RDKit::MolOps::details Namespace Reference

Functions
RDKIT_GRAPHMOL_EXPORT void	KekulizeFragment (RWMol &mol, const boost::dynamic_bitset<> &atomsToUse, boost::dynamic_bitset<> bondsToUse, bool markAtomsBonds=true, unsigned int maxBackTracks=100)
	not recommended for use in other code
RDKIT_GRAPHMOL_EXPORT std::vector< int >	hapticBondEndpoints (const Bond *bond)
RDKIT_GRAPHMOL_EXPORT unsigned int	addExplicitAttachmentPoint (RWMol &mol, unsigned int atomIdx, unsigned int val, bool addAsQuery=true, bool addCoords=true)
RDKIT_GRAPHMOL_EXPORT bool	isAttachmentPoint (const Atom *atom, bool markedOnly=true)
	returns whether or not an atom is an attachment point

Function Documentation

addExplicitAttachmentPoint()

RDKIT_GRAPHMOL_EXPORT unsigned int RDKit::MolOps::details::addExplicitAttachmentPoint	(	RWMol &	mol,
		unsigned int	atomIdx,
		unsigned int	val,
		bool	addAsQuery = true,
		bool	addCoords = true )

attachment points encoded as attachPt properties are added to the graph as dummy atoms

Parameters

mol	the molecule of interest
atomIdx	the index of the atom to which the attachment point should be added
val	the attachment point value. Should be 1 or 2
addAsQueries	if true, the dummy atoms will be added as null queries (i.e. they will match any atom in a substructure search)
addCoords	if true and the molecule has one or more conformers, positions for the attachment points will be added to the conformer(s).

hapticBondEndpoints()

RDKIT_GRAPHMOL_EXPORT std::vector< int > RDKit::MolOps::details::hapticBondEndpoints

(

const Bond *

bond

)

isAttachmentPoint()

RDKIT_GRAPHMOL_EXPORT bool RDKit::MolOps::details::isAttachmentPoint	(	const Atom *	atom,
		bool	markedOnly = true )

returns whether or not an atom is an attachment point

Parameters

mol	the molecule of interest
markedOnly	if true, only dummy atoms with the _fromAttachPoint property will be collapsed

In order for a dummy atom to be considered for collapsing it must have:

• degree 1 with a single or unspecified bond
• the bond to it can not be wedged
• either no query or be an AtomNullQuery

KekulizeFragment()

RDKIT_GRAPHMOL_EXPORT void RDKit::MolOps::details::KekulizeFragment	(	RWMol &	mol,
		const boost::dynamic_bitset<> &	atomsToUse,
		boost::dynamic_bitset<>	bondsToUse,
		bool	markAtomsBonds = true,
		unsigned int	maxBackTracks = 100 )

not recommended for use in other code