Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Addition of water selection documentation #4881

Merged
merged 3 commits into from
Jan 6, 2025
Merged

Addition of water selection documentation #4881

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
3b88344
Update selections.rst
talagayev Jan 4, 2025
8bbe560
Update selections.rst
talagayev Jan 5, 2025
7259197
Update package/doc/sphinx/source/documentation_pages/selections.rst
talagayev Jan 6, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 9 additions & 0 deletions package/doc/sphinx/source/documentation_pages/selections.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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.
hmacdope marked this conversation as resolved.
Show resolved Hide resolved
Currently the following water resnames are supported:
3 letter resnames: ``H2O``, ``HOH``, ``OH2``, ``HHO``, ``OHH``, ``TIP``,
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I'm not sure this will render out amazingly well - unfortunately the docs build seems to have failed.

``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``
Expand Down
Loading