Unable to import BioSimSpace after mamba installation about biosimspace HOT 12 CLOSED

Yup, that works. Thanks for your help!

from biosimspace.

No problem, thanks for reporting. Once the full 2023.1.0 release is available I'll delete the pre-release packages. This will avoid other people running into the same issue in future.

from biosimspace.

ah! my bad! but yes the the fix works (I was installing it like this: conda install -c conda-forge biosimspace - that's where my confusion came from)

from biosimspace.

Yes, it looks like we've incorrectly specified the Sire version range for our 2023 pre-release version of BioSimSpace. You should also be able to fix things by specifying the Sire version. For example, I think the 2023.0.2 development version of Sire should work with the latest devel conda package.

mamba create -n biosimspace23-dev -c conda-forge -c michellab/label/dev sire=2023.0.2 biosimspace

from biosimspace.

Hej, fyi: I have the same problem with your conda-forge version :(

from biosimspace.

Thanks, we don't have a package on conda-forge. Does the solution posted above not work for you?

from biosimspace.

Hi, I have installed biosimspace on this way. However when I am analyzing the relative free-energy value it gives an error.

AnalysisError Traceback (most recent call last)
Cell In[12], line 1
----> 1 pmf_free, overlap_matrix_free = BSS.FreeEnergy.Relative.analyse(f'o_xylene_benzene/free')
2 pmf_bound, overlap_matrix_bound = BSS.FreeEnergy.Relative.analyse(f'o_xylene_benzene/bound')
3 freenrg_rel = BSS.FreeEnergy.Relative.difference(pmf_bound, pmf_free)

File /cluster/ddu/cmmartinez001/miniconda3/envs/biosimspace-dev/lib/python3.9/site-packages/BioSimSpace/FreeEnergy/_relative.py:431, in Relative.analyse(work_dir)
429 # SOMD.
430 if len(data) > 0:
--> 431 return Relative._analyse_somd(work_dir)
433 # Now check for GROMACS output.
434 else:
435 data = glob(work_dir + "/lambda*/gromacs.xvg")

File /cluster/ddu/cmmartinez001/miniconda3/envs/biosimspace-dev/lib/python3.9/site-packages/BioSimSpace/FreeEnergy/_relative.py:605, in Relative._analyse_somd(work_dir)
598 proc = _subprocess.run(
599 _Utils.command_split(command),
600 shell=False,
601 stdout=_subprocess.PIPE,
602 stderr=_subprocess.PIPE,
603 )
604 if proc.returncode != 0:
--> 605 raise _AnalysisError("SOMD free-energy analysis failed!")
607 # Re-run without subsampling if the subsampling has resulted in less than 50 samples.
608 with open("%s/mbar.txt" % work_dir) as file:

AnalysisError: SOMD free-energy analysis failed!

In a previosu version it worked without any problem. Not sure if the code has been updated. Thanks

Cesar

from biosimspace.

Thanks, I'll try to reproduce this later and get back to you.

from biosimspace.

Hmmm, it's working for me with some existing ethane/methanol solvation free energy data. Is it possible to share the data for which it's failing. You could also edit the file shown in the error message above to print the standard output and error, e.g.:

print(proc.stdout)
print(proc.stderr)

(Do the above after adding text=True to the subprocess.run parameters.)

from biosimspace.

For reference, I did find an issue with our GROMACS analysis which resulted from the new (well, not so new) way we split command-line arguments for subprocess. This means that we now need to expand the glob for xvg files prior to running gmx bar. This is now fixed. For the few cases I've tested, SOMD analysis still appears to work just fine.

from biosimspace.

Also, when we figure out what the actual problem is I'll move it to a new issue thread, since it appears to have nothing to do with the original question. In future, please open a new issue when the query us unrelated. It makes book-keeping much easier.

Cheers.

from biosimspace.

I've tested using some example output from here (same system as you are looking at) and it still works for me.

from biosimspace.