diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures index e2cb51438e14a15d67ec9558b43368c6211eaeaf..6650d96648ea80c6696e68cb60010017ea2b572c 100644 --- a/actions/ost-compare-structures +++ b/actions/ost-compare-structures @@ -5,13 +5,13 @@ Example: ost compare-structures -m model.pdb -r reference.cif Loads the structures and performs basic cleanup: - * Assign elements according to the PDB compound dictionary + * Assign elements according to the PDB Chemical Component Dictionary * Map nonstandard residues to their parent residues as defined by the PDB - compound dictionary, e.g. phospho-serine => serine + Chemical Component Dictionary, e.g. phospho-serine => serine * Remove hydrogens * Remove OXT atoms * Remove unknown atoms, i.e. atoms that are not expected according to the PDB - compound dictionary + Chemical Component Dictionary * Select for peptide/nucleotide residues The cleaned structures are optionally dumped using -d/--dump-structures @@ -51,7 +51,7 @@ enabling -rna/--residue-number-alignment is recommended. Each score is opt-in and can be enabled with optional arguments. -Example to compute local and per-residue lDDT values as well as QS-score: +Example to compute global and per-residue lDDT values as well as QS-score: ost compare-structures -m model.pdb -r reference.cif --lddt --local-lddt \ --qs-score diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst index df447090b880c865fa8ef2b99d78f018bf3c22cb..8156c788652973791139df2b1cba53f484f19519 100644 --- a/modules/doc/actions.rst +++ b/modules/doc/actions.rst @@ -19,7 +19,8 @@ Comparing two structures -------------------------------------------------------------------------------- You can compare two structures from the command line with the -``ost compare-structures`` action. +``ost compare-structures`` action. This can be considered a command line +interface to :class:`ost.mol.alg.scoring.Scorer` .. warning:: @@ -47,16 +48,16 @@ Details on the usage (output of ``ost compare-structures --help``): Example: ost compare-structures -m model.pdb -r reference.cif Loads the structures and performs basic cleanup: - - * Assign elements according to the PDB compound dictionary + + * Assign elements according to the PDB Chemical Component Dictionary * Map nonstandard residues to their parent residues as defined by the PDB - compound dictionary, e.g. phospho-serine => serine + Chemical Component Dictionary, e.g. phospho-serine => serine * Remove hydrogens * Remove OXT atoms * Remove unknown atoms, i.e. atoms that are not expected according to the PDB - compound dictionary + Chemical Component Dictionary * Select for peptide/nucleotide residues - + The cleaned structures are optionally dumped using -d/--dump-structures Output is written in JSON format (default: out.json). In case of no additional @@ -94,7 +95,7 @@ Details on the usage (output of ``ost compare-structures --help``): Each score is opt-in and can be enabled with optional arguments. - Example to compute local and per-residue lDDT values as well as QS-score: + Example to compute global and per-residue lDDT values as well as QS-score: ost compare-structures -m model.pdb -r reference.cif --lddt --local-lddt --qs-score diff --git a/modules/mol/alg/pymod/qsscore.py b/modules/mol/alg/pymod/qsscore.py index db5079ef9fd8a3b4ddeb70bf3b0fa77d60db9182..e7d8a0b563afc85555780924d3e728cac3c18ded 100644 --- a/modules/mol/alg/pymod/qsscore.py +++ b/modules/mol/alg/pymod/qsscore.py @@ -246,7 +246,7 @@ class QSScorer: chain_mapper = ChainMapper(ent_1) mapping_result = chain_mapper.GetlDDTMapping(ent_2) qs_scorer = QSScorer.FromMappingResult(mapping_result) - score_result = qs_scorer.GetQSScore(mapping_result.mapping) + score_result = qs_scorer.Score(mapping_result.mapping) print("score:", score_result.QS_global) QS-score computation in :func:`QSScorer.Score` implements caching.