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feat/docs/cases: Covalent Bond Input #329

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@YaoYinYing YaoYinYing commented Aug 29, 2024

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.

drop: buildin logger

fix: template try-except bugs

fix: output logs

refactor: deduplicate code

fix: hetatm input raise from smiles

fix: hetatm input raise and dialognoses

docs&cases: covalent bonds

feat: covalent bond

fix: covalent bond

add: use_3d opt for ligand
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