T015_protein_ligand_docking Using OPAL Attribute error: Nonetype object has no attribute atttrs about teachopencadd

[Carlbullish]

I figured it out! perhaps You need to add
conda install -c conda-forge smina

to the opening import library section
it'll help learners like me know that having it installed is necessary to get the dock output. Just a suggestion though.i was able to run the notebook just fine now. Thanks

[dominiquesydow]

Hi @Carlbullish,

In order to have less troubles with missing packages, I recommend to install a conda environment with all packages needed for the t011-base branch:

# Change to your TeachOpenCADD directory
cd path/to/TeachOpenCADD
# Checkout t011-base branch
git checkout t011-base
# Create the environment
conda env create -f devtools/test_env.yml -n teachopencadd
# Activate the environment
conda activate teachopencadd
# Start notebooks within the activated environment
jupyter lab  # or jupyter notebook

[AndreaVolkamer]

@Carlbullish can you tell us which PR you are using. Because in the newest T015, we moved away from OPAL and are using smina as docking engine. The functioning notebook additions are all in PR #74 in the T011-base branch.
Tagging @schallerdavid here also, who reworked T015.

[Carlbullish]

Hi @AndreaVolkamer. Thanks . i got to find the newest T015, I still ran into an issue when i tried to use smina This is the code below:
output_text = run_smina(
DATA / "ligand.pdbqt",
DATA / "protein.pdbqt",
DATA / "docking_poses.sdf",
pocket_center,
pocket_size,
)
print(output_text)

The error i get :

FileNotFoundError Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_8688/2258732981.py in
----> 1 output_text = run_smina(
2 DATA / "ligand.pdbqt",
3 DATA / "protein.pdbqt",
4 DATA / "docking_poses.sdf",
5 pocket_center,

~\AppData\Local\Temp/ipykernel_8688/2585986300.py in run_smina(ligand_path, protein_path, out_path, pocket_center, pocket_size, num_poses, exhaustiveness)
27 The output of the Smina calculation.
28 """
---> 29 output_text = subprocess.check_output(
30 [
31 "smina",

~\anaconda3\envs\introductiontopython\lib\subprocess.py in check_output(timeout, *popenargs, **kwargs)
413 kwargs['input'] = empty
414
--> 415 return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
416 **kwargs).stdout
417

~\anaconda3\envs\introductiontopython\lib\subprocess.py in run(input, capture_output, timeout, check, *popenargs, **kwargs)
491 kwargs['stderr'] = PIPE
492
--> 493 with Popen(*popenargs, **kwargs) as process:
494 try:
495 stdout, stderr = process.communicate(input, timeout=timeout)

~\anaconda3\envs\introductiontopython\lib\subprocess.py in init(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors, text)
856 encoding=encoding, errors=errors)
857
--> 858 self._execute_child(args, executable, preexec_fn, close_fds,
859 pass_fds, cwd, env,
860 startupinfo, creationflags, shell,

~\anaconda3\envs\introductiontopython\lib\subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_start_new_session)
1309 # Start the process
1310 try:
-> 1311 hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
1312 # no special security
1313 None, None,

FileNotFoundError: [WinError 2] The system cannot find the file specified

I look forward to your help as usual guys. Thanks