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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.
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.
fjclark
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Oct 23, 2023
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:Gives:
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.
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