get.symbol returns the chemical symbol for an atom.
get.point3d returns the 3D coordinates of the atom
get.point2d returns the 2D coordinates of the atom
get.atomic.number returns the atomic number of the atom
get.hydrogen.count returns the number of implicit H's on the atom.
Depending on where the molecule was read from this may be NULL or an integer
greater than or equal to 0
get.charge returns the partial charge on the atom. If charges have not been set the
return value is NULL, otherwise the appropriate charge.
get.formal.charge is returns the formal charge on the atom. By default the formal
charge will be 0 (i.e., NULL is never returned)
is.aromatic returns TRUE if the atom is aromatic, FALSE
otherwise
is.aliphatic returns TRUE if the atom is part of an aliphatic chain,
FALSE otherwise
is.in.ring returns TRUE if the atom is in a ring, FALSE
otherwise
get.atom.index returns the index of the atom in the molecule (starting from 0)
get.connected.atoms returns a list of atoms that are connected to the specified atom
get.symbol(atom)
get.point3d(atom)
get.point2d(atom)
get.atomic.number(atom)
get.hydrogen.count(atom)
get.charge(atom)
get.formal.charge(atom)
get.connected.atoms(atom, mol)
get.atom.index(atom, mol)
is.aromatic(atom)
is.aliphatic(atom)
is.in.ring(atom)A jobjRef representing an IAtom object
A jobjRef representing an IAtomContainer object
In the case of get.point3d the return value is a
3-element vector containing the X, Y and Z coordinates of the
atom. If the atom does not have 3D coordinates, it returns a
vector of the form c(NA,NA,NA). Similarly for
get.point2d, in which case the return vector is of
length 2.