Generate structure connectivity

The primary public function offered by the connectivity shared library is connect_structure() (declared in connectivity/connect.h along with other supporting functions/classes):

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).