feat: account for radical cofactors

[joanimato]

Description

This is a potential solution to #416 . Currently meeko doesn't handle radical cofactors very well (like nitric oxide in the issue). This adds a flag that relaxes some of the checks in chemtempgen.py so rdkit properly handles radical cofactors without assigning implicit hydrogens.

Enabling this flag may break handling of other cofactors (maybe), hence why it is optional. It might be better to also require the user to input the resid of the cofactor, so this is not global. Not sure....

Type of change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Other (please describe):

Checklist:

Please go through the following checklist before submitting the PR:

• Written a description of the feature or bug fix above.
• Ran pytest locally and all tests have passed.
• If applicable, documentation was updated with new feature.
• Docstring included for any new classes/functions/methods, or for significantly modifed existing functions.
• (Optional) new test added to account for new feature.

Additional Information