stormm::chemistry::IndigoFragment Class Reference

A fragment of a structure detailed with the Indigo scoring function. More...

#include <indigo.h>

Public Member Functions
	IndigoFragment (const std::vector< int > &centers_list_in, const std::vector< IndigoAtomCenter > &all_centers, int score_delta=default_indigo_energy_gap)
	Constructor takes a list of atoms, then determines the bonds between them and whatever connections to other fragments. The identities of other fragments are not determined at the time of construction, but space to store them is allocated.
int	getCenterCount () const
	Get the number of centers in this fragment.
int	getStateCount () const
	Get the number of states in this fragment.
std::vector< int2 >	getState (int state_index) const
	Return the vector of {atom center number, atom center state} tuples describing a particular state of this fragment. This list will have to be interpreted in light of the complete list of atom centers to know what formal charge states and bond orders the fragment state actually implies.
int	getGlobalCenter (int center_index) const
	Get the index of a center in the fragment within the molecule system as a whole.
int	getCharge (int state_index) const
	Get the charge of this fragment in a particular state. There total charges were compute when the object was constructed, hence no further references to a master list of atom centers and their individual states is necessary.
int	getScore (int state_index) const
	Return the score associated with a particular state of this atom center.
std::vector< int >	getChargeStates () const
	Create a vector of the unique charge states in a fragment.
std::vector< int3 >	getChargesAndBestEnergies () const
	Get the range of charges and the minimum energy states that can produce each charge offered by this fragment. The vector of results is a list of tuples providing the fragment charge (in the x member), the minimum energy state (in the y member), and the index of the fragment state for that minimum energy and charge combination (in the z member).
std::vector< int2 >	getStatesBearingCharge (int charge_value) const
	Get all states in a fragment bearing a particular charge. The energy of each state satisfying the net charge condition is returned in the x member of each tuple. The index of the state is returned in the y member.
bool	testEquivalence (const IndigoFragment &other, const std::vector< int > &real_atom_map, const AtomGraph *ag_pointer, const std::vector< IndigoAtomCenter > &atom_centers) const
	Assess whether two fragments are equivalent, just with different atom indices. Return the result as a boolean expression.
int	cullStatesBearingCharge (int charge_value)
	Cull states of a fragment that bear a specific charge.
int	cullHigherEnergyStatesByCharge (int charge_value, int score_delta=default_indigo_energy_gap)
	Cull non-optimal states of a fragment that bear a specific charge.

Detailed Description

A fragment of a structure detailed with the Indigo scoring function.

Constructor & Destructor Documentation

IndigoFragment()

stormm::chemistry::IndigoFragment::IndigoFragment	(	const std::vector< int > &	centers_list_in,
		const std::vector< IndigoAtomCenter > &	all_centers,
		int	score_delta = default_indigo_energy_gap )

Constructor takes a list of atoms, then determines the bonds between them and whatever connections to other fragments. The identities of other fragments are not determined at the time of construction, but space to store them is allocated.

Parameters

idg_tab
atom_list	Subset of atoms that will make up this fragment
score_delta	The maximum score above some ground state, for a particular charge increment, to continue catalogging new states. Other above this threshold will be ignored.

Member Function Documentation

cullHigherEnergyStatesByCharge()

int stormm::chemistry::IndigoFragment::cullHigherEnergyStatesByCharge	(	int	charge_value,
		int	score_delta = default_indigo_energy_gap )

Cull non-optimal states of a fragment that bear a specific charge.

Parameters

charge_value	Cull states bearing this net charge with sub-optimal energies
score_delta	Threshold at which to cull non-optimal states (default 3187 implies an energy difference of 10 kcal/mol)

cullStatesBearingCharge()

int stormm::chemistry::IndigoFragment::cullStatesBearingCharge

(

int

charge_value

)

Cull states of a fragment that bear a specific charge.

Parameters

charge_value

Cull states bearing this net charge

getCharge()

int stormm::chemistry::IndigoFragment::getCharge

(

int

state_index

)

const

Get the charge of this fragment in a particular state. There total charges were compute when the object was constructed, hence no further references to a master list of atom centers and their individual states is necessary.

Parameters

state_index

Index of the state in question

getChargesAndBestEnergies()

std::vector< int3 > stormm::chemistry::IndigoFragment::getChargesAndBestEnergies

(

)

const

Get the range of charges and the minimum energy states that can produce each charge offered by this fragment. The vector of results is a list of tuples providing the fragment charge (in the x member), the minimum energy state (in the y member), and the index of the fragment state for that minimum energy and charge combination (in the z member).

Parameters

state_index

Index of the state in question

getGlobalCenter()

int stormm::chemistry::IndigoFragment::getGlobalCenter

(

int

center_index

)

const

Get the index of a center in the fragment within the molecule system as a whole.

Parameters

center_index

Index of the center of interest

getScore()

int stormm::chemistry::IndigoFragment::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()

std::vector< int2 > stormm::chemistry::IndigoFragment::getState

(

int

state_index

)

const

Return the vector of {atom center number, atom center state} tuples describing a particular state of this fragment. This list will have to be interpreted in light of the complete list of atom centers to know what formal charge states and bond orders the fragment state actually implies.

Parameters

state_index

Index of the fragment state in question

getStatesBearingCharge()

std::vector< int2 > stormm::chemistry::IndigoFragment::getStatesBearingCharge

(

int

charge_value

)

const

Get all states in a fragment bearing a particular charge. The energy of each state satisfying the net charge condition is returned in the x member of each tuple. The index of the state is returned in the y member.

Parameters

charge_value

The charge criterion for selecting states

testEquivalence()

bool stormm::chemistry::IndigoFragment::testEquivalence	(	const IndigoFragment &	other,
		const std::vector< int > &	real_atom_map,
		const AtomGraph *	ag_pointer,
		const std::vector< IndigoAtomCenter > &	atom_centers ) const

Assess whether two fragments are equivalent, just with different atom indices. Return the result as a boolean expression.

Parameters

other	Another fragment
real_atom_map	Map of fragment atoms into the original topology
ag_pointer	Pointer to the original topology
atom_centers	Array of all atom centers in the IndigoTable containing these fragments

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

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