search

MobleyLab / Lomap

Alchemical mutation scoring map
MIT License
37 stars 17 forks source link

Installing lomap via mobleylab conda channel #36

Closed ppxasjsm closed 2 years ago

ppxasjsm commented 6 years ago

Hi,

I am trying to use the conda install of lomap from the Mobley lab channel is this still a valid way to install things? I find it quite worrying that conda can simply downgrade my python from 3.5 to 2.7:

The following packages will be DOWNGRADED:

    python:                        3.5.5-h5001a0f_2      conda-forge --> 2.7.15-h43f7c74_0 conda-forge

If you don't know what you are doing this may mess with your conda environments quite badly.

davidlmobley commented 6 years ago

That's not good. Probably we need to work on our conda builds, but it will take me some time to get to this. I suggest installing from source in the meantime. You perhaps also want to try out the code avaialble in #34 .

ppxasjsm commented 6 years ago

I installed from source and am happy to switch to #34.

davidlmobley commented 5 years ago

OK, try it out and let us know if it seems like it improves the situation; @shuail and I have both been tied up with other things and haven't been able to invest much effort on this in a while but if it seems to be helping we can try to get it merged in sooner.

nitroamos commented 5 years ago

@ppxasjsm were you able to get it to work?

I've been asked to look into lomap for my project so I'm interested in advice on the best approach.

ppxasjsm commented 5 years ago

I have installed the networkx2 branch of lomap successfully.

Been testing bits of it since. No massive issues, apart from it running quite slowly on large number of compounds and been adding some network plotting bits to my scripts.

davidlmobley commented 5 years ago

Great. So you think that PR is ready to merge?

We welcome any contributions back you would like to make. :)

davidlmobley commented 5 years ago

@ppxasjsm - did you think #34 should be merged? Is that the brnach you're working from?

ppxasjsm commented 5 years ago

I am working on the networkxd2 branch. I haven't run into any major issues currently. I did change the network visualisation to just compound names on the nodes rather than drawing the structures as they are not displayed in a way that is useful. If I have time I can add bits to this towards the end of the week, if that is useful and can give a proper feedback. Mostly been trialing the perturbation map generation for the current D3R challenge, but happy to make some contributions.

davidlmobley commented 5 years ago

OK, that sounds great, @ppxasjsm . Thanks!

davidlmobley commented 2 years ago

Closing this; maintenance moved to github.com/OpenFreeEnergy/Lomap.