From 536a39018ac29a3d288ed24fbd00fd13f3ee22c6 Mon Sep 17 00:00:00 2001 From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com> Date: Mon, 6 Jan 2025 16:54:52 +0100 Subject: [PATCH] Addition of water selection documentation (#4881) * Update selections.rst addition of water in simple selection with its description added mention of all available resnames for water that are recognized --------- Co-authored-by: Irfan Alibay --- .../doc/sphinx/source/documentation_pages/selections.rst | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/package/doc/sphinx/source/documentation_pages/selections.rst b/package/doc/sphinx/source/documentation_pages/selections.rst index 6ee7f26bc2d..124e231207d 100644 --- a/package/doc/sphinx/source/documentation_pages/selections.rst +++ b/package/doc/sphinx/source/documentation_pages/selections.rst @@ -114,6 +114,15 @@ protein, backbone, nucleic, nucleicbackbone is identfied by a hard-coded set of residue names so it may not work for esoteric residues. +water + selects all atoms that belong to a set of water residues; water + is defined with a set of common water abbreviations present in + topology files and may not work with certain water residue names. + Currently the following water resnames are supported: + 3 letter resnames: ``H2O``, ``HOH``, ``OH2``, ``HHO``, ``OHH``, ``TIP``, + ``T3P``, ``T4P``, ``T5P``, ``SOL``, ``WAT``. + 4 letter resnames: ``TIP2``, ``TIP3``, ``TIP4``. + segid *seg-name* select by segid (as given in the topology), e.g. ``segid 4AKE`` or ``segid DMPC``