`patches`

Patches to add essential features to the CCD.

Module Attributes

`ACIDIC_PROTONS`	Map from residue name to a list of atom names of abstractable hydrogens.
`BASIC_ATOMS`	Protonation variants that add an atom to the CCD.
`ATOM_NAME_SYNONYMS`	Map from residue name and then canonical atom name to a list of synonyms

Functions

`fix_caps`	Fix `"NON-POLYMER"` residues so they can be used as caps for peptides.
`add_protonation_variants`	Add protonation variants from the ACIDIC_PROTONS and BASIC_ATOMS constants.
`add_synonyms`	Patch a residue definition to include synonyms from `ATOM_NAME_SYNONYMS`.
`disambiguate_alt_ids`	CCD patch: put alt atom ids in their own residue definitions if needed
`add_disulfide_crosslink`	Add a disulfide crosslink to a thiol sulfur atom named "SG".
`add_dephosphorylated_5p_terminus`	Add a definition representing a dephosphorylated 5' nucleic acid terminus.
`set_hop3_leaving`	Mark the HOP3 leaving atom in nucleic acid residues as such.
`patch_his_sidechain_zwitterion`	Patch the histidine side chain so that it is neutral, not zwitterionic.
`delete_doubly_deprotonated_arginine`	HH12 and HH22 are both acidic, but only one can leave at a time.
`add_nh2_leaving_atom`	Add the missing leaving atom to the NH3 residue.
`strip_linkless_leavers`	Set `leaving=False` on all atoms if `res` has no linking bond or crosslink.