Unable to Search for Atom Names Containing '

[fjclark]

Describe the bug

I am trying to modify BioSimSpace so that specifying restraint="backbone" also works for nucleic acids. However, several nucleic acid backbone atoms contain ' in their names, which results in an error:

sys.search("atomname O5'")

Gives:

ValueError: 'Invalid search query: "atomname O5'" : SireMol::parse_error: Failed to parse any of the selection 'atomname 
O5''. (call sire.error.get_last_error_details() for more info)

I am doing this correctly? Apologies if I have missed this in the tutorials. Thanks very much.

To Reproduce

Here is my RNA test system.

• OS: Ubuntu 22.04
• Version of Python: 3.11
• Version of sire: 2023.4.0
• I confirm that I have checked this bug still exists in the latest released version of sire: yes

[chryswoods]

Thanks for reporting - the issue is that ' is used as the quote character for strings in the parser. So you could search for atomname 'C 1' etc.

To escape the quote, we need to switch to the regular expression mode in the grammar (https://sire.openbiosim.org/cheatsheet/search.html#strings).

You put regular expressions within / characters. So searching for atomname /O5'/ would work.

Note you could also use *, ? and other regular expression glob patterns as well.

[fjclark]

Thanks very much for the quick reply. Sorry I missed this in the docs.

[chryswoods]

No need to apologise - I didn't know the code could do that either ;-)

Initially I thought that I would have to write code to let us escape single quotes, e.g. atomname O5\'. Then, as I was writing a reply saying this wasn't supported, I thought maybe it would be ok in the regex code, so gave it a try. I was surprised and happy it worked.

I'm going to add some docs to the regex code and the tutorial to show how we can escape single quotes this way. I may also think about how to add proper escaping to the syntax, as it is surprising that it doesn't escape quotes.