Skip to main content

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

Project description

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 git@bitbucket.org: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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for sblu, version 0.7.2
Filename, size File type Python version Upload date Hashes
Filename, size sblu-0.7.2-py3.6.egg (110.5 kB) File type Egg Python version 3.6 Upload date Hashes View
Filename, size sblu-0.7.2-py3-none-any.whl (51.4 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size sblu-0.7.2.tar.gz (10.1 MB) File type Source Python version None Upload date Hashes View

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page