is required).

Extract the archive and copy the psfgen binary to /usr/local/bin/ (or, if you wish, any other location listed in your PATH environment variable):

tar zxf NAMD_2.12_Linux-x86_64-multicore.tar.gz && sudo cp NAMD_2.12_Linux-x86_64-multicore/psfgen "/usr/local/bin/"

Python modules

If you’re using Anaconda or already have NumPy installed from any other source, then you should be fine just running pip install -r requirements/development.txt.

If you don’t have NumPy, you might get a cryptic No files/directories in /tmp/pip-install-xxxxx/ProDy/pip-egg-info (from PKG-INFO) error during this step.

To resolve it, just install NumPy manually: pip install numpy>=1.10, and then re-run the command above.

Usage

Some basic examples are included in the examples directory.