From 96b6c97ff151a39634523dc634c9d535116da045 Mon Sep 17 00:00:00 2001 From: Gabriel Studer <gabriel.studer@unibas.ch> Date: Thu, 21 Apr 2022 09:06:56 +0200 Subject: [PATCH] lDDT: docu updates --- modules/doc/actions.rst | 7 +++---- modules/mol/alg/doc/lddt.rst | 2 +- modules/mol/alg/doc/molalg.rst | 2 +- 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst index 6d7391a21..9444c519a 100644 --- a/modules/doc/actions.rst +++ b/modules/doc/actions.rst @@ -13,7 +13,7 @@ you can type ``ost <ACTION> -h`` to get a description on its usage. Here we list the most prominent actions with simple examples. -.. ost-compare-structures: +.. _ost compare structures: Comparing two structures -------------------------------------------------------------------------------- @@ -39,13 +39,12 @@ In summary it performs the following steps: if 100% sequence identity is expected. - Compute scores requested by user (CA-RMSD of oligomer, :mod:`QS scores of oligomer <ost.mol.alg.qsscoring>`, - :class:`single chain lDDT scores <ost.mol.alg.lDDTScorer>`, - :attr:`weighted average of single chain lDDT scores <ost.mol.alg.qsscoring.OligoLDDTScorer.weighted_lddt>`, + :class:`single chain lDDT scores <ost.mol.alg.qsscoring.OligoLDDTScorer.sc_lddt>`, :attr:`lDDT score of oligomer <ost.mol.alg.qsscoring.OligoLDDTScorer.oligo_lddt>`). Note that while the QS score is symmetric (same result when swapping reference and model), the lDDT scores are not. Extra atoms in the model for mapped chains have no effect on the score, while extra atoms in the reference reduce - the score. For the oligomeric variants (weighted-lDDT & oligo-lDDT), we do + the score. For oligo_lddt, we do :attr:`penalize for extra chains <ost.mol.alg.qsscoring.OligoLDDTScorer.penalize_extra_chains>` in both reference and model. diff --git a/modules/mol/alg/doc/lddt.rst b/modules/mol/alg/doc/lddt.rst index 55a6516ab..1d0587104 100644 --- a/modules/mol/alg/doc/lddt.rst +++ b/modules/mol/alg/doc/lddt.rst @@ -8,7 +8,7 @@ lDDT `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 - (:ref:`ost-compare-structures`) which utilizes the latest lDDT implementation + (: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 d60e1f459..f0251e915 100644 --- a/modules/mol/alg/doc/molalg.rst +++ b/modules/mol/alg/doc/molalg.rst @@ -22,7 +22,7 @@ Local Distance Test scores (lDDT, DRMSD) 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 + ``compare-structures`` action (:ref:`ost compare structures`) to compute lDDT with pre-processing and support for quaternary structures. -- GitLab