rcdk (version 2.9.19)

Molecule: Operations on molecules

Description

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

convert.implicit.explicit converts implicit hydrogens to explicit hydrogens. This function does not return any value but rather modifies the molecule object passed to it

Usage

get.exact.mass(molecule)
get.natural.mass(molecule)
convert.implicit.to.explicit(molecule)

Arguments

molecule

A jObjRef representing an IAtomContainer or IMolecule object

Value

• exact.mass returns a numeric

  get.natural.mass returns a numeric

  convert.implicit.to.explicit has no return value

See Also

get.atoms

Examples

m <- parse.smiles('c1ccccc1')

  ## Need to configure the molecule
  do.aromaticity(m)
  do.typing(m)
  do.isotopes(m)

  get.exact.mass(m)
  get.natural.mass(m)

  convert.implicit.to.explicit(m)
  get.natural.mass(m) 
  do.isotopes(m) # Configure isotopes of newly added hydrogens
  get.exact.mass(m)