From 12189444289c3a9ca794ee0a5e2127d8ee07606f Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 24 Mar 2023 16:32:16 +0100
Subject: [PATCH] doc: attempt to clarify issues.
---
modules/io/doc/profile.rst | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/modules/io/doc/profile.rst b/modules/io/doc/profile.rst
index bb6d41e27..9ab8a395c 100644
--- a/modules/io/doc/profile.rst
+++ b/modules/io/doc/profile.rst
@@ -151,14 +151,15 @@ The IOProfile Class
:type: bool
- Only relevant when reading PDB format. When set to true, reads CONECT
- statements and applies them in the pdb reader. This can result in
- hydrogen bonds salt bridges etc. to be connected. Check the PDB format
- definition for more info. This may cause issues in subsequent processing
- with the processor as we suddenly have two places where connectivity is
- built. For the use case of valid CONECT statements for all hetatms, you
- may want to disable processing of bonds between them in
- :attr:`ost.conop.Processor.connect_hetatm`
+ Only relevant when reading files in PDB format. When set to true, reads CONECT
+ statements and applies them in the PDB reader. This can result in
+ hydrogen bonds, salt bridges etc. to be connected. Check the PDB format
+ definition for more info. This may cause issues in subsequent processing,
+ such as bonds being overriden, or extra, inconsistent bonds, as the
+ processor suddenly has two separate sources of connectivity.
+ For the use case where the input PDB file contains valid CONECT
+ statements for all hetatms, you may want to disable processing of bonds
+ between them in :attr:`ost.conop.Processor.connect_hetatm`
.. attribute:: processor
--
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