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Created with Raphaël 2.2.013May830Apr292624232215121110953220Mar1586129Feb2820191615141312765432131Jan2925242322211712111098543231Dec30222120181398753130Nov2928272322211615149831Oct242322Sep2120191186429Aug2824231817161511109831Jul2726252422211918141210765329Jun282320191512652131May302625242316121110954221Apr2019629Mar28242317161310976532128Feb222120171615109876131Jan3027262524232220191817fix: set is_ligand based on entity.typelddt-pli: cleanuplddt-pli: enable added mdl contactsdoc: fix typosdoc: remove warnings about duplicate object descriptionDocumentation updatefind membrane: guard against cases with zero solvent accessibilitieslddt: make main lDDT() function more slimligand scoring: fix infinite loop in assignmentligand scoring: prevent infinite loop in assignmentligand scoring: increase and clarify model binding site radiusfix --full-bs-search argument in ligand scoringtest: add full_bs_search=False testsfix: prevent combination of global chain mapping and full_bs_search=FalseClarify doc of arguments of ligand scoringligand scoring: add partial binding site enumation to actionligand scoring: use partial binding site enumeration by defaultAdd my latest changes from develop to changelogdoc: more details for full_bs_searchtest: place MG closer to the correct positiondoc: reflect changes to model_representation with new full_bs_search=Falseligand scoring: refactorligand scoring: change iteration orderligand scoring: speedups (triggers a unit test, to be fixed in later commits)lDDT: bugfixlDDT: enable added mdl contacts in Scorer and compare-structures actionfix CI - avoid kwarg in numpy.vstack which has been introduced in numpy 1.24lddt: add experimental flag: add_mdl_contactstypotypebranch link refactorrefactor rigid scoring - introduce GDT implementation similar to LGAcosmeticsremove quack_mode property from IOProfiledisable numpy support in C++ layerAdd logging output to the scoringdockq: enable parameterization for peptides as recommended by CAPRIChangelog entry for DOD being recognised as water.Make heavy water 'water' like the RCSB wants it.Set RMSD assignment as default in scorer too