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_last_error to learn about the error. chfl_topology_from_frame(const CHFL_FRAME *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_last_error to learn about the error. chfl_topology_copy(const CHFL_TOPOLOGY *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_last_error to learn about the error. chfl_topology_atoms_count(const CHFL_TOPOLOGY *topology, uint64_t *size)¶Get the number of atoms in the topology in the integer pointed to by size.
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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_resize(CHFL_TOPOLOGY *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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_add_atom(CHFL_TOPOLOGY *topology, const CHFL_ATOM *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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_remove(CHFL_TOPOLOGY *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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_add_bond(CHFL_TOPOLOGY *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_ATOM* atom = chfl_atom("F");
chfl_topology_add_atom(topology, atom);
chfl_topology_add_atom(topology, atom);
chfl_atom_free(atom);
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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_remove_bond(CHFL_TOPOLOGY *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_ATOM* atom = chfl_atom("F");
for (size_t i=0; i<5; i++) {
chfl_topology_add_atom(topology, atom);
}
chfl_atom_free(atom);
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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_bonds_count(const CHFL_TOPOLOGY *topology, uint64_t *nbonds)¶Get the number of bonds in the topology in nbonds.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_ATOM* atom = chfl_atom("F");
for (size_t i=0; i<5; i++) {
chfl_topology_add_atom(topology, atom);
}
chfl_atom_free(atom);
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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_angles_count(const CHFL_TOPOLOGY *topology, uint64_t *nangles)¶Get the number of angles in the topology in nangles.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_ATOM* atom = chfl_atom("F");
for (size_t i=0; i<5; i++) {
chfl_topology_add_atom(topology, atom);
}
chfl_atom_free(atom);
// 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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_dihedrals_count(const CHFL_TOPOLOGY *topology, uint64_t *ndihedrals)¶Get the number of dihedral angles in the topology in ndihedrals.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_ATOM* atom = chfl_atom("F");
for (size_t i=0; i<5; i++) {
chfl_topology_add_atom(topology, atom);
}
chfl_atom_free(atom);
// 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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_impropers_count(const CHFL_TOPOLOGY *topology, uint64_t *nimpropers)¶Get the number of improper dihedral angles in the topology in nimpropers.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_ATOM* atom = chfl_atom("F");
for (size_t i=0; i<5; i++) {
chfl_topology_add_atom(topology, atom);
}
chfl_atom_free(atom);
chfl_topology_add_bond(topology, 1, 0);
chfl_topology_add_bond(topology, 1, 2);
chfl_topology_add_bond(topology, 1, 3);
uint64_t impropers = 0;
chfl_topology_impropers_count(topology, &impropers);
assert(impropers == 1);
chfl_topology_free(topology);
chfl_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_bonds(const CHFL_TOPOLOGY *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. The bonds are sorted in the array.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_ATOM* atom = chfl_atom("F");
for (size_t i=0; i<5; i++) {
chfl_topology_add_atom(topology, atom);
}
chfl_atom_free(atom);
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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_angles(const CHFL_TOPOLOGY *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. The angles are sorted in the array.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_ATOM* atom = chfl_atom("F");
for (size_t i=0; i<5; i++) {
chfl_topology_add_atom(topology, atom);
}
chfl_atom_free(atom);
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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_dihedrals(const CHFL_TOPOLOGY *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. The dihedrals are sorted in the array.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_ATOM* atom = chfl_atom("F");
for (size_t i=0; i<5; i++) {
chfl_topology_add_atom(topology, atom);
}
chfl_atom_free(atom);
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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_impropers(const CHFL_TOPOLOGY *topology, uint64_t (*data)[4], uint64_t nimpropers)¶Get the list of improper dihedral angles in the topology in the pre-allocated array data of size nimpropers.
data size must be passed in the nimpropers parameter, and be equal to the result of chfl_topology_impropers_count. The impropers are sorted in the array.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_ATOM* atom = chfl_atom("F");
for (size_t i=0; i<5; i++) {
chfl_topology_add_atom(topology, atom);
}
chfl_atom_free(atom);
chfl_topology_add_bond(topology, 3, 0);
chfl_topology_add_bond(topology, 3, 1);
chfl_topology_add_bond(topology, 3, 2);
uint64_t impropers[1][4] = {{0}};
chfl_topology_impropers(topology, impropers, 1);
assert(impropers[0][0] == 0);
assert(impropers[0][1] == 3);
assert(impropers[0][2] == 1);
assert(impropers[0][3] == 2);
chfl_topology_free(topology);
chfl_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_add_residue(CHFL_TOPOLOGY *topology, const CHFL_RESIDUE *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");
chfl_topology_add_residue(topology, residue);
chfl_residue_free(residue);
chfl_topology_free(topology);
chfl_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_residues_count(const CHFL_TOPOLOGY *topology, uint64_t *residues)¶Get the number of residues in the topology in the integer pointed to by residues.
CHFL_TOPOLOGY* topology = chfl_topology();
CHFL_RESIDUE* residue = chfl_residue("res");
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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_residues_linked(const CHFL_TOPOLOGY *topology, const CHFL_RESIDUE *first, const CHFL_RESIDUE *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_last_error to learn about the error if the status code is not CHFL_SUCCESS. chfl_topology_free(CHFL_TOPOLOGY *topology)¶Free the memory associated with a topology.
CHFL_TOPOLOGY* topology = chfl_topology();
if (topology == NULL) {
/* handle error */
}
chfl_topology_free(topology);
CHFL_SUCCESS