Molecule: Operations on molecules

MoleculeR Documentation

Operations on molecules


Various functions to perform operations on molecules.

get.exact.mass returns the exact mass of a molecule get.natural.mass returns the natural exact mass of a molecule converts implicit hydrogens to explicit hydrogens. This function does not return any value but rather modifies the molecule object passed to it is.neutral returns TRUE if all atoms in the molecule have a formal charge of 0, otherwise FALSE


In some cases, a molecule may not have any hydrogens (such as when read in from an MDL MOLfile that did not have hydrogens). In such cases, will add implicit hydrogens and then convert them to explicit ones. In addition, for such cases, make sure that the molecule has been typed beforehand.


get.exact.mass(mol) get.natural.mass(mol) is.neutral(mol)


mol A jobjRef representing an IAtomContainer or IMolecule object


get.exact.mass returns a numeric get.natural.mass returns a numeric has no return value is.neutral returns a boolean.


Rajarshi Guha (

See Also

get.atoms, set.atom.types

rcdk documentation built on Sept. 26, 2022, 5:09 p.m.