This is preliminary repository for databank of IDP simulations developed in the FAIRMD project.

This works in the same way a the NMRlipids databank

AddData creates README files where proteins are defined using FASTA sequence

CalcProperties currently calculates contact, distance and backbone correlation maps, radius of gyration distributions, dynamic landscapes and spin relaxation times.

Installation

The library is distributed as the fairmd.idp package (distribution name fairmd-idp), following the layout of FAIRMD_lipids:

pip install git+https://github.com/ohsOllila/IDPdatabank.git

or, from a clone of this repository, as an editable install:

pip install -e .

Alternatively, create a conda environment with all dependencies from conda-forge and install the package into it:

mamba env create -f environment.yml
mamba activate fairmd-idp
pip install --no-deps -e .

The scripts in Scripts/ import the library as fairmd.idp, e.g.

from fairmd.idp.core import *
from fairmd.idp.protein_functions import *

When the package is not installed from a clone of this repository, set NMLDB_ROOT_PATH to the cloned repository folder (or NMLDB_DATA_PATH to its Data folder) so that the data can be found.

Development

Linting, tests, package build and documentation are run with tox:

pip install tox
tox -e lint    # ruff + sphinx-lint
tox -e tests   # pytest
tox -e build   # build sdist/wheel and check the manifest
tox -e docs    # build the documentation into docs/build/html

The documentation is published at https://ohsollila.github.io/IDPdatabank/ on every push to master. See docs/src/development.rst and docs/README.md for details.