feat/docs/cases: Covalent Bond Input

[YaoYinYing]

This is one of the separated PRs from #321 .

Full PR roadmap

id	purpose	# commits	Affected
1	Hydra-Omegaconf and Pip module	6	Code, Config, Doc
2	BFD supports and MSA parallelism fixes	5	Code, Config, Case
3	Small molecule inputs and covalent bonds	4	Code, Case, Doc

Changelog

Added

• Support for SDF file inputs for small molecules and additional file formats.
• Expanded set of demo cases.
• PTM Inputs (phosphorylations, isopeptides, metal bindings, disulfide bridges, glycosylations, etc.)

Fixed

• Implemented automatic binary search within the PATH if not explicitly specified.
• Resolved an issue with dummy assertions of ref_atom_name_chars and problematic atoms that caused errors.
• Addressed the None-value in TemplateAtomMaskAllZerosError to prevent incorrect warning triggers.