CHFL_TOPOLOGY¶CHFL_TOPOLOGY¶An opaque type handling a topology.
A `CHFL_TOPOLOGY` contains the definition of all the atoms in the system, and the liaisons between the atoms (bonds, angles, dihedrals, ...). It will also contain all the residues information if it is available.
chfl_topology(void)¶Create a new empty topology.
The caller of this function should free the associated memory using `chfl_topology_free`.
CHFL_TOPOLOGY* topology = chfl_topology();
if (topology == NULL) {
/* handle error */
}
chfl_topology_free(topology);
chfl_topology_from_frame(const CHFL_FRAME *const frame)¶Get a copy of the topology of a `frame`.
The caller of this function should free the associated memory using `chfl_topology_free`.
CHFL_FRAME* frame = chfl_frame();
CHFL_TOPOLOGY* topology = chfl_topology_from_frame(frame);
if (topology == NULL) {
/* handle error */
}
chfl_topology_free(topology);
chfl_frame_free(frame);
chfl_topology_copy(const CHFL_TOPOLOGY *const topology)¶Get a copy of a `topology`.
The caller of this function should free the associated memory using `chfl_topology_free`.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_ATOM* atom = chfl_atom("F");
chfl_topology_add_atom(topology, atom);
chfl_topology_add_atom(topology, atom);
chfl_topology_add_atom(topology, atom);
chfl_atom_free(atom);
CHFL_TOPOLOGY* copy = chfl_topology_copy(topology);
if (copy == NULL) {
/* handle error */
}
chfl_topology_free(copy);
chfl_topology_free(topology);
chfl_topology_atoms_count(const CHFL_TOPOLOGY *const topology, uint64_t *natoms)¶Get the number of atoms in the `topology` in the integer pointed to by `natoms`.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_ATOM* atom = chfl_atom("F");
chfl_topology_add_atom(topology, atom);
chfl_topology_add_atom(topology, atom);
chfl_topology_add_atom(topology, atom);
chfl_atom_free(atom);
uint64_t atoms = 0;
chfl_topology_atoms_count(topology, &atoms);
assert(atoms == 3);
chfl_topology_free(topology);
chfl_topology_resize(CHFL_TOPOLOGY *const topology, uint64_t natoms)¶Resize the `topology` to hold `natoms` atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type. If it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.
CHFL_TOPOLOGY* topology = chfl_topology();
chfl_topology_resize(topology, 67);
uint64_t atoms = 0;
chfl_topology_atoms_count(topology, &atoms);
assert(atoms == 67);
chfl_topology_free(topology);
chfl_topology_add_atom(CHFL_TOPOLOGY *const topology, const CHFL_ATOM *const atom)¶Add a copy of an `atom` at the end of a `topology`.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_ATOM* O = chfl_atom("O");
CHFL_ATOM* H = chfl_atom("H");
chfl_topology_add_atom(topology, O);
chfl_topology_add_atom(topology, H);
chfl_topology_add_atom(topology, H);
chfl_atom_free(O);
chfl_atom_free(H);
chfl_topology_free(topology);
chfl_topology_remove(CHFL_TOPOLOGY *const topology, uint64_t i)¶Remove the atom at index `i` from a `topology`.
This shifts all the atoms indexes after `i` by 1 (n becomes n-1).
CHFL_TOPOLOGY* topology = chfl_topology();
// Add a fex atoms to the topology
CHFL_ATOM* O = chfl_atom("O");
CHFL_ATOM* H = chfl_atom("H");
chfl_topology_add_atom(topology, O);
chfl_topology_add_atom(topology, H);
chfl_topology_add_atom(topology, H);
chfl_topology_add_atom(topology, O);
chfl_atom_free(O);
chfl_atom_free(H);
uint64_t atoms = 0;
chfl_topology_atoms_count(topology, &atoms);
assert(atoms == 4);
chfl_topology_remove(topology, 2);
chfl_topology_atoms_count(topology, &atoms);
assert(atoms == 3);
chfl_topology_free(topology);
chfl_topology_add_bond(CHFL_TOPOLOGY *const topology, uint64_t i, uint64_t j)¶Add a bond between the atoms at indexes `i` and `j` in the `topology`.
CHFL_TOPOLOGY* topology = chfl_topology();
chfl_topology_add_bond(topology, 0, 1);
uint64_t bonds = 0;
chfl_topology_bonds_count(topology, &bonds);
assert(bonds == 1);
chfl_topology_free(topology);
chfl_topology_remove_bond(CHFL_TOPOLOGY *const topology, uint64_t i, uint64_t j)¶Remove any existing bond between the atoms at indexes `i` and `j` in the `topology`.
This function does nothing if there is no bond between `i` and `j`.
CHFL_TOPOLOGY* topology = chfl_topology();
chfl_topology_add_bond(topology, 0, 1);
chfl_topology_add_bond(topology, 1, 2);
chfl_topology_add_bond(topology, 2, 3);
uint64_t bonds = 0;
chfl_topology_bonds_count(topology, &bonds);
assert(bonds == 3);
chfl_topology_remove_bond(topology, 1, 2);
chfl_topology_bonds_count(topology, &bonds);
assert(bonds == 2);
chfl_topology_free(topology);
chfl_topology_isbond(const CHFL_TOPOLOGY *const topology, uint64_t i, uint64_t j, bool *result)¶Check if the atoms at indexes `i` and `j` are bonded together, and store the result in `result`.
CHFL_TOPOLOGY* topology = chfl_topology();
chfl_topology_add_bond(topology, 0, 1);
bool result = false;
chfl_topology_isbond(topology, 0, 1, &result);
assert(result == true);
chfl_topology_isbond(topology, 0, 2, &result);
assert(result == false);
chfl_topology_free(topology);
chfl_topology_isangle(const CHFL_TOPOLOGY *const topology, uint64_t i, uint64_t j, uint64_t k, bool *result)¶Check if the atoms at indexes `i`, `j` and `k` form an angle, and store the result in `result`.
CHFL_TOPOLOGY* topology = chfl_topology();
chfl_topology_add_bond(topology, 0, 1);
chfl_topology_add_bond(topology, 1, 2);
bool result = false;
chfl_topology_isangle(topology, 0, 1, 2, &result);
assert(result == true);
chfl_topology_isangle(topology, 0, 2, 1, &result);
assert(result == false);
chfl_topology_free(topology);
chfl_topology_isdihedral(const CHFL_TOPOLOGY *const topology, uint64_t i, uint64_t j, uint64_t k, uint64_t m, bool *result)¶Check if the atoms at indexes `i`, `j`, `k` and `m` form a dihedral angle, and store the result in `result`.
CHFL_TOPOLOGY* topology = chfl_topology();
chfl_topology_add_bond(topology, 0, 1);
chfl_topology_add_bond(topology, 1, 2);
chfl_topology_add_bond(topology, 2, 3);
bool result = false;
chfl_topology_isdihedral(topology, 0, 1, 2, 3, &result);
assert(result == true);
chfl_topology_isdihedral(topology, 0, 2, 1, 3, &result);
assert(result == false);
chfl_topology_free(topology);
chfl_topology_bonds_count(const CHFL_TOPOLOGY *const topology, uint64_t *nbonds)¶Get the number of bonds in the `topology` in `nbonds`.
CHFL_TOPOLOGY* topology = chfl_topology();
chfl_topology_add_bond(topology, 0, 1);
chfl_topology_add_bond(topology, 2, 3);
uint64_t bonds = 0;
chfl_topology_bonds_count(topology, &bonds);
assert(bonds == 2);
chfl_topology_free(topology);
chfl_topology_angles_count(const CHFL_TOPOLOGY *const topology, uint64_t *nangles)¶Get the number of angles in the `topology` in `nangles`.
CHFL_TOPOLOGY* topology = chfl_topology();
// We have two angles: 0-1-2 and 1-2-3
chfl_topology_add_bond(topology, 0, 1);
chfl_topology_add_bond(topology, 1, 2);
chfl_topology_add_bond(topology, 2, 3);
uint64_t angles = 0;
chfl_topology_angles_count(topology, &angles);
assert(angles == 2);
chfl_topology_free(topology);
chfl_topology_dihedrals_count(const CHFL_TOPOLOGY *const topology, uint64_t *ndihedrals)¶Get the number of dihedral angles in the `topology` in `ndihedrals`.
CHFL_TOPOLOGY* topology = chfl_topology();
// We have one dihedral angle: 0-1-2-3
chfl_topology_add_bond(topology, 0, 1);
chfl_topology_add_bond(topology, 1, 2);
chfl_topology_add_bond(topology, 2, 3);
uint64_t dihedrals = 0;
chfl_topology_dihedrals_count(topology, &dihedrals);
assert(dihedrals == 1);
chfl_topology_free(topology);
chfl_topology_bonds(const CHFL_TOPOLOGY *const topology, uint64_t (*data)[2], uint64_t nbonds)¶Get the list of bonds in the `topology` in the pre-allocated array `data` of size `nbonds`.
`data` size must be passed in the `nbonds` parameter, and be equal to the result of `chfl_topology_bonds_count`.
CHFL_TOPOLOGY* topology = chfl_topology();
chfl_topology_add_bond(topology, 0, 1);
chfl_topology_add_bond(topology, 2, 3);
uint64_t bonds[2][2] = {{0}};
chfl_topology_bonds(topology, bonds, 2);
assert(bonds[0][0] == 0);
assert(bonds[0][1] == 1);
assert(bonds[1][0] == 2);
assert(bonds[1][1] == 3);
chfl_topology_free(topology);
chfl_topology_angles(const CHFL_TOPOLOGY *const topology, uint64_t (*data)[3], uint64_t nangles)¶Get the list of angles in the `topology` in the pre-allocated array `data` of size `nangles`.
`data` size must be passed in the `nangles` parameter, and be equal to the result of `chfl_topology_angles_count`.
CHFL_TOPOLOGY* topology = chfl_topology();
chfl_topology_add_bond(topology, 0, 1);
chfl_topology_add_bond(topology, 1, 2);
chfl_topology_add_bond(topology, 2, 3);
uint64_t angles[2][3] = {{0}};
chfl_topology_angles(topology, angles, 2);
assert(angles[0][0] == 0);
assert(angles[0][1] == 1);
assert(angles[0][2] == 2);
assert(angles[1][0] == 1);
assert(angles[1][1] == 2);
assert(angles[1][2] == 3);
chfl_topology_free(topology);
chfl_topology_dihedrals(const CHFL_TOPOLOGY *const topology, uint64_t (*data)[4], uint64_t ndihedrals)¶Get the list of dihedral angles in the `topology` in the pre-allocated array `data` of size `ndihedrals`.
`data` size must be passed in the `ndihedrals` parameter, and be equal to the result of `chfl_topology_dihedrals_count`.
CHFL_TOPOLOGY* topology = chfl_topology();
chfl_topology_add_bond(topology, 0, 1);
chfl_topology_add_bond(topology, 1, 2);
chfl_topology_add_bond(topology, 2, 3);
uint64_t dihedrals[1][4] = {{0}};
chfl_topology_dihedrals(topology, dihedrals, 1);
assert(dihedrals[0][0] == 0);
assert(dihedrals[0][1] == 1);
assert(dihedrals[0][2] == 2);
assert(dihedrals[0][3] == 3);
chfl_topology_free(topology);
chfl_topology_add_residue(CHFL_TOPOLOGY *const topology, const CHFL_RESIDUE *const residue)¶Add a copy of `residue` to this `topology`.
The residue id must not already be in the topology, and the residue must contain only atoms that are not already in another residue.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_RESIDUE* residue = chfl_residue("res", 1);
chfl_topology_add_residue(topology, residue);
chfl_residue_free(residue);
chfl_topology_free(topology);
chfl_topology_residues_count(const CHFL_TOPOLOGY *const topology, uint64_t *nresidues)¶Get the number of residues in the `topology` in the integer pointed to by `nresidues`.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_RESIDUE* residue = chfl_residue("res", 1);
chfl_topology_add_residue(topology, residue);
chfl_residue_free(residue);
uint64_t residues = 0;
chfl_topology_residues_count(topology, &residues);
assert(residues == 1);
chfl_topology_free(topology);
chfl_topology_residues_linked(const CHFL_TOPOLOGY *const topology, const CHFL_RESIDUE *const first, const CHFL_RESIDUE *const second, bool *result)¶Check if the two residues `first` and `second` from the `topology` are linked together, *i.e.* if there is a bond between one atom in the first residue and one atom in the second one, and store the result in `result.`
CHFL_TOPOLOGY* topology = chfl_topology();
// Build the topology ...
CHFL_RESIDUE* first = chfl_residue_from_topology(topology, 0);
CHFL_RESIDUE* second = chfl_residue_from_topology(topology, 1);
bool linked = false;
chfl_topology_residues_linked(topology, first, second, &linked);
chfl_residue_free(first);
chfl_residue_free(second);
chfl_topology_free(topology);
chfl_topology_free(CHFL_TOPOLOGY *const topology)¶Free the memory associated with a `topology`.
CHFL_TOPOLOGY* topology = chfl_topology();
if (topology == NULL) {
/* handle error */
}
chfl_topology_free(topology);