OpenStructure 2.4
Release Notes
- Add fast and flexible lDDT implementation. The new code is purely Python based, natively supports complexes and is able to score DNA/RNA. The deprecated lDDT implementation remains for consistency.
- Add algorithms to establish one to one mappings between chains in a reference structure and a model. Chain mappings can be derived by optimizing oligomeric lDDT, RMSD or QS-score.
- Substitution matrixes for RNA/DNA to compute alignments: seq.alg.IDENTITY and seq.alg.NUC44.
- Add binding to DockQ (https://github.com/bjornwallner/DockQ) as well as an OpenStructure specific implementation of it. Also allows to extract CAPRI specific oligo scores (fnat, fnonnat, irmsd, lrmsd etc.)
- Reimplentation of QS-score in mol.alg.qsscore. Implements speedups and heavy caching which benefits heavy enumeration approaches in chain mapping.
- Stereochemistry related algorithms in mol.alg.stereochemistry. Identifies clashes and non-sensible bond lengths/angles based on parameterizations from CCP4 MON_LIB.
- Add non-polymer/small molecule ligand scoring algorithm with lDDT-PLI and symmetry-corrected ligand RMSD scores that were used in CASP15.
- Better compression in OMF structure format.
- Two central scoring objects to access to all OpenStructure specific scoring capabilities. Tertiary and quaternary structures and interactions, including required pre-processing of model/reference (cleanup, stereochemistry checks, chain mapping etc.) with mol.alg.scoring.Scorer. Non-polymer/small molecule ligands with mol.alg.ligand_scoring.LigandScorer.
- Re-write of compare-structures action to include newly developed chain mapping and scores. The old action is available as compare-structures-legacy.
- Add compare-ligand-structures action which computes lDDT-PLI and symmetry-corrected ligand RMSD scores in protein complexes.
- Several minor bug fixes and improvements.
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Download the latest version of OpenStructure.
Compilation instructions for this version can be found here.