HydrogenTools Class Reference

Public Types
enum	Adjustment {   Add = 0 ,   Remove ,   AddAndRemove }

Static Public Member Functions
static void	removeAllHydrogens (RWMolecule &molecule)
static void	adjustHydrogens (RWMolecule &molecule, Adjustment adjustment=AddAndRemove)
static void	adjustHydrogens (RWAtom &atom, Adjustment adjustment=AddAndRemove)
static int	valencyAdjustment (const RWAtom &atom)
static int	extraHydrogenIndices (const RWAtom &atom, int numberOfHydrogens, std::vector< size_t > &indices)
static void	generateNewHydrogenPositions (const RWAtom &atom, int numberOfHydrogens, std::vector< Vector3 > &positions)

Member Enumeration Documentation

Adjustment

enum Adjustment

Enum values that control the adjustHydrogen function's behavior.

Enumerator
Add	Only add hydrogens to underbonded atoms.
Remove	Only remove hydrogens from overbonded atoms.
AddAndRemove	Add hydrogens to underbonded atoms and remove hydrogens from overbonded atoms.

Member Function Documentation

removeAllHydrogens()

void removeAllHydrogens ( RWMolecule & molecule )

static

Remove all hydrogen atoms from molecule.

adjustHydrogens() [1/2]

void adjustHydrogens ( RWMolecule & molecule, Adjustment adjustment = AddAndRemove )

static

Add/remove hydrogens on molecule to satisfy valency.

adjustHydrogens() [2/2]

void adjustHydrogens ( RWAtom & atom, Adjustment adjustment = AddAndRemove )

static

Add/remove hydrogens on atom to satisfy valency.

valencyAdjustment()

int valencyAdjustment ( const RWAtom & atom )

static

Returns

The number of bonds that need to be added or removed from atom to satisfy valency. A positive number indicates the number of bonds to add, a negative number indicates the number of bonds that need to be removed.

extraHydrogenIndices()

int extraHydrogenIndices ( const RWAtom & atom, int numberOfHydrogens, std::vector< size_t > & indices )

static

Obtain the indices of hydrogens that can be removed from atom.

Parameters

atom	The atom from which to prune hydrogens.
numberOfHydrogens	The maximum number of hydrogens to prune.
indices	A vector that will be appended with the indices of the hydrogens to remove.

Returns

The number of hydrogen indices appended to indices.

Note

This function modifies neither atom nor its parent molecule. It only pushes the indices of hydrogens to remove to the end of indices.

generateNewHydrogenPositions()

void generateNewHydrogenPositions ( const RWAtom & atom, int numberOfHydrogens, std::vector< Vector3 > & positions )

static

Generate positions for numberOfHydrogens hydrogens bonded to atom.

Parameters

positions

Vector of positions that will be appended with numberOfHydrogens hydrogen locations.

Note

There is nothing intelligent going on here. The new positions are randomly oriented and have a length that is the sum of atom's and hydrogen's covalent radii. Effort is made to prevent overlap with other bonded atoms, but this is not guaranteed.

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The documentation for this class was generated from the following file:

• hydrogentools.h