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
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
schwede
openstructure
Commits
5a05bb4b
Commit
5a05bb4b
authored
5 months ago
by
Studer Gabriel
Browse files
Options
Downloads
Patches
Plain Diff
docu update
parent
2fc9db7a
Loading
Loading
No related merge requests found
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
modules/mol/alg/pymod/ligand_scoring_base.py
+12
-0
12 additions, 0 deletions
modules/mol/alg/pymod/ligand_scoring_base.py
with
12 additions
and
0 deletions
modules/mol/alg/pymod/ligand_scoring_base.py
+
12
−
0
View file @
5a05bb4b
...
...
@@ -285,6 +285,17 @@ class LigandScorer:
to be used by the :class:`LigandScorer` based on
"
non-polymer
"
entity types.
In case of PDB file format, ligands must be loaded separately as SDF files.
Only polymers (protein and nucleic acids) of model and target are considered
for ligand binding sites. The
:class:`ost.mol.alg.chain_mapping.ChainMapper` is used to enumerate possible
mappings of these chains. In short: identical chains in the target are
grouped based on pairwise sequence identity
(see pep_seqid_thr/nuc_seqid_thr param). Each model chain is assigned to
one of these groups (see mdl_map_pep_seqid_thr/mdl_map_nuc_seqid_thr param).
To avoid spurious matches, only polymers of a certain length are considered
in this matching procedure (see min_pep_length/min_nuc_length param).
Shorter polymers are never mapped and do not contribute to scoring.
Here is an example of how to setup a scorer::
from ost.mol.alg.ligand_scoring_scrmsd import SCRMSDScorer
...
...
@@ -313,6 +324,7 @@ class LigandScorer:
print(
"
model cleanup:
"
, sc.model_cleanup_log)
print(
"
target cleanup:
"
, sc.target_cleanup_log)
:param model: Model structure - a deep copy is available as :attr:`model`.
The model undergoes the following cleanup steps which are
dependent on :class:`ost.conop.CompoundLib` returned by
...
...
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
register
or
sign in
to comment