From e4264ca3b61dbb6fa5d3a3b1d288b30bfc60248c Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 20 Mar 2024 14:45:07 +0100
Subject: [PATCH] Set RMSD assignment as default in scorer too
---
modules/mol/alg/pymod/ligand_scoring.py | 21 ++++++++++-----------
1 file changed, 10 insertions(+), 11 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 0f73d2005..07ebe9a15 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -56,14 +56,12 @@ class LigandScorer:
Note that this global chain mapping currently ignores non polymer entities
such as small ligands, and may result in overly pessimistic scores.
- By default, target-model ligand assignments are computed independently
- for the RMSD and lDDT-PLI scores. For RMSD, each model ligand is uniquely
- assigned to a target ligand, starting from the "best" possible mapping
- (lowest RMSD) and using each target and model ligand in a single
- assignment. Ties are resolved by best (highest) lDDT-PLI. Similarly,
- for lDDT-PLI, the assignment is based on the highest lDDT-PLI, and ties
- broken by lowest RMSD. Setting `rmsd_assignment=True` forces a single
- ligand assignment, based on RMSD only. Ties are broken arbitrarily.
+ By default, target-model ligand assignments are computed identically
+ for the RMSD and lDDT-PLI scores. Each model ligand is uniquely assigned
+ to a target ligand, starting from the lowest RMSD and using each target and
+ model ligand in a single assignment. If `rmsd_assignment` is set to False,
+ RMSD and lDDT-PLI are assigned separately to optimize each score, and the
+ other score is used as a tiebreaker.
By default, only exact matches between target and model ligands are
considered. This is a problem when the target only contains a subset
@@ -236,9 +234,10 @@ class LigandScorer:
chain names as value. Only has an effect if
*global_chain_mapping* is True.
:type custom_mapping: :class:`dict`
- :param rmsd_assignment: assign ligands based on RMSD only. The default
- (False) is to use a combination of lDDT-PLI and
- RMSD for the assignment.
+ :param rmsd_assignment: set to False to assign lDDT-PLI and RMSD separately
+ using a combination of these two scores to
+ optimize the assignment. By default (True), only
+ RMSD is considered for the ligand assignment.
:type rmsd_assignment: :class:`bool`
:param n_max_naive: Parameter for global chain mapping. If *model* and
*target* have less or equal that number of chains,
--
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