Things that might be wrong

[ericmjl]

After checking with real structural biologist:

add_cation_pi_interactions_: Phenylalanine ring is a bit negatively charged; interacting with slight positive charge of amine group of Lysine or Arginine.

Some molecular interaction calculators use different criteria.

Bugs found:

• B26THR/OG1 should have an H-bond with A24LEU/O (2.8A apart)
• B8ARG should have an ionic interaction with A29ASP
  • This bug comes from https://github.com/ericmjl/protein-interaction-network/blob/master/proteingraph/pin.py#L418, should be if not (condition1 and condition2)
• Another bug in https://github.com/ericmjl/protein-interaction-network/blob/master/proteingraph/pin.py#L327, should not have hydrogen bonds between N-N, O-O, O-S or S-S. i.e. should only be N-O or N-S pairing for hydrogen bonds.

[yara944]

hi , I have this problem when I operate the code usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help

error: no commands supplied
File "C:\Users\Lenovo\Desktop\protein-interaction-network-master\setup.py", line 40, in
long_description_content_type="text/markdown",

[ericmjl]

@yara944 thanks for chiming in.

I think you might want to install directly from PyPI rather than from source:

pip install protein-interaction-network

Alternatively, @a-r-j is working on a package that is a superset of this one, Graphein, so I think you might want to take a look at it. It's still in heavy development, so if you still use protein-interaction-network as a stopgap, that's not a problem, but do know that I'll be deprecating this package as soon as Graphein is fully tested and released 😄.

[a-r-j]

Hi @yara944 :) I've just made a quick tutorial for graphein that may be helpful: https://mybinder.org/v2/gh/a-r-j/graphein/c2ef3f74c88a17f1b4c838e82dbdd1e105e4e813 (the tutorial lives in notebooks/residue_graphs.ipynb)

As Eric says, it's still in heavy development but we're not expecting the overall flow to change much at this point.

[yara944]

@ericmjl I have tried this solution but i still have the same problem

[ericmjl]

@yara944 to debug I'm going to need a copy/paste of the commands you used at the terminal and the exact output that came from it. When it comes to installing things, programming environments are complex enough that I have to know whether the assumptions I'm working with hold true for your particular system. Can you paste below here the commands that you used to install with pip, and the exact output that came from it? Also, paste in something that shows me what your computing environment looks like. (And please make sure to format it nicely using the markdown backtick syntax, which will make it easier to parse.)

Also, are you installing into a conda environment? I'm not well-versed in idioms outside of the conda world, and if you're using a system Python rather than an isolated environment's Python, then all bets are off, I definitely won't be able to help here. (We all have our own lives outside of open-source software.) If these terms are foreign to you, I'd recommend reading my Data Science Bootstrap Notes to learn more.