Atoms: Operations on Atoms

AtomsR Documentation

Operations on Atoms


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 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 returns TRUE if the atom is in a ring, FALSE otherwise get.atom.index eturns 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) set.atom.types(mol)


atom A jobjRef representing an IAtom object mol 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 co-ordinates 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.


Rajarshi Guha (

rcdk documentation built on July 9, 2023, 7:27 p.m.