From fda78a1535ac875bf0a1ed986229d7e25fc49ec3 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 31 May 2024 18:20:26 +0200
Subject: [PATCH] ligand_scoring: docu update
---
modules/mol/alg/pymod/ligand_scoring_base.py | 20 +++++++++++++++++---
1 file changed, 17 insertions(+), 3 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring_base.py b/modules/mol/alg/pymod/ligand_scoring_base.py
index 60a2b3bb3..8d3882c0e 100644
--- a/modules/mol/alg/pymod/ligand_scoring_base.py
+++ b/modules/mol/alg/pymod/ligand_scoring_base.py
@@ -40,6 +40,22 @@ class LigandScorer:
with a delta of 0.2, a low-score match with coverage 0.96 would be
preferred over a high-score match with coverage 0.70.
+ All versus all scores are available through the lazily computed
+ :attr:`score_matrix`. However, many things can go wrong... be it even
+ something as simple as two ligands not matching. Error states therefore
+ encode scoring issues. Issues with a particular ligand are indicated by a
+ non-zero state in :attr:`model_ligand_states`/:attr:`target_ligand_states`.
+ This invalidates pairwise scores of such a ligand with all other ligands.
+ This and other issues in pairwise score computation are reported in
+ :attr:`state_matrix` which has the same size as :attr:`score_matrix`.
+ Only if the respective location is 0, a valid pairwise score can be
+ expected. The states and their meaning can be explored with code::
+
+ for state_code, (short_desc, desc) in scorer_obj.items():
+ print(state_code)
+ print(short_desc)
+ print(desc)
+
Assumptions:
:class:`LigandScorer` generally assumes that the
@@ -267,9 +283,7 @@ class LigandScorer:
Ligand pairs can be matched and a valid score can be expected if
respective location in this matrix is 0.
Target ligands are in rows, model ligands in columns. States are encoded
- as integers <= 9. Larger numbers encode errors for child classes.
-
- Human readable description is accessible as `scorer.state_decoding[2]`
+ as integers <= 9. Larger numbers encode errors for child classes.
:rtype: :class:`~numpy.ndarray`
"""
--
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