diff --git a/CHANGELOG.txt b/CHANGELOG.txt index 45543aa00e52f3ad79f2c502e78dcd6bc0cc4093..b7b9879aa97e04ca459f9a1151efc97fd73ba529 100644 --- a/CHANGELOG.txt +++ b/CHANGELOG.txt @@ -4,9 +4,6 @@ Changes in Release x.x.x * heavy water (DOD) is now recognised as 'water' instead of 'non-polymer' by the compounds library. * Added a '--version' argument to the 'ost' executable - * Changed default value of '--rmsd-assignment' to False for ligand scoring - * Added 'full_bs_search' argument in ligand scoring to optionally speed up - computations in large complexes. * SEQRES information is now read from the entity_poly_seq category in mmCIF. The canonical as well as semi-canonical (with 3 letter-codes in bracket) SEQRES are now available from the MMCifInfo object. The @@ -18,10 +15,24 @@ Changes in Release x.x.x score within 3 GDTTS points when compared to LGA results). Oligo/RNA support comes for free when using the ost.mol.alg.scoring.Scorer object. + * Introduce ilDDT score in scoring.Scorer and compare-structures action. + It's an all atom lDDT score which only considers interface contacts. * Rigid superposition based scores (RMSD, GDT) in ost.mol.alg.scoring.Scorer now use RMSD based chain mapping when scoring oligos. + * scoring.Scorer and compare-structures action can now optionally enable + peptide specific parameterizations as defined by the CAPRI community for + DockQ related scores (fnat, fnonnat, irmsd, lrmsd). + * ChainMapper.GetMapping now uses backbone only lDDT with inclusion radius + 30A as target function if nucleotide chains are present. Protein only + structures still use QS-score as target function as before. * Ligand scoring refactoring. lDDT-PLI and symmetry corrected RMSD are now completely separated. + * Breaking changes in compare-ligand-structures action output - run + 'ost compare-ligand-structures -h' for more information. + * Added 'full_bs_search' argument in ligand scoring. Binding sites for + symmetry corrected RMSD computation are now searched by only considering + polymer chains in proximity of ligands to speed up computations on large + complexes. The old behavior can be restored by enabling this flag. * Added model contacts in lDDT. lDDT is not symmetric in a sense that added/wrong contacts in the model do not penalize the score. lDDT now comes with a flag to add such contacts, i.e. contacts between atom pairs in the