pydockrmsd 1.0.0

Description:

pydockrmsd 1.0.0

DockRMSD




Abstract
Docked Root-mean-square deviation of atomic positions Paper
DockRMSD is capable of deterministically identifying the minimum symmetry-corrected RMSD and is able to do so without significant loss of computational efficiency compared to other methods. The open-source DockRMSD program can be conveniently integrated with various docking pipelines to assist with accurate atomic mapping and RMSD calculations, which can therefore help improve docking performance, especially for ligand molecules with complicated structural symmetry
Descriptions





Paper extract

Computer-aided drug design, in particular protein–ligand docking, has brought about the discovery of many biologically active drugs [1, 2]. In many protein–ligand docking programs, a flexible small molecule structure is docked in a rigid protein receptor structure in order to find the optimal binding conformation and affinity of the small molecule within the protein binding pocket. Since the ability of these programs to accurately assess binding affinity is dependent on their ability to find the optimal conformation of the ligand in the protein binding pocket, docking programs are often benchmarked by their ability to reproduce the native binding pose of a ligand from a protein–ligand complex crystal structure. A common metric used to evaluate distance between the predicted pose and the native pose, given a superposition of their protein receptor structures, is the root mean square deviation (RMSD) between their respective atoms

DockRMSD PDF paper
Usage
Please use mamba for fast download and installation
conda install mamba -n base -c conda-forge

Local Install
*NIX systems only:
Linux and MacOS
Remove all previous pydockrmsd installation

If you have MacOS with apple silicon 'M' processor, please use manual installation.
Github Action cannot handle apple silicon yet

pip uninstall pydockrmsd

mamba env create --name pydockrmsd --file condaenv/requirement.yml
conda activate pydockrmsd
mamba env update --name pydockrmsd --file condaenv/ci-cd.yml --prune
./scripts/install.sh

Pypi install
Build Requirement
pip install -r requirements.txt

Direct Download
pip install pydockrmsd # pypi source

Example

crystal_bench.py

rdkit, pandas, numpy, pyarrow required


crystal_bench.ipynb
DockRMSD Website python Wrapper: docking pose distance calculation

Python atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. Journal of Cheminformatics, 11:40 (2019).
PyDockRMSD Written by Barre Kevin, DockRMSD Written by Eric Bell
Os supported

Linux
Mac OS
Windows

Tools used



cython
pdoc3
pandoc
pandas
pyarrow (file.parquet as file storage system)
cibuildwheel (cross compilation)

Documentation
Simple Usage
from pydockrmsd.dockrmsd import PyDockRMSD
import pydockrmsd.hungarian as hungarian
dockrmsd = PyDockRMSD("./data/targets/1a8i/crystal.mol2",
"./data/targets/1a8i/vina1.mol2")
print(dockrmsd.rmsd)
print(dockrmsd.total_of_possible_mappings)
print(dockrmsd.optimal_mapping)
print(dockrmsd.error)
print(hungarian("./data/targets/1a8i/crystal.mol2",
"./data/targets/1a8i/vina1.mol2"))

License
This project is open source licensed under the EUROPEAN UNION PUBLIC LICENCE v. 1.2 EUPL © the European Union 2007, 2016 License. Please see the LICENSE file for more information.
Local documentation
pdoc3 pydockrmsd --http localhost:8080

Tag:

v: Version
d: Documentation
b: Build
p: Publish
t: Test

Issues
Corresponding issues:

neudinger/pyDockRMSD#3

CHANGELOG file