Library for munging data files from ClusPro/FTMap/etc.
Python library and associated scripts for munging data files from ClusPro/FTMap/etc.
Ensure you have pip, then run:
[sudo] pip install sblu
First, install psfgen (see below) if you’re planning to use pdbprep functionality.
Clone the repository to your local machine:
git clone email@example.com: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).
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/"
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.
Some basic examples are included in the examples directory.
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