An object to store information about chemical motifs: participation in rings, planarity, chirality, aromaticity, conjugation, planarity, and bonds with different rotatability. More...

#include <chemical_features.h>

Public Member Functions
int	getAtomCount () const
	Get the total number of atoms.

int	getPlanarAtomCount () const
	Get the number of planar atoms.

int	getRingCount () const
	Get the number of rings in the system.

int	getFusedRingCount () const
	Get the number of fused rings in the system.

int	getMutableRingCount () const
	Get the number of malleable, non-aromatic twistable rings in the system.

int	getAromaticGroupCount () const
	Get the number of aromatic groups in the system.

int	getPolarHydrogenCount () const
	Get the number of polar hydrogens in the system.

int	getHydrogenBondDonorCount () const
	Get the number of hydrogen bond donors in the system.

int	getHydrogenBondAcceptorCount () const
	Get the number of hydrogen bond acceptors in the system.

int	getChiralCenterCount () const
	Get the number of chiral centers in the system.

int	getRotatableBondCount () const
	Get the number of rotatable bonds in the system.

int	getCisTransBondCount () const
	Get the number of bonds involved in cis-trans isomerization.

bool	rotatableGroupsMapped () const
	Indicate whether the rotatable groups (including rotatable bonds as well as cis-trans bonds) have been computed.

bool	chiralitiesComputed () const
	Indicate whether chiralities have been determined for this set of chemical features.

std::vector< uint >	getRingMask (int min_ring_size, int max_ring_size) const
	Return a mask of rings within a given size range for this system.

std::vector< uint >	getAromaticMask (int min_pi_electrons, int max_pi_electrons) const
	Return a mask of atomatic atoms in the system.

std::vector< int >	getPolarHydrogenList () const
	Get a list of all polar hydrogen atoms.

std::vector< int >	getHydrogenBondDonorList () const
	Get a list of all hydrogen bond donor atoms.

std::vector< int >	getHydrogenBondAcceptorList () const
	Get a list of all hydrogen bond acceptor atoms.

std::vector< uint >	getPolarHydrogenMask () const
	Get a bit mask of all polar hydrogen atoms in the system, acceptable for inputs to creating new atom masks.

std::vector< uint >	getHydrogenBondDonorMask () const
	Get a bit mask of all hydrogen bond donors in the system, acceptable for inputs to creating new atom masks.

std::vector< uint >	getHydrogenBondAcceptorMask () const
	Get a bit mask of all hydrogen bond acceptors in the system, acceptable for inputs to creating new atom masks.

std::vector< int >	getChiralCenters (ChiralOrientation direction=ChiralOrientation::NONE) const
	List the chiral centers in a system, using topological indices.

std::vector< int4 >	getChiralArmBaseAtoms () const
	Get the bases of each arm for all chiral centers. The result returns the lowest priority arm in the "x" member, the highest in the "y" member, and the second- and third-highest priority arms in the "z" and "w" members of each tuple, respectively.

std::vector< uint >	getChiralityMask (ChiralOrientation direction) const
	Return a mask of chiral centers in the system.

std::vector< double >	getFormalCharges () const
	Return a vector containing the formal charges on all particles in the system (this includes virtual sites, which will have formal charges of zero since they are not real atoms).

std::vector< double >	getBondOrders () const
	Return a vector containing the orders of all bonds in the system (this includes bonds to virtual sites only if they are defined in the topology's connectivity, and such bonds will have order zero).

const std::vector< int > &	getZeroKelvinFormalCharges () const
	Return the formal charges for a representative Lewis structure of the molecules in this topology.

const std::vector< int > &	getZeroKelvinBondOrders () const
	Return the bond orders for a representative Lewis structure of the molecules in this topology.

const std::vector< int > &	getZeroKelvinFreeElectrons () const
	Return the free electron content of atoms in a representative Lewis structure of the molecules in this topology.

std::vector< IsomerPlan >	getCisTransIsomerizationGroups () const
	Get the moving atom groups and bond endpoints involved in cis-trans isomerization. This function clones the simple form of getRotatableBondGroups but the reliance on so many different arrays and counters makes it fruitless to abstract.

std::vector< IsomerPlan >	getChiralInversionGroups () const
	Get the group of atoms that can invert a chiral center by a C2 symmetry rotation. This re-uses the IsomerPlan struct, this time casting the root and pivot atoms as the origins of the heaviest and second-heaviest branches, respectively, which will again not move even as the rest of the atoms rotate.

const AtomGraph *	getTopologyPointer () const
	Get a pointer to the AtomGraph which built this object.

const ChemicalFeatures *	getSelfPointer () const
	Get a const pointer to the object itself in host memory.

ChemicalFeaturesReader	data (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the abstract.

void	findChiralOrientations (const CoordinateFrameReader &cfr)
	Find the chiral orientations of the system's chiral centers. This function will be called once by the constructor but can be called additional times if the coordinates of the system change. It will update the object's internal array of chiral centers, which combines orientational information with the centers' topological indices.

void	findRotatableBondGroups (StopWatch *timer=nullptr)
	Find the rotatable (and cis-trans invertible, and chiral invertible) atom groups in the topology based on rotatable bonds or chiral centers found by the rest of the chemical perception calculations.


	ChemicalFeatures (const AtomGraph ag_in=nullptr, MapRotatableGroups map_groups_in=MapRotatableGroups::NO, double temperature_in=300.0, StopWatch timer_in=nullptr)
	The constructor requires a topology and some coordinate set.

	ChemicalFeatures (const AtomGraph &ag_in, MapRotatableGroups map_groups_in=MapRotatableGroups::NO, double temperature_in=300.0, StopWatch *timer_in=nullptr)

	ChemicalFeatures (const AtomGraph ag_in, const CoordinateFrameReader &cfr, MapRotatableGroups map_groups_in=MapRotatableGroups::NO, double temperature_in=300.0, StopWatch timer_in=nullptr)

	ChemicalFeatures (const AtomGraph ag_in, const CoordinateFrame &cf, MapRotatableGroups map_groups_in=MapRotatableGroups::NO, double temperature_in=300.0, StopWatch timer_in=nullptr)

	ChemicalFeatures (const AtomGraph ag_in, const PhaseSpace &ps, MapRotatableGroups map_groups_in=MapRotatableGroups::NO, double temperature_in=300.0, StopWatch timer_in=nullptr)

	ChemicalFeatures (const AtomGraph &ag_in, const CoordinateFrame &cf, MapRotatableGroups map_groups_in=MapRotatableGroups::NO, double temperature_in=300.0, StopWatch *timer_in=nullptr)

	ChemicalFeatures (const AtomGraph &ag_in, const PhaseSpace &ps, MapRotatableGroups map_groups_in=MapRotatableGroups::NO, double temperature_in=300.0, StopWatch *timer_in=nullptr)


	ChemicalFeatures (const ChemicalFeatures &original)
	Copy and move constructors.

	ChemicalFeatures (ChemicalFeatures &&original)


ChemicalFeatures &	operator= (const ChemicalFeatures &other)
	Copy assignment and move assignment operators.

ChemicalFeatures &	operator= (ChemicalFeatures &&other)


ChiralOrientation	getAtomChirality (int atom_index) const
	Return the chiral orientations for one or more atoms in the system.

std::vector< ChiralOrientation >	getAtomChirality (int low_index, int high_index) const

std::vector< ChiralOrientation >	getAtomChirality () const


double	getFreeElectrons (int atom_index) const
	Return the (resonance-averaged) free electron content for one or more atoms in the system.

std::vector< double >	getFreeElectrons (int low_index, int high_index) const

std::vector< double >	getFreeElectrons () const


ullint	getRingInclusion (int atom_index) const
	Return the ring inclusion specifications for one or more atoms in the system.

std::vector< ullint >	getRingInclusion (int low_index, int high_index) const

std::vector< ullint >	getRingInclusion () const


bool	bondIsInRing (int atom_i, int atom_j) const
	Return whether a bond in the system is in a ring group or not.

bool	bondIsInRing (int bond_index) const


std::vector< IsomerPlan >	getRotatableBondGroups () const
	Get the atom endpoints of a rotatable bond. The bond root atom is returned in the x member of the tuple, the pivot atom (the second atom, closest to atoms that will turn) is listed in the y member.

std::vector< IsomerPlan >	getRotatableBondGroups (int cutoff, int mol_index=0) const


std::vector< ChiralInversionProtocol >	getChiralInversionMethods () const
	Get the means for inverting one or more chiral centers.

ChiralInversionProtocol	getChiralInversionMethods (int index) const

Detailed Description

An object to store information about chemical motifs: participation in rings, planarity, chirality, aromaticity, conjugation, planarity, and bonds with different rotatability.

Constructor & Destructor Documentation

◆ ChemicalFeatures() [1/2]

stormm::chemistry::ChemicalFeatures::ChemicalFeatures	(	const AtomGraph *	ag_in = nullptr,
		MapRotatableGroups	map_groups_in = MapRotatableGroups::NO,
		double	temperature_in = 300.0,
		StopWatch *	timer_in = nullptr )

The constructor requires a topology and some coordinate set.

Overloaded:

Create a blank object
Create a with a topology only (provided by const pointer or by const reference)
Create with a topology and one of the basic (single-system) coordinate objects

Parameters

ag_in	Pointer to the system topology. This topology will not be modified by submitting it to this constructor, but it is needed as a constant pointer so that the object itself can store a valid pointer to the original topology (passing by const reference would not create a valid pointer).
cfr	Coordinates of the system
ps	Coordinates of the system (a CoordinateFrameReader will be extracted)
map_groups_in	Indicator of whether to map rotatable groups (this is an O(N^2) algorithm in memory as well as computation, as larger structures will have more rotatable bonds and the entirety of the structure must be traced in relation to each of them)
temperature_in	Temperature at which to take Boltzmann weights of different resonance states

◆ ChemicalFeatures() [2/2]

stormm::chemistry::ChemicalFeatures::ChemicalFeatures ( const ChemicalFeatures & original )

Copy and move constructors.

Parameters

original The ChemicalFeatures object to copy

Member Function Documentation

◆ bondIsInRing()

bool stormm::chemistry::ChemicalFeatures::bondIsInRing	(	int	atom_i,
		int	atom_j ) const

Return whether a bond in the system is in a ring group or not.

Overloaded:

Provide the two atoms at either endpoint of the bond (checked for existence of an actual bond)
Provide the topological index of the bond (faster method if a means of interpreting the context of each bond is prepared)

Parameters

atom_i	Topological index of the first atom in the bond
atom_j	Topological index of the second atom in the bond
bond_index	Topological index of the bond of interest

◆ data()

ChemicalFeaturesReader stormm::chemistry::ChemicalFeatures::data ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get the abstract.

Parameters

tier	Extract pointers to data on either the CPU host or GPU device

◆ findChiralOrientations()

void stormm::chemistry::ChemicalFeatures::findChiralOrientations ( const CoordinateFrameReader & cfr )

Find the chiral orientations of the system's chiral centers. This function will be called once by the constructor but can be called additional times if the coordinates of the system change. It will update the object's internal array of chiral centers, which combines orientational information with the centers' topological indices.

Parameters

cfr	Present coordinates of the system

◆ findRotatableBondGroups()

void stormm::chemistry::ChemicalFeatures::findRotatableBondGroups ( StopWatch * timer = nullptr )

Find the rotatable (and cis-trans invertible, and chiral invertible) atom groups in the topology based on rotatable bonds or chiral centers found by the rest of the chemical perception calculations.

Parameters

timer Timekeeping object for performance profiling

◆ getAromaticMask()

std::vector< uint > stormm::chemistry::ChemicalFeatures::getAromaticMask	(	int	min_pi_electrons,
		int	max_pi_electrons ) const

Return a mask of atomatic atoms in the system.

Parameters

min_pi_electrons	Minimum number of electrons in the aromatic ring system to report
max_pi_electrons	Maximum number of electrons in the aromatic ring system to report

◆ getAtomChirality()

ChiralOrientation stormm::chemistry::ChemicalFeatures::getAtomChirality ( int atom_index ) const

Return the chiral orientations for one or more atoms in the system.

Overloaded:

Get the chiral orientation for a specific atom
Get the chiral orientations for a range of atoms
Get the chiral orientations for all atoms

Parameters

atom_index	The one atom of interest, based on the topological ordering
low_index	The start of a series of atoms for which to get ring inclusions
high_index	The upper limit of a series of atoms for which to get ring inclusions

◆ getChiralCenters()

std::vector< int > stormm::chemistry::ChemicalFeatures::getChiralCenters ( ChiralOrientation direction = ChiralOrientation::NONE ) const

List the chiral centers in a system, using topological indices.

Parameters

direction Preferred chiral orientation of the centers to return (D-, L-, or both)

◆ getChiralInversionMethods()

std::vector< ChiralInversionProtocol > stormm::chemistry::ChemicalFeatures::getChiralInversionMethods ( ) const

Get the means for inverting one or more chiral centers.

Overloaded:

Get all chiral inversion instructions
Get the instruction for a specific center, numbered according to the list of all chiral centers in the molecule.

Parameters

index The index of the chiral center of interest

◆ getChiralityMask()

std::vector< uint > stormm::chemistry::ChemicalFeatures::getChiralityMask ( ChiralOrientation direction ) const

Return a mask of chiral centers in the system.

Parameters

direction Allows one to select R- (D-), S- (L-), or both chiralities for the mask

◆ getFreeElectrons()

double stormm::chemistry::ChemicalFeatures::getFreeElectrons ( int atom_index ) const

Return the (resonance-averaged) free electron content for one or more atoms in the system.

Overloaded:

Get the free electron content for a specific atom
Get the free electron content for a range of atoms
Get the free electron content for all atoms

Parameters

atom_index	The one atom of interest
low_index	The start of a series of atoms for which to get ring inclusions
high_index	The upper limit of a series of atoms for which to get ring inclusions

◆ getRingInclusion()

ullint stormm::chemistry::ChemicalFeatures::getRingInclusion ( int atom_index ) const

Return the ring inclusion specifications for one or more atoms in the system.

Overloaded:

Get the ring inclusion for a specific atom
Get the ring inclusion for a range of atoms
Get the ring inclusion for all atoms

Parameters

atom_index	The one atom of interest
low_index	The start of a series of atoms for which to get ring inclusions
high_index	The upper limit of a series of atoms for which to get ring inclusions

◆ getRingMask()

std::vector< uint > stormm::chemistry::ChemicalFeatures::getRingMask	(	int	min_ring_size,
		int	max_ring_size ) const

Return a mask of rings within a given size range for this system.

Parameters

min_ring_size	The minimum number of atoms in the rings that will be reported
max_ring_size	The maximum number of atoms in the rings that will be reported

◆ getRotatableBondGroups()

std::vector< IsomerPlan > stormm::chemistry::ChemicalFeatures::getRotatableBondGroups ( ) const

Get the atom endpoints of a rotatable bond. The bond root atom is returned in the x member of the tuple, the pivot atom (the second atom, closest to atoms that will turn) is listed in the y member.

Overloaded:

Get all rotatable bonds without re-ordering the list.
Get a list of all rotatable bonds upon which a minimum number of atoms turn.
Get a list of rotatable bonds for which the pivot is within a specific cutoff of the current conformation's center of mass.
Get a list of rotatable bonds for which the pivot is within a specific cutoff of the center of mass of some atom mask (the mask must be supplied as a raw bitmask of the entire system, a std::vector of unsigned ints, to prevent making a circular dependency whereby the AtomMask object depends on ChemicalFeatures and vice-versa).
Get a list of the N largest rotatable groups of atoms.

Parameters

cutoff	The threshold at which to accept rotatable bond groups. The meaning depends on the value of the choice enumeration (see below). If the choice is COM_PROXIMITY, then cutoff is a distance with units of Angstroms. If the choice is GROUP_SIZE, then cutoff is a minimium number of rotating atoms.
mol_index	The molecule of interest (the system may have multiple molecules).

◆ operator=()

ChemicalFeatures & stormm::chemistry::ChemicalFeatures::operator= ( const ChemicalFeatures & other )

Copy assignment and move assignment operators.

Parameters

other The ChemicalFeatures object to copy (a different name for a better semantic fit in the context of the = sign)

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

Constructor & Destructor Documentation

◆ ChemicalFeatures() [1/2]

◆ ChemicalFeatures() [2/2]

Member Function Documentation

◆ bondIsInRing()

◆ data()

◆ findChiralOrientations()

◆ findRotatableBondGroups()

◆ getAromaticMask()

◆ getAtomChirality()

◆ getChiralCenters()

◆ getChiralInversionMethods()

◆ getChiralityMask()

◆ getFreeElectrons()

◆ getRingInclusion()

◆ getRingMask()

◆ getRotatableBondGroups()

◆ operator=()