CHFL_ATOM
ΒΆchfl_atom
(const char * name)Create an atom from an atomic name.
name
- The new atom name
chfl_atom_from_frame
(const CHFL_FRAME * frame, size_t idx)Get a specific atom from a frame.
idx
is out of bounds frame
- The frame
idx
- The atom index in the frame
chfl_atom_from_topology
(const CHFL_TOPOLOGY * topology, size_t idx)Get a specific atom from a topology.
idx
is out of bounds topology
- The topology
idx
- The atom index in the topology
chfl_atom_mass
(const CHFL_ATOM * atom, float * mass)Get the mass of an atom, in atomic mass units.
atom
- The atom
mass
- The atom mass
chfl_atom_set_mass
(CHFL_ATOM * atom, float mass)Set the mass of an atom, in atomic mass units.
atom
- The atom
mass
- The new atom mass
chfl_atom_charge
(const CHFL_ATOM * atom, float * charge)Get the charge of an atom, in number of the electron charge e.
atom
- The atom
charge
- The atom charge
chfl_atom_set_charge
(CHFL_ATOM * atom, float charge)Set the charge of an atom, in number of the electron charge e.
atom
- The atom
charge
- The new atom charge
chfl_atom_name
(const CHFL_ATOM * atom, char * name, size_t buffsize)Get the name of an atom.
atom
- The atom
name
- A string buffer to be filled with the name
buffsize
- The size of the string buffer
chfl_atom_set_name
(CHFL_ATOM * atom, const char * name)Set the name of an atom.
atom
- The atom
name
- A null terminated string containing the new name
chfl_atom_full_name
(const CHFL_ATOM * atom, char * name, size_t buffsize)Try to get the full name of an atom from the short name.
atom
- The atom
name
- A string buffer to be filled with the name
buffsize
- The size of the string buffer
chfl_atom_vdw_radius
(const CHFL_ATOM * atom, double * radius)Try to get the Van der Waals radius of an atom from the short name.
atom
- The atom
radius
- The Van der Waals radius of the atom or -1 if no value could be found.
chfl_atom_covalent_radius
(const CHFL_ATOM * atom, double * radius)Try to get the covalent radius of an atom from the short name.
atom
- The atom
radius
- The covalent radius of the atom or -1 if no value could be found.
chfl_atom_atomic_number
(const CHFL_ATOM * atom, int * number)Try to get the atomic number of an atom from the short name.
atom
- The atom
number
- The atomic number, or -1 if no value could be found.
Available types of atoms.
Values:
CHFL_ATOM_ELEMENT
= = 0
- Element from the periodic table of elements.
CHFL_ATOM_COARSE_GRAINED
= = 1
- Coarse-grained atom are composed of more than one element: CH3 groups, amino-acids are coarse-grained atoms.
CHFL_ATOM_DUMMY
= = 2
- Dummy site, with no physical reality.
CHFL_ATOM_UNDEFINED
= = 3
- Undefined atom type.
chfl_atom_type
(const CHFL_ATOM * atom, chfl_atom_type_t * type)Get the atom type.
atom
- the atom to read
type
- the type of the atom
chfl_atom_set_type
(CHFL_ATOM * atom, chfl_atom_type_t type)Set the atom type.
atom
- the atom to modify
type
- the new type of the atom
chfl_atom_free
(CHFL_ATOM * atom)Destroy an atom, and free the associated memory.
atom
- The atom to destroy