Daniel Parton
Daniel Parton
While I'm doing this, should I also make timestep, temperature and collision rate controllable from the CLI? They are currently only controllable via the API. And pressure and barostat period?...
Thanks - I've implemented a couple of functions to deal with this, which might also be helpful be in yank: https://gist.github.com/danielparton/562973c33cf25870e474 # `parse_api_params_string()` The idea behind this is to have...
Thanks, I've fixed the print statements. There are a large number of other py3k compatibility issues though, so it will be a bit longer yet before I get py3k builds...
Ok, Travis and the `ensembler-dev` package are looking good now. I've also implemented functionality for specifying protonation states and for generating models with hydrogens prior to the refinement stage. I'm...
Sure, shouldn't be too much work. My plan is to implement a "project_settings.yaml" file to contain this sort of info. This would go in the project top-level directory, and would...
What if the target is not a standard UniProt sequence?
Yes currently nonstandard sequences would have to be added manually in a FASTA file, which does not allow for residue numbering. There is a script for outputting topologies with residues...
Ok, could you write this as a separate issue?
Sure - I think I have this working. It runs quite a bit slower, since it takes a few seconds to load each structure with `mdtraj`. I'm regenerating the packaged...