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
is.in.ring 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
Usage
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) set.atom.types(mol)
Arguments
atom A jobjRef representing an IAtom object mol A jobjRef representing an IAtomContainer object
Value
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.
Author
Rajarshi Guha (rajarshi.guha@gmail.com)