Package com.actelion.research.chem
Class MoleculeNeutralizer
- java.lang.Object
-
- com.actelion.research.chem.MoleculeNeutralizer
-
public class MoleculeNeutralizer extends java.lang.Object
-
-
Constructor Summary
Constructors Constructor Description MoleculeNeutralizer()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
neutralizeChargedMolecule(StereoMolecule mol)
Tries to neutralize all charged atoms of the molecule unless a charged atom has a neighbour atom with opposite charge.
-
-
-
Method Detail
-
neutralizeChargedMolecule
public int neutralizeChargedMolecule(StereoMolecule mol)
Tries to neutralize all charged atoms of the molecule unless a charged atom has a neighbour atom with opposite charge. Quarternary ammonium or B(-) won't be touched. If positive charges remain, this method tries to deprotonate halogenes and acidic oxygen atoms to neutralize the molecule.- Parameters:
mol
-- Returns:
- remaining overall charge, which may be different from 0 if complete neutralization cannot be achieved
-
-