BPTI example or any Protein

[amrhamedp]

Hello Dr Noe,
Can you please provide an example in the notebooks demonstrating the transformation of protein into whitened Cartesian and internal coordinates?
I know that BPTI trajectory is provided by Dr Shaw. I am just looking for the model itself.

[psolsson]

Hi. You can download a self-contained example here

[amrhamedp]

Hi. You can download a self-contained example here

There are missing classes:
from deep_boltzmann.models.openmm import OpenMMEnergy
from deep_boltzmann.models.proteins import mdtraj2Z
Those are not here i believe

[franknoe]

This is the original submission (not revision). Please check out the latest code there:

 https://zenodo.org/record/3242635#.XhTkd-t7lTY

The link is also given in the paper under "code availability", close to the acknowledgements. Unfortunately it is very hidden, but it is journal style to put it there.

[amrhamedp]

Thank you very much...I really appreciate this. The work is really great.

[xiaoyinyang]

Hi, can I know the version of tensorflow you used? Thanks!

[ParthGoyal1508]

Hi @franknoe,

I'm facing an issue while executing the file particle_dimer_test.py

Traceback (most recent call last): File "particle_dimer_test.py", line 6, in <module> from deep_boltzmann.models import ParticleDimer File "<frozen zipimport>", line 259, in load_module File "/home/parth/env/lib/python3.8/site-packages/Deep_Boltzmann_Package-0.1-py3.8.egg/deep_boltzmann/__init__.py", line 3, in <module> from deep_boltzmann.models.double_well import DoubleWell ModuleNotFoundError: No module named 'deep_boltzmann.models'

Could you please help with this? Thanks

[amrhamedp]

Use the code in science article and not this one.

[ParthGoyal1508]

Hi @amrhamedp,

I have used the code which was mentioned in the paper under "code availability".
https://zenodo.org/record/3242635#.XhTkd-t7lTY

For setup, I ran two commands

python3 setup.py build
python3 setup.py install

but after executing the particle_dimer_test.py file it throws the above error, Is there any installation step am I missing?