Tags: plinder-org/plinder
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ligand_fixes (#70) * chore: minor bugfix in rascalMCES bond checking * chore: avoid redundant calculations for const_size * refactor: smallmols * chore: update logger warn -> warning * refactor core.structure.smallmols_utils from data annotation rdkit_utils * feat: smiles2inchikey upgrade + testing * feat: ligand uncharger + chore: smallmols_utils cleanup * chore: remove duplicated code * feat: add mmp based test-train similarity + feat: return most similar smiles (ecfp and mmp) * chore: fix eval stratify test + cleanup * chore: upgrade rdkit version to 2024.03.6 (#89) * feat: patch up entry_release_date + update README
Updated Splits.py, added Custom_split example (#81) (#87) * Updated Splits.py, added Custom_split example (#81) * Updated Splits.py, added Custom_split example * Updated apo and pred structure links * Updated plot.py, Added plots to custom_split notebook * chore: mystnb execution_mode "off" Trying to set execution mode off for the documentation CI * chore: fix selected_systems type --------- Co-authored-by: Vladas Oleinikovas <v.oleinikovas@gmail.com> * chore: lint * chore: add static split_plots * posebusters eval fix (#86) * bugfix: handling named sdf files for posebusters * feat: add matched reference ligand chain to single ligand scores * chore: add best_matched_reference_chain to test_eval * chore: handle none for "bisy_rmsd" * chore: flexible -> score_receptor; ligand_file_list -> ligand_file * fix: posebusters for flexible receptor scoring * chore: eval doc update * fix: PoseBusters requires a PDB file for receptor * fix: num_proteins only for CHAINTYPE_POLY_PEPTIDE_L * chore: cheatfix for num_model_proteins CI * chore: add explicit BindingDB/ChemBl license to README * chore: add known bugs + dates.csv --------- Co-authored-by: Jay <48680156+Ninjani@users.noreply.github.com> * chore: rm ipynb that fails CI * chore: add ipynb * chore: rm 6_custom_split.md file * chore: up rdkit pin * chore: plip pin at 2.3 * chore: update plip pins and main test report detection --------- Co-authored-by: Franz Görlich <102743232+frgoe003@users.noreply.github.com> Co-authored-by: Jay <48680156+Ninjani@users.noreply.github.com>
posebusters eval fix (#86) * bugfix: handling named sdf files for posebusters * feat: add matched reference ligand chain to single ligand scores * chore: add best_matched_reference_chain to test_eval * chore: handle none for "bisy_rmsd" * chore: flexible -> score_receptor; ligand_file_list -> ligand_file * fix: posebusters for flexible receptor scoring * chore: eval doc update * fix: PoseBusters requires a PDB file for receptor * fix: num_proteins only for CHAINTYPE_POLY_PEPTIDE_L * chore: cheatfix for num_model_proteins CI * chore: add explicit BindingDB/ChemBl license to README * chore: add known bugs + dates.csv --------- Co-authored-by: Jay <48680156+Ninjani@users.noreply.github.com>
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