Package: papyrus-scripts
Papyrus-scriptsCollection of scripts to interact with the Papyrus bioactivity dataset.Associated Article:10.1186/s13321-022-00672-xBéquignon OJM, Bongers BJ, Jespers W, IJzerman AP, van de Water B, van Westen GJP.
Papyrus - A large scale curated dataset aimed at bioactivity predictions.
J Cheminform 15, 3 (2023). https://doi.org/10.1186/s13321-022-00672-xAssociated Preprint:10.33774/chemrxiv-2021-1rxhkBéquignon OJM, Bongers BJ, Jespers W, IJzerman AP, van de Water B, van Westen GJP.
Papyrus - A large scale curated dataset aimed at bioactivity predictions.
ChemRxiv. Cambridge: Cambridge Open Engage; 2021;
This content is a preprint and has not been peer-reviewed.Installationpipinstallpapyrus-scripts:warning: If pip gives the following error and resolves in import errorsDefaultingtouserinstallationbecausenormalsite-packagesisnotwriteableThen uninstall and reinstalling the library with the following commands:pipuninstall-ypapyrus-scripts
python-mpipinstallpapyrus-scriptsAdditional dependencies can be installed to allow:similarity and substructure searchescondainstallFPSim2openbabelh5pycupy-cconda-forgetraining DNN models:condainstallpytorchtorchvisiontorchaudiocudatoolkit=11.3-cpytorchDonwload the datasetThe Papyrus data can be donwload in three different ways.The use of the command line interface is strongly recommended to download the data.- Using the command line interface (CLI)Once the library is installed (seeInstallation),
one can easily download the data.The following command will download the Papyrus++ bioactivities and protein targets (high-quality Ki and KD data as well as IC50 and EC50 of reproducible assays) for the latest version.papyrusdownload-VlatestThe following command will donwload the entire set of high-, medium-, and low-quality bioactivities and protein targets along with all precomputed molecular and protein descriptors for version 05.5.papyrusdownload-V05.5--more--dallThe following command will download Papyrus++ bioactivities, protein targets and compound structures for both version 05.4 and 05.5.papyrusdownload-V05.5-V05.4-SMore options can be found usingpapyrusdownload--helpBy default, the data is downloaded topystow's default directory.One can override the folder path by specifying the-oswitch in the above commands.- Using the application programming interface (API)frompapyrus_scriptsimportdownload_papyrus# Donwload the latest version of the entire dataset with all precomputed descriptorsdownload_papyrus(version='latest',only_pp=False,structures=True,descriptors='all')- Directly from online archivesDifferent online servers host the Papyrus data based on release and ChEMBL version (table below).Papyrus versionChEMBL versionZenodo4TUGoogle Drive05.429:x::heavy_check_mark::heavy_check_mark:05.530:heavy_check_mark::x::heavy_check_mark:05.631:heavy_check_mark::x::x:Precomputed molecular and protein descriptors along with molecular structures (2D for default set and 3D for low quality set with stereochemistry) are not available for version 05.4 from 4TU but are from Google Drive.As stated in the pre-printwe strongly encouragethe use of the dataset in which stereochemistry was not considered.
This corresponds to files containing the mention "2D" and/or "without_stereochemistry".Interconversion of the compressed filesThe available LZMA-compressed files (.xz) may not be supported by some software (e.g. Pipeline Pilot).Decompressing the data is strongly discouraged!Though Gzip files were made available at 4TU for version 05.4, we now provide a CLI option to locally interconvert from LZMA to Gzip and vice-versa.To convert from LZMA to Gzip (or vice-versa) use the following command:papyrusconvert-vlatestRemoval of the dataOne can remove the Papyrus data using either the CLI or the API.The following exerts exemplify the removal of all Papyrus data files, including all versions utility files.papyrusclean--remove_rootfrompapyrus_scriptsimportremove_papyrusremove_papyrus(papyrus_root=True)Easy handling of the datasetOnce installed the Papyrus-scripts allow for the easy filtering of the data.Simple examples can be found in thesimple_examples.ipynbnotebook.An example on matching data with the Protein Data Bank can be found in thesimple_examples.ipynbnotebook.More advanced examples will be added to theadvanced_querying.ipynbnotebook.Reproducing results of the pre-printThe scripts used to extract subsets, generate models and obtain visualizations can be foundhere.Features to comeSubstructure and similarity molecular searchesability to use DNN modelsability to repeat model training over multiple seedsy-scramblingadapt models to QSPRpredExamples to comeUse of custom grouping schemes for training/test set splitting and cross-validationUse custom molecular and protein descriptors (either Python function or file on disk)LogosLogos can be found underfigures/logoTwo version exist depending on the background used.:warning: GitHub does not render the white logo properly in the table below but should not deter you from using it!On white backgroundOn colored background