From f6c110be16c1d40f23bd34eb31783b33f101b2a2 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Mon, 24 Jul 2023 11:58:25 +0200
Subject: [PATCH] doc: SCHWED-5954 document unassigned ligand reporting
---
actions/ost-compare-ligand-structures | 8 +++++---
modules/doc/actions.rst | 7 ++++++-
modules/mol/alg/pymod/ligand_scoring.py | 7 +++----
3 files changed, 14 insertions(+), 8 deletions(-)
diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index 667927fb3..a246b13af 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -48,7 +48,8 @@ options, this is a dictionary with three keys:
Each score is opt-in and, be enabled with optional arguments and is added
to the output. Keys correspond to the values in "model_ligands" above.
-Only assigned (mapped) ligands are reported.
+Unassigned ligands are reported with a message in "unassigned_model_ligands"
+and "unassigned_reference_ligands".
"""
import argparse
@@ -199,8 +200,9 @@ def _ParseArgs():
dest="unassigned",
default=False,
action="store_true",
- help=("Report unassigned ligands in the output together with assigned "
- "ligands."))
+ help=("Report unassigned model ligands in the output together with "
+ "assigned ligands, with a null score, and reason for not being "
+ "assigned."))
parser.add_argument(
"--lddt-pli",
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index dbda82e83..5deeca860 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -353,7 +353,8 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
Each score is opt-in and, be enabled with optional arguments and is added
to the output. Keys correspond to the values in "model_ligands" above.
- Only assigned (mapped) ligands are reported.
+ Unassigned ligands are reported with a message in
+ "unassigned_model_ligands" and "unassigned_reference_ligands".
options:
-h, --help show this help message and exit
@@ -406,6 +407,10 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
if global-chain-mapping flag is set.
-ra, --rmsd-assignment
Use RMSD for ligand assignment.
+ -u, --unassigned Report unassigned model ligands in the output
+ together with assigned ligands, with a null score,
+ and reason for not being assigned.
+
--lddt-pli Compute lDDT-PLI score and store as key "lddt-pli".
--rmsd Compute RMSD score and store as key "rmsd".
--radius RADIUS Inclusion radius for the binding site. Any residue
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 90ff2f81a..d78a439c8 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -229,10 +229,9 @@ class LigandScorer:
the optimum. A heuristic is used otherwise.
:type n_max_naive: :class:`int`
:param unassigned: If True, unassigned model ligands are reported in
- the output together with assigned ligands, with the
- a score of None, and reason for not being assigned
- in the \*_details matrix.
- Defaults to False.
+ the output together with assigned ligands, with a score
+ of None, and reason for not being assigned in the
+ \*_details matrix. Defaults to False.
:type unassigned: :class:`bool`
"""
def __init__(self, model, target, model_ligands=None, target_ligands=None,
--
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