fix covalent detection, comment out unused code

[OleinikovasV]

Attempted to fix covalent annotation including some detection bugs. This should be ready and more consistent with the expected behaviour. Lots of redundant code could be stripped away. Commented it for now for visibility. Potentilaly more tests could be written.

covalent_linkages are now reported in annotation like this (receptorligand): `{auth_resid}:{resname}{assym_id}{seq_resid}{atom_name}{auth_resid}:{resname}{assym_id}{seq_resid}{atom_name}`

Example: {'145:CYS:B:145:SG__404:Q0I:N:.:C'} Note that a ligand does not have the uniprot sequence residue number - thus is returned as '.'.

[github-actions[bot]]

Coverage report

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File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
src/plinder/core
__init__.py
src/plinder/data
__init__.py
get_system_annotations.py
splits.py
src/plinder/data/pipeline
config.py
io.py
utils.py
src/plinder/data/utils/annotations
aggregate_annotations.py
extras.py
get_ligand_validation.py
interaction_utils.py					150-151, 199-202
ligand_utils.py
rdkit_utils.py
save_utils.py
src/plinder/eval/docking
utils.py
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