From a72c57e9a51fb15c69a50a021d563da67cd504d2 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Apr 2022 08:47:12 +0200
Subject: [PATCH] lDDT: docu updates
---
modules/mol/alg/doc/lddt.rst | 2 +-
modules/mol/alg/doc/molalg.rst | 11 +++++++++--
2 files changed, 10 insertions(+), 3 deletions(-)
diff --git a/modules/mol/alg/doc/lddt.rst b/modules/mol/alg/doc/lddt.rst
index dad25005f..55a6516ab 100644
--- a/modules/mol/alg/doc/lddt.rst
+++ b/modules/mol/alg/doc/lddt.rst
@@ -7,7 +7,7 @@ lDDT
The executable that refers to
`Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_
is considered deprecated. This documentation still exists for
- reference but you should consider using the `compare-structures` action
+ reference but you should consider using the ``compare-structures`` action
(:ref:`ost-compare-structures`) which utilizes the latest lDDT implementation
that can deal with quaternary structures and compounds beyond the 20
standard proteinogenic amino acids.
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index be8b184d0..d60e1f459 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -16,6 +16,15 @@ Local Distance Test scores (lDDT, DRMSD)
proteinogenic amino acids. The old code is still available and documented
:doc:`here <lddt_deprecated>`.
+.. note::
+
+ :class:`lddt.lDDTScorer` provides the raw Python API to compute lDDT but
+ stereochemistry checks as described in
+ `Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_
+ must be done seperately. You may want to check out the
+ ``compare-structures`` action (:ref:`ost-compare-structures`) to
+ compute lDDT with pre-processing and support for quaternary structures.
+
.. autoclass:: ost.mol.alg.lddt.lDDTScorer
:members:
@@ -25,8 +34,6 @@ Local Distance Test scores (lDDT, DRMSD)
.. autofunction:: ost.mol.alg.lddt.GetDefaultSymmetrySettings
-
-
.. function:: CheckStructure(ent, \
bond_table, \
angle_table, \
--
GitLab