Easy creation of ResidueChemTemplates

[diogomart]

The default dict from the meeko data folder ("residue_chem_templates.json") can be loaded with

templates = ResidueChemTemplates.create_from_defaults()

Additional templates can be added with

templates.add_json_file("NAKB_templates")

it looks for files in the current working directory, and in the meeko data folder where "residue_chem_templates.json" and "NAKB_templates.json" are currently located. For files in the meeko data folder the ".json" suffix is optional, as per the example above.

[diogomart]

Additionally, this PR deletes old data files that are no longer in use. It also deletes a few methods in "PDBQTReceptor.py" that were used for receptor preparation before the chorizos (now polymers) were created. I tested adding interaction fingerprints to vina results with ringtail, and that worked. I tested ringtail because ringtail depends on PDBQTReceptor.py to add interactions.

[rwxayheee]

This looks good, thanks!

[rwxayheee]

Works for Python3.10. There's a small problem with importlib.resources.files (maybe only with Python3.9):

/Users/amyhe/micromamba/envs/meeko_tutorial_py39/bin/mk_prepare_receptor.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').require('meeko==0.6.0a3')
Traceback (most recent call last):
  File "/Users/amyhe/micromamba/envs/meeko_tutorial_py39/bin/mk_prepare_receptor.py", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/Users/amyhe/Downloads/tutorial2/Meeko/scripts/mk_prepare_receptor.py", line 12, in <module>
    from meeko.reactive import atom_name_to_molsetup_index, assign_reactive_types_by_index
  File "/Users/amyhe/Downloads/tutorial2/Meeko/meeko/__init__.py", line 28, in <module>
    from .polymer import Polymer
  File "/Users/amyhe/Downloads/tutorial2/Meeko/meeko/polymer.py", line 34, in <module>
    data_path = resources.files("meeko.data")
  File "/Users/amyhe/micromamba/envs/meeko_tutorial_py39/lib/python3.9/importlib/resources.py", line 147, in files
    return _common.from_package(_get_package(package))
  File "/Users/amyhe/micromamba/envs/meeko_tutorial_py39/lib/python3.9/importlib/_common.py", line 14, in from_package
    return fallback_resources(package.__spec__)
  File "/Users/amyhe/micromamba/envs/meeko_tutorial_py39/lib/python3.9/importlib/_common.py", line 18, in fallback_resources
    package_directory = pathlib.Path(spec.origin).parent
  File "/Users/amyhe/micromamba/envs/meeko_tutorial_py39/lib/python3.9/pathlib.py", line 1082, in __new__
    self = cls._from_parts(args, init=False)
  File "/Users/amyhe/micromamba/envs/meeko_tutorial_py39/lib/python3.9/pathlib.py", line 707, in _from_parts
    drv, root, parts = self._parse_args(args)
  File "/Users/amyhe/micromamba/envs/meeko_tutorial_py39/lib/python3.9/pathlib.py", line 691, in _parse_args
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType

bfc2a2e uses the importlib_resources backport as a walkaround for py3.9.

50f9c29 is a small fix for #221

[diogomart]

importlib_resources is not on standard library, and importlib.resources is working for me on python 3.9.20. Could you double check?

[rwxayheee]

It didn't work on Mac with Python 3.9.20. Maybe it's OS specific. Is the backport not a default library on Linux?

importlib.resources is introduced in Py3.9. It also won't work with earlier python.

[diogomart]

importlib.resources doesn't work on 3.8, and some of the type hints we are using also don't work on 3.8. So we should restrict to python3.9 or later anyway.

importlib_resources is not standard on linux. At least not with python packaged by conda-forge, I don't know if that makes a difference. So on a Mac, Python3.9 comes with importlib_resources but not with importlib.resources? If that's the case, which is weird, we could simply

try:
    from importlib.resources import files
except:
    from importlib_resources import files

[diogomart]

Just for the record, we settled on #225 a0193ab