valdes-tresanco-ms/autodocktools_py3

Python3 translation of AutoDockTools

AutoDockTools_py3

Python3 translation of AutoDockTools

Install

Linux

python -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3

Windows

python.exe -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3

This version is under test.

autodocktools_py3's Issues

'<' not supported between instances of 'Residue' and 'Residue'

I have found an issue at:

MolKit\tree.py", line 940, in sort
sorted(self.data)

Error:

'<' not supported between instances of 'Residue' and 'Residue'

Using the script prepare_flexreceptor4.py

How I can fix this issue?
Many thanks in advance.

prepare_flexreceptor4.py no output

I found a possible issue at:

AutoDockTools\Utilities24\prepare_flexreceptor4.py

I try the following command on AutoDockTools_py3
python.exe AutoDockTools\Utilities24\prepare_flexreceptor4.py -r "Fib_MGTOOL.pdbqt" -g "Fib_RIGID.pdbqt" -x "Fib_FLEX.pdbqt" -s Fib_MGTOOL:P:THR22,Fib_MGTOOL:Q:GLY51

without any error, but also without any of the expected files as output. I try the same arguments and file on the official AutoDockTools and it generates the expected output.

Here is the pbdqt file of the example https://anonymousfiles.io/x0WrqlTn/

How I can fix this issue?
Many thanks in advance.

ModuleNotFoundError: No module named 'AutoDockTools.Utilities24.prepare_dpf4'

Dear developer,

Thanks for sharing the code.
There isn't prepare_dpf4.py in Utilities24 directory but prepare_dpf42.py is.
Is it typo of setup.py?

   'prepare_dpf4 = AutoDockTools.Utilities24.prepare_dpf4:main',

Thanks,

mol2 parsing doesn't work

Line 116 of MolKit/mol2Parser.py
atmlines = [x.strip() for x in self.allLines[self.keysAndLinesIndices['@<TRIPOS>ATOM'][
Should be
atmlines = [x.split() for x in self.allLines[self.keysAndLinesIndices['@<TRIPOS>ATOM'][
Indeed, further in, build4LevelsTree expects atomlines to be a list of list of strings, and not a list of strings

ModuleNotFoundError: No module named 'Support'

On Windows, the prepare_ligand4 and prepare_receptor4 scripts report error "ModuleNotFoundError: No module named 'Support'". Seems that the script is looking for the files not included.

Please include quick example of how to run prepare_ligand4.py

After installing your code with pip as described in the README file, how does one use prepare_ligand4.py?