A struct to serve as a tracker of progress through a molecule in the search for loops. Proceeding forward in the search, every link will have come from one and only one previous link, but could go in multiple directions thereafter. More...

#include <chemical_features.h>

Public Member Functions
	BondedNode ()
	Basic constructor simply initializes the members to blank values.

void	setBranchPointer (std::vector< int > *vi, size_t pos, size_t max_branches)
	Take a pre-existing std::vector<int> in order to set the object's own next_links pointer. This is in the interest of not repeatedly allocating and freeing many tiny std::vector<int> objects as BondedNodes are created and destroyed to grow a chain of atoms.

void	addToTree (int previous_in, int current_atom, int current_layer, const NonbondedKit< double > &nbk, const std::vector< bool > &valid_atom_mask)
	Set this as the next link in the chain, or as the chain initiator.

void	addToTree (int previous_in, int current_atom, int current_layer, int previous_node_in, const NonbondedKit< double > &nbk, const std::vector< bool > &valid_atom_mask)

void	addBondOrder (const ValenceKit< double > &vk, const Hybrid< double > &bond_orders)
	Add the bond order between this atom and its previous atom.

int	getPreviousAtom () const
	Get the previous atom index.

int	getPreviousNode () const
	Get the previous node's list index.

int	getAtom () const
	Get the central atom for this BondedNode.

int	getLayer () const
	Get the layer of which this BondedNode is a part.

int	getBranchCount () const
	Get the number of branches associated with this BondedNode's central atom (this is the total number of other atoms that it bonds to, less the previous atom in the chain)

int	getBranchAtom (int index) const
	Get the topological atom index of a specific branch that can come off of this BondedNode.

int	findBranchAtom (int search_index) const
	Get the branch index of a specific atom in a BondedNode.

uint	getRingCompletion (int branch_index) const
	Get the ring completion status for a particular node.

double	getRootBondOrder () const
	Get the bond order of the bond between this atom and the previous atom in the tree.

void	setRingCompletion (int partner_index)
	Set the ring completion for this object (this relies on no atom having more bonds than the number of bits in an unsigned int)

void	wipeRingCompletion ()
	Wipe clean the ring completion for this object.

Detailed Description

A struct to serve as a tracker of progress through a molecule in the search for loops. Proceeding forward in the search, every link will have come from one and only one previous link, but could go in multiple directions thereafter.

Member Function Documentation

◆ addBondOrder()

void stormm::chemistry::BondedNode::addBondOrder	(	const ValenceKit< double > &	vk,
		const Hybrid< double > &	bond_orders )

Add the bond order between this atom and its previous atom.

Parameters

vk	Valence interactions abstract from the original topology
bond_orders	Orders of bonds determined by Lewis structure drawing

◆ addToTree()

void stormm::chemistry::BondedNode::addToTree	(	int	previous_in,
		int	current_atom,
		int	current_layer,
		const NonbondedKit< double > &	nbk,
		const std::vector< bool > &	valid_atom_mask )

Set this as the next link in the chain, or as the chain initiator.

Overloaded:

Optionally accept the index of the previous node for traceback purposes.

Parameters

previous_in	Index of the previous BondedNode leading to this one, or -1 if this is intended to be the chain initiator
current_atom	Topological index of the current atom this BondedNode describes
current_layer	The current layer in the growing tree
nbk	Nonbonded interactions abstract for the overarching topology (needed for list of 1:2 exclusions, which indicate bonds)
valid_atom_mask	Reference table of which atoms are valid to include in the tree

◆ findBranchAtom()

int stormm::chemistry::BondedNode::findBranchAtom ( int search_index ) const

Get the branch index of a specific atom in a BondedNode.

Parameters

search_index The topological atom index to search for within the node's branches

◆ getBranchAtom()

int stormm::chemistry::BondedNode::getBranchAtom ( int index ) const

Get the topological atom index of a specific branch that can come off of this BondedNode.

Parameters

index The branch index of interest (could be any topological atom)

◆ getRingCompletion()

uint stormm::chemistry::BondedNode::getRingCompletion ( int branch_index ) const

Get the ring completion status for a particular node.

Parameters

branch_index The branch index of the partner atom with which this node forms a ring (this index is not a topological index, and must be ascertained in advance by findBranchAtom() above)

◆ setBranchPointer()

void stormm::chemistry::BondedNode::setBranchPointer	(	std::vector< int > *	vi,
		size_t	pos,
		size_t	max_branches )

Take a pre-existing std::vector<int> in order to set the object's own next_links pointer. This is in the interest of not repeatedly allocating and freeing many tiny std::vector<int> objects as BondedNodes are created and destroyed to grow a chain of atoms.

Parameters

vi	Vector of integers in which this BondedNode will store some of its data
pos	Indicator of the space in the storage vector allocate to this object
max_branches	The maximum number of branches that this chain link shall support

◆ setRingCompletion()

void stormm::chemistry::BondedNode::setRingCompletion ( int partner_index )

Set the ring completion for this object (this relies on no atom having more bonds than the number of bits in an unsigned int)

Parameters

partner_index Topological index of the atom to which a ring has been formed

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

src/Chemistry/chemical_features.h
src/Chemistry/chemical_features.cpp

Public Member Functions

Detailed Description

Member Function Documentation

◆ addBondOrder()

◆ addToTree()

◆ findBranchAtom()

◆ getBranchAtom()

◆ getRingCompletion()

◆ setBranchPointer()

◆ setRingCompletion()