How to prohibit FreeSASA warning

[xiaolinpan]

Could you teach me to prohibit the waring message? thank you very much!
"""
FreeSASA: warning: guessing that atom 'H' is symbol ' H'
FreeSASA: warning: atom 'TRP H' unknown, guessing element is ' H', and radius 1.100 A
FreeSASA: warning: guessing that atom 'H' is symbol ' H'
FreeSASA: warning: atom 'TRP H' unknown, guessing element is ' H', and radius 1.100 A
FreeSASA: warning: guessing that atom 'H' is symbol ' H'
FreeSASA: warning: atom 'TRP H' unknown, guessing element is ' H', and radius 1.100 A
FreeSASA: warning: guessing that atom 'H' is symbol ' H'
FreeSASA: warning: atom 'TRP H' unknown, guessing element is ' H', and radius 1.100 A
FreeSASA: warning: guessing that atom 'H' is symbol ' H'
FreeSASA: warning: atom 'TRP H' unknown, guessing element is ' H', and radius 1.100 A
FreeSASA: warning: guessing that atom 'N' is symbol ' N'
FreeSASA: warning: guessing that atom 'C' is symbol ' C'
FreeSASA: warning: guessing that atom 'C' is symbol ' C'
FreeSASA: warning: guessing that atom 'O' is symbol ' O'
FreeSASA: warning: guessing that atom 'C' is symbol ' C'
FreeSASA: warning: guessing that atom 'O' is symbol ' O'
FreeSASA: warning: guessing that atom 'H' is symbol ' H'
"""

[mittinatten]

How are you calling freesasa to get this?

…

On Mon, 24 Aug 2020 at 16:08, xiaolinpan ***@***.***> wrote: Could you teach me to prohibit the waring message? thank you very much! """ FreeSASA: warning: guessing that atom 'H' is symbol ' H' FreeSASA: warning: atom 'TRP H' unknown, guessing element is ' H', and radius 1.100 A FreeSASA: warning: guessing that atom 'H' is symbol ' H' FreeSASA: warning: atom 'TRP H' unknown, guessing element is ' H', and radius 1.100 A FreeSASA: warning: guessing that atom 'H' is symbol ' H' FreeSASA: warning: atom 'TRP H' unknown, guessing element is ' H', and radius 1.100 A FreeSASA: warning: guessing that atom 'H' is symbol ' H' FreeSASA: warning: atom 'TRP H' unknown, guessing element is ' H', and radius 1.100 A FreeSASA: warning: guessing that atom 'H' is symbol ' H' FreeSASA: warning: atom 'TRP H' unknown, guessing element is ' H', and radius 1.100 A FreeSASA: warning: guessing that atom 'N' is symbol ' N' FreeSASA: warning: guessing that atom 'C' is symbol ' C' FreeSASA: warning: guessing that atom 'C' is symbol ' C' FreeSASA: warning: guessing that atom 'O' is symbol ' O' FreeSASA: warning: guessing that atom 'C' is symbol ' C' FreeSASA: warning: guessing that atom 'O' is symbol ' O' FreeSASA: warning: guessing that atom 'H' is symbol ' H' """ — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#50>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAVV4HCQJBYSJQLKYI5PSY3SCJX5VANCNFSM4QJRKI2A> .

[xiaolinpan]

I use structure.addAtom() to create a freesasa structure, and when i use atom symbol(C, H, O, N, etc) as atom name, it appeared, but the result calculated is right. I want to prohibit the message, could you help me? thank you very much!

[mittinatten]

The Python API does not support all options available yet, in the C API you can suppress these specific warnings. I should probably expose that in Python as well.

You can override all warnings using:

freesasa.setVerbosity(freesasa.nowarnings)

But, you should probably not include H atoms, the standard atomic radii are designed to work without hydrogens.

[xiaolinpan]

The hydrogen atom is added to match the atom index of other programs, thank you for your help!

[mittinatten]

Ok, I have created a task to add the mentioned functionality freesasa/freesasa-python#15