Sails::Topology

publicTopology() = default

publicTopology(gemmi::Structure * structure, Sails::ResidueDatabase & database)

publicGlycanfind_glycan_topology(Sails::Glycosite& glycosite)

Find the glycan topology in a given glycosite.

This method is responsible for finding the glycan topology in a given glycosite by using a provided structure and residue database. It iterates through each residue in the glycosite and checks for close donor-acceptor atom pairs.

Parameters

• glycosite The glycosite to search in

Returns

The glycan topology found in the glycosite

public inline voidset_structure(gemmi::Structure * structure)

public inline gemmi::Structureget_structure() const

Get the structure object.

This method returns the internal structure object.

Returns

The gemmi::Structure object.

private gemmi::Structure *m_structure

private ResidueDatabasem_database

private gemmi::NeighborSearchm_neighbor_search

private voidinitialise_neighbour_search(gemmi::Structure * structure)

private voidfind_residue_near_donor(Sails::Glycosite& glycosite,Sails::Glycan& glycan, std::queue<Glycosite> & queue)

Find nearby residue near a donor atom.

This method finds nearby residues for a given donor atom in a glycosite. It adds the found residues to the glycan and adds the corresponding linkages to the glycan as well.

Parameters

• glycosite The glycosite containing the donor atom.

• glycan The glycan to add the found residues and linkages to.

• queue The queue to store the found glycosites for further processing.

Exceptions

• std::runtime_error If the glycosite is not found in the database.