Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
O
openstructure
Manage
Activity
Members
Code
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Deploy
Releases
Container registry
Model registry
Analyze
Contributor analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
GitLab community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
schwede
openstructure
Commits
550ad549
Verified
Commit
550ad549
authored
5 months ago
by
Xavier Robin
Browse files
Options
Downloads
Patches
Plain Diff
There is no more DRMSD in LDDT
parent
235f2d39
No related branches found
No related tags found
No related merge requests found
Changes
1
Show whitespace changes
Inline
Side-by-side
Showing
1 changed file
modules/mol/alg/doc/lddt.rst
+6
-6
6 additions, 6 deletions
modules/mol/alg/doc/lddt.rst
with
6 additions
and
6 deletions
modules/mol/alg/doc/lddt.rst
+
6
−
6
View file @
550ad549
Local Distance
Test scores (lDDT, DRMSD
)
Local Distance
Difference Test (LDDT
)
================================================================================
.. note::
This is a new implementation of
l
DDT, introduced in OpenStructure 2.4 with
This is a new implementation of
L
DDT, introduced in OpenStructure 2.4 with
focus on supporting quaternary structure and compounds beyond the 20
standard proteinogenic amino acids.
The :doc:`previous
l
DDT code <lddt_deprecated>` that comes with
The :doc:`previous
L
DDT code <lddt_deprecated>` that comes with
`Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_ is
considered deprecated.
.. note::
:class:`lddt.lDDTScorer` provides the raw Python API to compute
l
DDT but
:class:`lddt.lDDTScorer` provides the raw Python API to compute
L
DDT 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
l
DDT with pre-processing and support for quaternary structures.
compute
L
DDT with pre-processing and support for quaternary structures.
.. autoclass:: ost.mol.alg.lddt.lDDTScorer
...
...
@@ -36,7 +36,7 @@ Local Distance Test scores (lDDT, DRMSD)
cutoffs=(0.5, 1.0, 2.0, 4.0), \
label="locallddt")
Object containing the settings used for
l
DDT calculations.
Object containing the settings used for
L
DDT calculations.
:param radius: Sets :attr:`radius`.
:param sequence_separation: Sets :attr:`sequence_separation`.
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
sign in
to comment