The pH addition code has some major problems, and is arguably not fit for
purpose. It's on my list of things to do (but not at the top right now as
fixing it doesn't require an API change). The code isn't that complex
though, and I encourage others to accept the challenge. There are several
bug reports on this list and on our bug tracker to help guide a rethink.
It's not so much a coding problem as a question of stepping back and
rethinking the approach.
On 17 August 2017 at 17:43, Stefano Forli <fo...@scripps.edu> wrote:
> Hi all,
>
> I've found that when adding hydrogens with pH correction using Python I
> get a segmentation fault on the structure attached.
>
> Hard to debug, since the code kills the interpreter, but the few tests
> I've done with Begin/EndModify() do not make much difference.
>
> Adding hydrogens with this code bit me several times already, so if
> anybody has advice on how to prevent the crash or improve the code, it
> would be appreciated.
>
> Thanks
>
> S
>
>
>
>
> --
>
> Stefano Forli, PhD
>
> Assistant Professor
> Dept. of Integrative Structural
> and Computational Biology, MB-112A
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, CA 92037-1000, USA.
>
> tel: +1 (858)784-2055
> fax: +1 (858)784-2860
> email: fo...@scripps.edu
> http://www.scripps.edu/~forli/
>
>
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