Installation

SPyCi-PDB uses only Python-based APIs for which we expect it to run native on any system Python can run, as long as third-party back-calculator installation requirements are met.

Please note that the IDPConformerGenerator library is required for parsing PDB structure coordinates. Details for IDPConformerGenerator can be found here.

Full installation instructures are highlighted below.

Note

As highlighted in requirements.txt, listed below are all of the Python packages required. Please note that the Python version must be between 3.8 and 3.11, inclusive. The following list will be updated if more packages are added:

numpy >= 1.22.4, < 2

numba >= 0.53.0, < 1

pybind11 >= 2.9.2, < 3

pandas >= 1.2.4, < 2

scipy >= 1.8.1, < 2

matplotlib >= 3.5.2, < 4

natsort >= 8, < 9

tox == 4

As mentioned above, IDPConformerGenerator libraries are required.

If you already have an idpconfgen environment

It is recommended to install IDPConformerGenerator first to have the environment prepared for SPyCi-PDB. Please visit the IDPConformerGenerator repository to install IDPConformerGenerator environment first.

Activate the idpconfgen environment (conda or virtualenv) and update the environment with the dependencies seen in SPyCi-PDB:

pip install -r existing_requirements.txt --upgrade

Install SPyCi-PDB on top of IDPConformerGenerator:

python setup.py develop --no-deps

Standalone From Source

Clone from the official repository:

git clone https://github.com/julie-forman-kay-lab/SPyCi-PDB

Navigate to the new SPyCi-PDB folder:

cd SPyCi-PDB

Run the following commands to install spycipdb dependencies if Anaconda is used as your Python package manager:

conda env create -f requirements.yml
conda activate spycipdb

Note

If you don’t use Anaconda to manage your Python installations, you can use virtualenv and the requirements.txt file following the commands:

virtualenv spycienv --python=3.11

source spycienv/bin/activate

pip install -r requirements.txt

If you have difficulties installing spycipdb, raise an issue in the main GitHub repository, and we will help you.

Install spycipdb in development mode in order for your installation to be always up-to-date with the repository:

python setup.py develop --no-deps

Note

The above applies also if you used virtualenv instead of conda.

Remember to activate the spycipdb environment every time you open a new terminal window, from within the repository folder, choose yours:

# Installation with Anaconda
conda activate spycipdb

# Installation with virtualenv
source spycienv/bin/activate

To update to the latest version, navigate to the repository folder, activate the spycipdb python environment as described above, and run the commands:

git pull

# if you used anaconda to create the python environment, run:
conda env update -f requirements.yml

# if you used virtual env to create the python environment, run:
pip install -r requirements.txt  --upgrade

python setup.py develop --no-deps

Your installation will become up to date with the latest developments.

Please note that IDPConformerGenerator will be installed alongside SPyCi-PDB as the library is required for processing PDB files. You can find the installation of IDPConformerGenerator in src/idpconfgen/.

Updating SPyCi-PDB

When new back-calculators are added or when dependencies change from the GitHub, please update your environment with the latest dependencies after performing a git pull.

To update an anaconda environment:

conda env update --file requirements.yml --prune

To update a virtualenv environment:

pip install -r requirements.txt --upgrade

Then perform setup.py again for good measure:

python setup.py develop --no-deps

Installing Third-party Software

Some functionalities of SPyCi-PDB require third-party software. These are not mandatory to install unless you want to use such operations.

DEERPREdict

Note

A default PRE calculator will be installed along with SPyCi-PDB.

However, if you would like to use DEERPREdict as an alternative predictor for PRE values, specifically, predicting intensity ratios instead of the default distance calculation, please see below.

If you’ve installed a recent version of SPyCi-PDB (past v0.5.X), DEERPREdict should already be installed in your Python environment.

If you do not have DEERPREdict as a package, the installation of DEERPREdict can be done by using pip as highlighted on their `website<https://deerpredict.readthedocs.io/_docs/installation.html>`_.

Specifically you can install DEERpredict on-top of the SPyCi-PDB environment.:

pip install DEERPREdict

UCBShift

Note

Module is only required if you wish to perform Chemical Shift back-calculations.

You should be in the parent directory where SPyCi-PDB was cloned to with the Python environment is deactivated.

Clone the UCBShift repository from Zi Hao Liu’s fork on GitHub.:

git clone https://github.com/menoliu/CSpred

Enter the CSpred folder and make a models directory, then download and extract the latest trained models to CSpred/models directory.

Move back into the SPyCi-PDB directory and enter the thirdparty/ucbshift_reqs folder:

cd ..
cd SPyCi-PDB
cd ./thirdparty/ucbshift_reqs

Run the following commands to install UCBShift dependencies if Anaconda is used as your Python package manager:

conda env update --name spycipdb --file ucbshift_requirements.yml --prune

Run the following commands to install UCBShift dependencies if virtualenv was used to install SPyCi-PDB:

pip install -r ucbshift_requirements.txt

Go back to the SPyCi-PDB directory and reinstall spycipdb and idpconfgen if needed.:

conda activate spycipdb
cd ../..
python setup.py develop --no-deps
cd ./src/idpconfgen/
python setup.py develop --no-deps

The following is the same with virtualenv:

source spycienv/bin/activate
cd ../..
python setup.py develop --no-deps
cd ./src/idpconfgen/
python setup.py develop --no-deps

Currently, reinstallation is required as UCBShift changes the Python version. We will be working on a fix to streamline this process soon by using package handlers such as PyPi. Thank you for your patience.

If you’re running into DSSP errors, please make sure you only have one version of DSSP installed and the preferred DSSP version is 3.X. Please refer to this issue for troubleshooting an older version of DSSP on a newer version of Ubuntu.

ATSAS v3.1.1 - CRYSOL v3.0

Note

ATSAS installation is only required for the saxs module.

Please visit the ATSAS website to download v3.1.1 of ATSAS. Theoretically, SPyCi-PDB will work if you already have ATSAS v3.X installed.

Test your installation via:

crysol -h

PALES v6.0

Note

PALES installation is only required for the rdc module.

A package of PALES v6.0 for Linux is already included in the thirdparty/ folder. Downloaded and extracted from the Ad Bax Group.

For use with x64 bit Linux Ubuntu 20.04.X LTS and 18.04.X, you must install the i386 architecture along with required package libraries:

sudo dpkg --add-architecture i386
sudo apt update
sudo apt install libc6:i386 libncurses5:i386 libstdc++6:i386 libx11-6:i386

If the last command above fails, run the following instead:

sudo apt install multiarch-support