Residue class¶

class chemfiles::Residue¶

A Residue is a group of atoms belonging to the same logical unit. They can be molecules, amino-acids in a protein, monomers in polymers, etc.

Iterating over a Residue gives the indexes of the atoms in the associated Topology.

auto residue = Residue("CLU");

residue.add_atom(56);
residue.add_atom(22);
residue.add_atom(31);

std::vector<size_t> atoms;
for (auto atom: residue) {
    atoms.push_back(atom);
}

assert(atoms == std::vector<size_t>({22, 31, 56}));

Public Functions

Residue(std::string name)¶

Create a new residue with a given name and no residue id.

auto residue = Residue("ALA");

assert(residue.name() == "ALA");
assert(residue.id() == nullopt);

Residue(std::string name, uint64_t resid)¶

Create a new residue with a given name and residue id resid.

auto residue = Residue("ALA", 456);

assert(residue.name() == "ALA");
assert(residue.id().value() == 456);

const std::string &name() const¶

Get the name of the residue

auto residue = Residue("FOO");
assert(residue.name() == "FOO");

optional<uint64_t> id() const¶

Get the residue identifier if it exists.

This function returna an chemfiles::optional value that is close to C++17 std::optional.

auto residue = Residue("FOO");
assert(!residue.id());

residue = Residue("BAR", 33);
assert(residue.id());
assert(residue.id().value() == 33);

size_t size() const¶

Get the size of the residue, i.e. the number of atoms in this residue.

auto residue = Residue("FOO");
assert(residue.size() == 0);

residue.add_atom(2);
residue.add_atom(22);
residue.add_atom(42);
residue.add_atom(36);

assert(residue.size() == 4);

void add_atom(size_t i)¶

Add an atom with index i to this residue

If the atom is already in the residue, this does nothing.

auto residue = Residue("FOO");
assert(residue.size() == 0);

residue.add_atom(2);
residue.add_atom(22);
residue.add_atom(42);
residue.add_atom(36);

assert(residue.size() == 4);

residue.add_atom(36);
assert(residue.size() == 4);

bool contains(size_t i) const¶

Check if the residue contains a given atom with index i

auto residue = Residue("FOO");

residue.add_atom(2);
residue.add_atom(22);
residue.add_atom(42);
residue.add_atom(36);

assert(residue.contains(22) == true);
assert(residue.contains(23) == false);