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BPTI example or any Protein #3

Open amrhamedp opened 4 years ago

amrhamedp commented 4 years ago

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 commented 4 years ago

Hi. You can download a self-contained example here

amrhamedp commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

xiaoyinyang commented 4 years ago

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

ParthGoyal1508 commented 2 years ago

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 commented 2 years ago

Use the code in science article and not this one.

ParthGoyal1508 commented 2 years ago

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?