Package: pydockrmsd
DockRMSDAbstractDocked Root-mean-square deviation of atomic positionsPaperDockRMSD 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 symmetryDescriptionsPaper extractComputer-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 atomsDockRMSD PDF paperUsagePlease use mamba for fast download and installationcondainstallmamba-nbase-cconda-forgeLocal Install*NIX systems only:
Linux and MacOSRemove all previous pydockrmsd installationIf you have MacOS with apple silicon 'M' processor, please use manual installation.
Github Action cannot handle apple silicon yetpipuninstallpydockrmsdmambaenvcreate--namepydockrmsd--filecondaenv/requirement.yml
condaactivatepydockrmsd
mambaenvupdate--namepydockrmsd--filecondaenv/ci-cd.yml--prune
./scripts/install.shPypi installBuild Requirementpipinstall-rrequirements.txtDirect Downloadpipinstallpydockrmsd# pypi sourceExamplecrystal_bench.pyrdkit, pandas, numpy, pyarrowrequiredcrystal_bench.ipynbDockRMSD Websitepython Wrapper: docking pose distance calculationPython atom mapping and RMSD calculation of symmetric molecules throughgraphisomorphism.Journal of Cheminformatics, 11:40 (2019).PyDockRMSD Written by Barre Kevin, DockRMSD Written by Eric BellOs supportedLinuxMac OSWindowsTools usedcythonpdoc3pandocpandaspyarrow (file.parquet as file storage system)cibuildwheel(cross compilation)DocumentationSimple Usagefrompydockrmsd.dockrmsdimportPyDockRMSDimportpydockrmsd.hungarianashungariandockrmsd=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"))LicenseThis project is open source licensed under the EUROPEAN UNION PUBLIC LICENCE v. 1.2 EUPL © the European Union 2007, 2016 License. Please see theLICENSE filefor more information.Local documentationpdoc3pydockrmsd--httplocalhost:8080Tag:v: Versiond: Documentationb: Buildp: Publisht: TestIssuesCorresponding issues:neudinger/pyDockRMSD#3CHANGELOG file