AddHydrogenProcessor Class Reference
[Miscellaneous]

Saturate atoms with hydrogen atoms. More...

#include <addHydrogenProcessor.h>

Inheritance diagram for AddHydrogenProcessor:

List of all members.

Public Member Functions
	AddHydrogenProcessor (const AddHydrogenProcessor &hbp)
virtual bool	start ()
	start method
virtual Processor::Result	operator() (Composite &composite)
	operator ()
Size	getConnectivity (Atom &atom)
void	setRings (const vector< vector< Atom * > > &rings)
Size	getNumberOfAddedHydrogens ()
Protected Member Functions
Size	countBondOrders (Atom &atom)
void	addHydrogen_ (Atom &atom, Vector3 position)
bool	isRingAtom_ (Atom &atom)
vector< Atom * >	getPartners_ (Atom &atom)
Vector3	getNormal_ (const Vector3 &v)
bool	normalize_ (Vector3 &v)
bool	hasMultipleBond_ (Atom &atom)
float	getBondLength_ (Position element)
Protected Attributes
HashSet< Atom * >	ring_atoms_
Position	atom_nr_
Atom *	last_atom_
Size	nr_hydrogens_

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Detailed Description

Saturate atoms with hydrogen atoms.

Only works with main group elements. The formal charge of the atoms are taken into account. The placement of the hydrogen atoms only depends on the direct neighbour atoms. No additional optimization of the atom placement is done. The optimal bond lengths are calculized by a modified Schomaker-Stevenson rule (adapted from the MMFF94 force field).
Usage:

      RingPerceptionProcessor rpp;
      vector<vector<Atom*> > rings;
      rpp.calculateSSSR(rings, system);
      rings = rpp.getAllSmallRings();
      AddHydrogenProcessor ap;
      ap.setRings(rings);
      system.apply(ap);