Cleanup dependencies

[yusuf1759]

• Remove unused dependencies
• Remove unused functions, classes, modules

[github-actions[bot]]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
src/plinder/data/structure
atoms.py
src/plinder/data/utils/annotations
ligand_utils.py
Project Total

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