From 970d8ca32d271833f86c4535764b60b7d47e9aad Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 18 Jan 2023 15:51:17 +0100
Subject: [PATCH] feat: SCHWED-5783 document more assumptions
---
modules/mol/alg/pymod/ligand_scoring.py | 16 ++++++++++++++++
1 file changed, 16 insertions(+)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index db2e1d307..3971195f2 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -37,6 +37,22 @@ class LigandScorer:
SWISS-MODEL), but it will most likely not work for most entities loaded
from PDB files.
+ Unlike most of OpenStructure, this class does not assume that the ligands
+ (either in the model or the target) are part of the PDB component
+ dictionary. They may have arbitrary residue names. Residue names do not
+ have to match between the model and the target.
+ It is up to the caller to ensure that the connectivity of atoms is properly
+ set before passing any ligands to this class. Ligands with improper
+ connectivity will lead to bogus results.
+
+ Note, however, that atom names should be unique within a residue (ie two
+ distinct atoms cannot have the same atom name).
+
+ This only applies to the ligand. The rest of the model and target
+ structures (protein, nucleic acids) must still follow the usual rules and
+ contain only residues from the compound library.
+
+
:param model: Model structure - a deep copy is available as :attr:`model`.
No additional processing (ie. Molck), checks,
stereochemistry checks or sanitization is performed on the
--
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