From 051c8e5dc46be7a6791d4160984423d1764d1d76 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 9 Mar 2023 17:23:27 +0100
Subject: [PATCH] docu updates
---
actions/ost-compare-structures | 8 ++++----
modules/doc/actions.rst | 15 ++++++++-------
modules/mol/alg/pymod/qsscore.py | 2 +-
3 files changed, 13 insertions(+), 12 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index e2cb51438..6650d9664 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 df447090b..8156c7886 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 db5079ef9..e7d8a0b56 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.
--
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