libatomstruct: C++ atomic structure classes

Generate structure connectivity

connect_structure() is declared in atomstruct/connect.h.

void connect_structure(AtomicStructure *as, std::vector<Residue *> *chain_starters, std::vector<Residue *> *chain_enders, std::set<Atom *> *conect_atoms, std::set<MolResId> *mod_res)
Parameters:
  • as – AtomicStructure to create Bonds for
  • chain_starters – Residues that start polymer chains
  • chain_enders – Residues that end polymer chains
  • conect_atoms – Atoms whose connectivity has been specified a priori (e.g. in PDB CONECT records). Bonds will not be generated for such atoms and are the responsibility of the caller
  • mod_res – MolResIds for residues with standard names that nonetheless have non-standard connectivity (e.g. those found in PDB MODRES records) and that therefore should not have template connectivity applied. A MolResId can be constructed from a Residue pointer. The standard_residue() function can be used to determine if a residue name is considered standard (arg is a string).