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Created with Raphaël 2.2.024Apr232215121110953220Mar1586129Feb2820191615141312765432131Jan2925242322211712111098543231Dec30222120181398753130Nov2928272322211615149831Oct242322Sep2120191186429Aug2824231817161511109831Jul2726252422211918141210765329Jun282320191512652131May302625242316121110954221Apr2019629Mar28242317161310976532128Feb222120171615109876131Jan30272625242322201918171613fix --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 tooUse RMSD only assignment by defaultfix: mixed up parameterschain mapping: adapt naive RMSD mapping threshold to what we describe in paperdoc: lddt_pli_radius should be >= radiuscleanup: ran black and reorganized the scriptfeat: add --version option to show OST versionbugfixchain mapping: enable subsampling as default for GetRMSDMappingchain mapping: introduce "heuristic" strategies in different optimizerschain mapping: modest refactorchain mapping: introduce naive_rmsd strategy in GetRigidMapping