Minor changes

.github/workflows/ci.yml

@@ -62,18 +62,18 @@ jobs:
         shell: bash -l {0}
         run: |
           echo "Download combinatorial library from zenodo..."
-          wget -q -O data/combinatorial_library/combinatorial_library.tar.bz2 https://zenodo.org/record/10843763/files/combinatorial_library.tar.bz2?download=1
+          wget -q -O data/combinatorial_library/combinatorial_library.tar.bz2 https://zenodo.org/record/17368450/files/combinatorial_library.tar.bz2?download=1
           ls -l data/combinatorial_library/
           echo "Decompress selected files..."
-          tar -xvf data/combinatorial_library/combinatorial_library.tar.bz2 combinatorial_library_deduplicated.json chembl_standardized_inchi.csv
-          mv combinatorial_library_deduplicated.json data/combinatorial_library/
-          mv chembl_standardized_inchi.csv data/combinatorial_library/
+          tar -xvf data/combinatorial_library/combinatorial_library.tar.bz2 combinatorial_library/combinatorial_library_deduplicated.json combinatorial_library/chembl_standardized_inchi.csv
+          mv combinatorial_library/combinatorial_library_deduplicated.json data/combinatorial_library/
+          mv combinatorial_library/chembl_standardized_inchi.csv data/combinatorial_library/
           ls -l data/combinatorial_library/
 
       - name: Run tests
         shell: bash -l {0}
         run: |
           PYTEST_ARGS="--nbval-lax --nbval-current-env --nbval-cell-timeout=3600"
-          PYTEST_IGNORE="--ignore=notebooks/custom_kinfraglib/2_3_custom_filters_paper.ipynb" 
+          PYTEST_IGNORE="--ignore=notebooks/custom_kinfraglib/2_4_custom_filters_paper.ipynb --ignore=notebooks/custom_kinfraglib/1_4_custom_filters_pairwise_retrosynthesizability.ipynb --ignore=notebooks/custom_kinfraglib/2_1_custom_filters_pipeline.ipynb" 
 
           pytest $PYTEST_ARGS $PYTEST_IGNORE

data/README.md

@@ -10,5 +10,5 @@ Overview of data content:
 - `combinatorial_library/`: Combinatorial library based on the reduced fragment library.
 - `external/`: Data from external resources.
 - `filters/`: Data used for custom filters.
-- `fragment_library_custom_filtered/`: Custom filtered fragment library: Pre-filtered (remove pool X,  deduplicate per subpocket, remove unfragmented ligands, remove all fragments that connect only to pool X), and filtered for unwanted substructures (PAINS and Brenk), drug-likeness (Ro3 and QED), synthesizability (buyable building blocks and SYBA) and pairwise retrosynthesizability (using ASKCOS).
+- `fragment_library_custom_filtered/`: Custom filtered fragment library: Pre-filtered (remove pool X, deduplicate per subpocket, remove unfragmented ligands, remove all fragments that connect only to pool X), and filtered for unwanted substructures (PAINS and Brenk), drug-likeness (Ro3 and QED), synthesizability (buyable building blocks and SYBA) and pairwise retrosynthesizability (using ASKCOS).
 - `fragment_library_old/`: Full fragment library v1.1.0 which was described in the KinFragLib paper. 

data/combinatorial_library/README.md

@@ -1,17 +1,17 @@
 # KinFragLib: Combinatorial library 
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15844170.svg)](https://doi.org/10.5281/zenodo.15844170)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17368450.svg)](https://doi.org/10.5281/zenodo.17368450)
 
 This folder is meant for the metadata and properties of the KinFragLib combinatorial library, which is based on the KinFragLib fragment library at https://github.com/volkamerlab/KinFragLib. This dataset is used for the analysis of the combinatorial library.
 
-**Note**: Since this dataset contains large files, we provide it outside this repository at https://zenodo.org/records/15844170 (DOI: 10.5281/zenodo.15844170, v2.0.1).
+**Note**: Since this dataset contains large files, we provide it outside this repository at https://zenodo.org/records/17368450 (DOI: 10.5281/zenodo.17368450, v2.0.2).
 In order to run the analysis notebooks, please download this dataset to this folder. 
 
 ## Raw data
 
 - `combinatorial_library.json`: Full combinatorial library, please refer to `notebooks/kinfraglib/4_1_combinatorial_library_data_preparation.ipynb` at https://github.com/volkamerlab/KinFragLib for detailed information about this data format
 - `combinatorial_library_deduplicated.json`: Deduplicated combinatorial library (based on InChIs)
-- `chembl_standardized_inchi.csv`: Standardized ChEMBL 33 molecules in the form of InChI strings.
+- `chembl_standardized_inchi.csv`: Standardized ChEMBL 36 molecules in the form of InChI strings.
 - `KLIFS_download_summary.csv`: PDB codes of all KLIFS structures used to generate the KinFragLib fragmentation library. 
 
 ## Processed data

data/external/README.md

@@ -1,3 +1,3 @@
 # External data
 
-- `pkidb_2020-07-15.sdf`: PKIDB dataset from 2020-07-15 downloaded from https://www.icoa.fr/pkidb/ (publications: DOI:10.3390/molecules23040908 and DOI: 10.3390/molecules25143226).
+- `pkidb_2025-04-15.sdf`: PKIDB dataset from 2025-04-15 downloaded from https://www.icoa.fr/pkidb/ (publications: DOI:10.3390/molecules23040908 and DOI: 10.3390/molecules25143226).