Atom
Class representing a single atom
- Properties:
-
- AtomType(AtomType)
- - Type of the atom
- Molecule (Molecule)
- - The molecule where the atoms belongs to
- Name(str)
- - Name of the atom
- Number(int)
- - Atom's serial number within all atoms of the molecule
- ID(int)
- - Atom's serial number within all atoms of the system
- Charge (float)
- - Charge of the atom in electron charges
- Mass (float)
- - Mass of the atom in a.u.
- R (np.ndarray)
- - Coordinates of the atom (A)
- Bonds
- - List of bonds (Pairwise and angle) where the atom is involved
- BondedAtoms (also PairBondedAtoms, AngleBondedAtoms)
- - List of atoms bonded to this one. Both angle- and pairwise bonds are taken into account
-
- Methods:
-
- IsBonded(that_atom)
- - Check if that atom is bonded to this one
- Distance(that_atom)
- - Calculate Euclidian Distance from that atom to this one
- PBC()
- - Apply periodic boundary conditions to the atom's coordinates (inplace!)
- Write2MCM(stream)
- - Write atom to the mcmfile-stream
