stormm::chemistry::IndigoAtomCenter Class Reference

Enumerate the possible combinations of formal charge state and the orders of bonds relevant to a particular atom. Also list the other atoms linked by those bonds. More...

#include <indigo.h>

Public Member Functions
	IndigoAtomCenter (int table_index_in, int z_number_in, int bond_count_in, int valence_electrons_in, const std::vector< int > &relevant_bonds_in, const std::vector< int > &partner_atoms_in, const std::vector< int > &atom_scores, const std::vector< int > &bond_scores)
	The constructor takes the parent IndigoTable's lists of atoms and bonds.
int	getIndigoTableIndex () const
	Let it be known which atom this center pertains to.
int	getStateCount () const
	Return the number of states this atomc center can take on.
uint	getState (int state_index) const
	Return the bitmask describing a particular state of this atom center.
int	getCharge (int state_index) const
	Get the charge of an atom center in a particular state.
int	getAtomicNumber () const
	Get the atomic number of the atom.
int	getScore (int state_index) const
	Return the score associated with a particular state of this atom center.
void	sortStates ()
	Sort the states to put the lowest energy (lowest scoring) state first.
int	getPartnerCount () const
	Get the number of partners in this atom center.
int	getRelevantBond (int index) const
	Get the index of the relevant bond connecting this atom to the partner of the same index. The index is produced into the original topology.
int	getPartner (int index) const
	Get one of the partners for a specific atom center. Return the atom center index of the partner in the overarching IndigoTable.
int	findPartnerIndex (int partner_atom_number) const
	Find a partner atom within the local list of this atom center. Return the index of the partner atom in the local list (also corresponds to the index of the bond that this atom will use to connect to that partner atom).
int	getBondOrderOfState (int bond_index, int state_index) const
	Get the order of a bond made by this atom center to a specified partner when the atom center lies in a particular state.
bool	queryBondToPartner (int partner_atom_number, int partner_bo) const
	Determine whether an atom center makes a bond of a certain order to a specific partner.
int	cullByPartners (const std::vector< IndigoAtomCenter > &acen)
	Cull states from a particular atom center if its partners cannot reciprocate with the correct bond order. Return the number of states culled.

Detailed Description

Enumerate the possible combinations of formal charge state and the orders of bonds relevant to a particular atom. Also list the other atoms linked by those bonds.

Member Function Documentation

cullByPartners()

int stormm::chemistry::IndigoAtomCenter::cullByPartners

(

const std::vector< IndigoAtomCenter > &

acen

)

Cull states from a particular atom center if its partners cannot reciprocate with the correct bond order. Return the number of states culled.

Parameters

acen	Array of all atom centers from the overarching IndigoTable (this array contains the atom center that is currently being operated on, but is passed as read-only)

getBondOrderOfState()

int stormm::chemistry::IndigoAtomCenter::getBondOrderOfState	(	int	bond_index,
		int	state_index ) const

Get the order of a bond made by this atom center to a specified partner when the atom center lies in a particular state.

Parameters

bond_index	Index of the bond in question, in the local list kept by this atom center This also indicates the local index of the partner of interest.
state_index	Index of the state of the atom center to query. Bond orders can change depending on different states of the atom center.

getCharge()

int stormm::chemistry::IndigoAtomCenter::getCharge

(

int

state_index

)

const

Get the charge of an atom center in a particular state.

Parameters

state_index

Index of the state in question

getPartner()

int stormm::chemistry::IndigoAtomCenter::getPartner

(

int

index

)

const

Get one of the partners for a specific atom center. Return the atom center index of the partner in the overarching IndigoTable.

Parameters

index

Index of the specific partner within the center's local list

getRelevantBond()

int stormm::chemistry::IndigoAtomCenter::getRelevantBond

(

int

index

)

const

Get the index of the relevant bond connecting this atom to the partner of the same index. The index is produced into the original topology.

Parameters

index

Index of the atom center's partner, to which the bond of interest connects

getScore()

int stormm::chemistry::IndigoAtomCenter::getScore

(

int

state_index

)

const

Return the score associated with a particular state of this atom center.

Parameters

state_index

Index of the state in question

getState()

uint stormm::chemistry::IndigoAtomCenter::getState

(

int

state_index

)

const

Return the bitmask describing a particular state of this atom center.

Parameters

state_index

Index of the state in question

queryBondToPartner()

bool stormm::chemistry::IndigoAtomCenter::queryBondToPartner	(	int	partner_atom_number,
		int	partner_bo ) const

Determine whether an atom center makes a bond of a certain order to a specific partner.

Parameters

partner_index	The index of the partner atom center in the overarching IndigoTable
partner_bo	The bond order that must be found in some state

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

• src/Chemistry/indigo.h
• src/Chemistry/indigo.cpp