Hi Adam,
On 2021-08-26 21:27, Adam Sjøgren wrote:
> Andrius writes:
>
>> These libraries do not have sonames, thus I reckon they are not a part
>> of public API.
>
> Ah, I see - I was thinking that there would be a reason I didn't know of.
>
> However if you run alphafold2 you get an exception where it tries to use
> libOpenMMAmoeba.so. Hm.
>
> (Unfortunately I don't have a small script to reproduce the problem.)
I see. If alphafold2 needs these libraries, then we better provide them
in Debian package after all.
>> On the other hand, reference libraries,
>>
>> libOpenMMAmoebaReference.so
>> libOpenMMDrudeReference.so
>> libOpenMMRPMDReference.so
>>
>> are provided in libopenmm-plugins binary package (>= 7.5.1+dfsg-1) at
>> /usr/lib/${DEB_HOST_MULTIARCH}/openmm/plugins.
>>
>> If this would be of use, libOpenMM{Amoeba,Drude,RPMD}.so could be
>> provided at /usr/lib/${DEB_HOST_MULTIARCH}/openmm, as
>> /usr/lib/${DEB_HOST_MULTIARCH} is reserved for libraries with sonames.
>
> Ah, ok, thanks for the explanation.
>
> I will give it a go locally, see if that works and return.
alphafold2 will probably have to be patched to look for
libOpenMM{Amoeba,Drude,RPMD}.so under /usr/lib/${DEB_HOST_MULTIARCH}/openmm.
Are you talking about this source of alphafold [1]? This one uses simtk
Python package which is part of OpenMM, but also not yet packaged for
Debian, and all calls to OpenMM are made through simtk.
[1] https://github.com/deepmind/alphafold
Best,
Andrius
