#include <indigox/classes/forcefield.hpp>

Public Types
enum	Family
	Enum for the different families of forcefields. More...

Public Member Functions
	Forcefield ()=default

	Forcefield (const Forcefield &)=default

	Forcefield (Forcefield &&)=default

	Forcefield (Family family, std::string name)
	Normal constructor. More...

	~ Forcefield ()=default

FFAngle	GetAngleType (AngleType type, int32_t id) const
	Get the type of angle with the given id. More...

FFAngle	GetAngleType (int32_t id) const
	Get the first angle type with the given id. More...

FFAtom	GetAtomType (std::string name) const
	Get the AtomType with the given name. More...

FFAtom	GetAtomType (int32_t id) const
	Get the AtomType with the given id. More...

FFBond	GetBondType (BondType type, int32_t id) const
	Get the type of bond with the given id. More...

FFBond	GetBondType (int32_t id) const
	Get the first bond type with the given id. More...

FFDihedral	GetDihedralType (DihedralType type, int32_t id) const
	Get the type of dihedral with the given id. More...

FFDihedral	GetDihedralType (int32_t id) const
	Get the first dihedral type with the given id. More...

Family	GetFamily () const
	Get the family of the forcefield. More...

std::string	GetName () const
	Get the name of the forcefield. More...

void	LinkAngleTypes (const FFAngle &a, const FFAngle &b)
	Link together two equivalent angle types. More...

void	LinkBondTypes (const FFBond &a, const FFBond &b)
	Link together two equivalent bond types. More...

FFAngle	NewAngleType (AngleType type, int32_t id, double a, double b)
	Adds a new angle type to the forcefield with two parameters. More...

FFAtom	NewAtomType (int32_t id, std::string name, const Element &element)
	Add a new atom type to the forcefield. More...

FFBond	NewBondType (BondType type, int32_t id, double a, double b)
	Adds a new bond type to the forcefield with two parameters. More...

FFDihedral	NewDihedralType (DihedralType type, int32_t id, double a, double b, double c)
	Adds a new dihedral type to the forcefield with three parameters. More...

FFDihedral	NewDihedralType (DihedralType type, int32_t id, double a, double b)
	Adds a new dihedral type to the forcefield with two parameters. More...

size_t	NumAngleTypes () const
	Get the number of angle types in the forcefield. More...

size_t	NumAngleTypes (AngleType type) const
	Get the number of angle types of the given functional form. More...

size_t	NumAtomTypes () const
	Get the number of atom types in the forcefield. More...

size_t	NumBondTypes () const
	Get the total number of bond types in the forcefield. More...

size_t	NumBondTypes (BondType type) const
	Get the number of bond types of the given functional form. More...

size_t	NumDihedralTypes () const
	Get the number of dihedral types in the forcefield. More...

size_t	NumDihedralTypes (DihedralType type) const
	Get the number of dihedral types of the given functional form. More...

	operator bool () const

bool	operator!= (const Forcefield &ff) const

bool	operator< (const Forcefield &ff) const

bool	operator<= (const Forcefield &ff) const

Forcefield &	operator= (const Forcefield &)=default

Forcefield &	operator= (Forcefield &&)=default

bool	operator== (const Forcefield &ff) const

bool	operator> (const Forcefield &ff) const

bool	operator>= (const Forcefield &ff) const

void	ReserveAngleTypes (AngleType type, size_t size)
	Reserve space for angle types. More...

void	ReserveAtomTypes (size_t size)
	Reserve space for atom types. More...

void	ReserveBondTypes (BondType type, size_t size)
	Reserve space for bond types. More...

void	ReserveDihedralTypes (DihedralType type, size_t size)
	Reserve space for dihedral types. More...

Friends
class	cereal::access
	Friendship allows serialisation. More...

std::ostream &	operator<< (std::ostream &os, const Forcefield &ff)

Member Enumeration Documentation

◆ Family

enum Family

strong

Enum for the different families of forcefields.

Though other values are provided, currently only the GROMOS family of forcefields are technically supported.

Enumerator
Empty
GROMOS
CHARMM
AMBER
Other

Constructor & Destructor Documentation

◆ Forcefield() [1/4]

Forcefield ( )

default

◆ Forcefield() [2/4]

Forcefield ( const Forcefield & )

default

◆ Forcefield() [3/4]

Forcefield ( Forcefield && )

default

◆ ~ Forcefield()

~ Forcefield ( )

default

◆ Forcefield() [4/4]

Forcefield	(	Family	family,
		std::string	name
	)

Normal constructor.

Create a new forcefield from the given family. The family dictates which types of functional forms are allowed. Currently implemented is the GROMOS family of forcefields, which allows harmonic and quartic bond types, harmonic and caosine-harmonic angle types, and proper and improper dihedral types.

Parameters

family	the family of forcefields to use.
name	the name of the forcefield.

Member Function Documentation

◆ GetAngleType() [1/2]

FFAngle GetAngleType	(	AngleType	type,
		int32_t	id
	)		const

Get the type of angle with the given id.

Parameters

type	the type of angle to get.
the	id of the angle type.

Returns: the requested angle type, or an empty shared_ptr.

◆ GetAngleType() [2/2]

FFAngle GetAngleType ( int32_t id ) const

Get the first angle type with the given id.

Searches through all allowed angle types in order and returns the first type with the given id.

Parameters

id	the id of the angle type.

Returns: the angle type, or an empty shared_ptr.

◆ GetAtomType() [1/2]

FFAtom GetAtomType ( std::string name ) const

Get the AtomType with the given name.

Parameters

name	the name of the atom type.

Returns: the atomtype with the name, or an empty shared_ptr.

◆ GetAtomType() [2/2]

FFAtom GetAtomType ( int32_t id ) const

Get the AtomType with the given id.

Parameters

id	the id of the atom type.

Returns: the atomtype with the id, or an empty shared_ptr.

◆ GetBondType() [1/2]

FFBond GetBondType	(	BondType	type,
		int32_t	id
	)		const

Get the type of bond with the given id.

Parameters

type	the type of bond to get.
the	id of the bond type.

Returns: the requested bond type, or an empty shared_ptr.

◆ GetBondType() [2/2]

FFBond GetBondType ( int32_t id ) const

Get the first bond type with the given id.

Searches through all allowed bond types in order and returns the first type with the id.

Parameters

id	the id of the bond type.

Returns: the bond type, or an empty shared_ptr.

◆ GetDihedralType() [1/2]

FFDihedral GetDihedralType	(	DihedralType	type,
		int32_t	id
	)		const

Get the type of dihedral with the given id.

Parameters

type	the type of dihedral to get.
the	id of the dihedral type.

Returns: the requested dihedral type, or an empty shared_ptr.

◆ GetDihedralType() [2/2]

FFDihedral GetDihedralType ( int32_t id ) const

Get the first dihedral type with the given id.

Searches through all allowed dihedral types in order and returns the first type with the given id.

Parameters

id	the id of the dihedral type.

Returns: the dihedral type, or an empty shared_ptr.

◆ GetFamily()

Family GetFamily ( ) const

Get the family of the forcefield.

Returns: the forcefields family.

◆ GetName()

std::string GetName ( ) const

Get the name of the forcefield.

Returns: the name of the forcefield.

◆ LinkAngleTypes()

void LinkAngleTypes	(	const FFAngle &	a,
		const FFAngle &	b
	)

Link together two equivalent angle types.

Two angle types can be linked together when they are regarded as the same type with different functional forms. For example, the GROMOS forcefield provides both harmonic and cosine-harmonic force constants for all angle types. This method will remove any existing links.

Parameters

a,b	the two types to link.

◆ LinkBondTypes()

void LinkBondTypes	(	const FFBond &	a,
		const FFBond &	b
	)

Link together two equivalent bond types.

Two bond types can be linked together when they are regarded as the same type with different functional forms. For example, the GROMOS forcefield provides both harmonic and quartic force constants for all bond types. This method will remove any existing links.

Parameters

a,b	the two types to link.

◆ NewAngleType()

FFAngle NewAngleType	(	AngleType	type,
		int32_t	id,
		double	a,
		double	b
	)

Adds a new angle type to the forcefield with two parameters.

This constructor should be used for AngleType::Harmonic and AngleType::CosineHarmonic bond types. In both cases, a is the force constant and b is the ideal angle.

Parameters

type	the type of the angle.
id	the id of the angle.
a,b	the two parameter values.

Returns: the newly created angle type.

◆ NewAtomType()

FFAtom NewAtomType	(	int32_t	id,
		std::string	name,
		const Element &	element
	)

Add a new atom type to the forcefield.

Parameters

id	the id of the atom type.
name	the name of the atom type.

Returns: the newly created atom type.

Exceptions

std::runtime_error if an atomtype with the given name or id already exists within the forcefield.

◆ NewBondType()

FFBond NewBondType	(	BondType	type,
		int32_t	id,
		double	a,
		double	b
	)

Adds a new bond type to the forcefield with two parameters.

This constructor should be used for BondType::Harmonic and BondType::Quartic bond types. In both cases, a is the force constant and b is the ideal length.

Parameters

type	the type of the bond.
id	the id of the bond.
a,b	the two parameter values.

Returns: the newly created bond type.

◆ NewDihedralType() [1/2]

FFDihedral NewDihedralType	(	DihedralType	type,
		int32_t	id,
		double	a,
		double	b,
		double	c
	)

Adds a new dihedral type to the forcefield with three parameters.

This constructor should be used for DihedralType::Proper dihedral types. In that case, a is the force constant, b is the phase and c is the multiplicity.

Parameters

type	the type of dihedral.
id	the id of the dihedral.
a,b,c	the three parameter values.

Returns: the newly created dihedral type.

◆ NewDihedralType() [2/2]

FFDihedral NewDihedralType	(	DihedralType	type,
		int32_t	id,
		double	a,
		double	b
	)

Adds a new dihedral type to the forcefield with two parameters.

This constructor should be used for DihedralType::Improper dihedral types. In that case, a is the force constant and b is the ideal dihedral angle

Parameters

type	the type of dihedral.
id	the id of the dihedral.
a,b	the three parameter values.

Returns: the newly created dihedral type.

◆ NumAngleTypes() [1/2]

size_t NumAngleTypes ( ) const

Get the number of angle types in the forcefield.

For forcefields with multiple allowed types, the count of each type are summed.

Returns: the number of angle types in the forcefield.

◆ NumAngleTypes() [2/2]

size_t NumAngleTypes ( AngleType type ) const

Get the number of angle types of the given functional form.

Determines how may of the given angle types are present in the forcefield. In the case that the provided type is not supposrted by the forcefield, 0 is returned.

Parameters

type	the type of angle to count.

Returns: the number of angle types in the forcefield.

◆ NumAtomTypes()

size_t NumAtomTypes ( ) const

Get the number of atom types in the forcefield.

Returns: the number of atom types in the forcefield.

◆ NumBondTypes() [1/2]

size_t NumBondTypes ( ) const

Get the total number of bond types in the forcefield.

For forcefields with multiple allowed types, the count of each type are summed.

Returns: the number of bond types in the forcefield.

◆ NumBondTypes() [2/2]

size_t NumBondTypes ( BondType type ) const

Get the number of bond types of the given functional form.

Determines how many of the given bond type funcitonal form are present in the forcefield. In the case that the provided type is not supported by the forcefield, 0 is returned.

Parameters

type	the type of bond to count.

Returns: the number of bond types in the forcefield.

◆ NumDihedralTypes() [1/2]

size_t NumDihedralTypes ( ) const

Get the number of dihedral types in the forcefield.

For forcefields with multiple allowed types, the count of each type are summed.

Returns: the number of bond types in the forcefield.

◆ NumDihedralTypes() [2/2]

size_t NumDihedralTypes ( DihedralType type ) const

Get the number of dihedral types of the given functional form.

Determines how many of the given dihedral types are present in the forcefield. In the case that the provided type is not supported by the forcefield, 0 is returned.

Parameters

type	the type of dihedral to count.

Returns: the number of dihedral types in the forcefield.

◆ operator bool()

operator bool ( ) const

inline

◆ operator!=()

bool operator!= ( const Forcefield & ff ) const

inline

◆ operator<()

bool operator< ( const Forcefield & ff ) const

◆ operator<=()

bool operator<= ( const Forcefield & ff ) const

inline

◆ operator=() [1/2]

Forcefield& operator= ( Forcefield && )

default

◆ operator=() [2/2]

Forcefield& operator= ( const Forcefield & )

default

◆ operator==()

bool operator== ( const Forcefield & ff ) const

◆ operator>()

bool operator> ( const Forcefield & ff ) const

◆ operator>=()

bool operator>= ( const Forcefield & ff ) const

inline

◆ ReserveAngleTypes()

void ReserveAngleTypes	(	AngleType	type,
		size_t	size
	)

Reserve space for angle types.

Parameters

type	the type of angle to reserve space for.
size	the amount of space to reserve.

◆ ReserveAtomTypes()

void ReserveAtomTypes ( size_t size )

Reserve space for atom types.

Parameters

size	the amount of space to reserve.

◆ ReserveBondTypes()

void ReserveBondTypes	(	BondType	type,
		size_t	size
	)

Reserve space for bond types.

Parameters

type	the type of bond to reserve space for.
size	the amount of space to reserve.

◆ ReserveDihedralTypes()

void ReserveDihedralTypes	(	DihedralType	type,
		size_t	size
	)

Reserve space for dihedral types.

Parameters

type	the type of dihedral to reserve space for.
size	the amount of space to reserve.

Friends And Related Function Documentation

◆ cereal::access

friend class cereal::access

friend

Friendship allows serialisation.

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		const Forcefield &	ff
	)

friend

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

include/indigox/classes/forcefield.hpp

Public Types

Public Member Functions

Friends

Member Enumeration Documentation

◆ Family

Constructor & Destructor Documentation

◆ Forcefield() [1/4]

◆ Forcefield() [2/4]

◆ Forcefield() [3/4]

◆ ~ Forcefield()

◆ Forcefield() [4/4]

Member Function Documentation

◆ GetAngleType() [1/2]

◆ GetAngleType() [2/2]

◆ GetAtomType() [1/2]

◆ GetAtomType() [2/2]

◆ GetBondType() [1/2]

◆ GetBondType() [2/2]

◆ GetDihedralType() [1/2]

◆ GetDihedralType() [2/2]

◆ GetFamily()

◆ GetName()

◆ LinkAngleTypes()

◆ LinkBondTypes()

◆ NewAngleType()

◆ NewAtomType()

◆ NewBondType()

◆ NewDihedralType() [1/2]

◆ NewDihedralType() [2/2]

◆ NumAngleTypes() [1/2]

◆ NumAngleTypes() [2/2]

◆ NumAtomTypes()

◆ NumBondTypes() [1/2]

◆ NumBondTypes() [2/2]

◆ NumDihedralTypes() [1/2]

◆ NumDihedralTypes() [2/2]

◆ operator bool()

◆ operator!=()

◆ operator<()

◆ operator<=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ operator>()

◆ operator>=()

◆ ReserveAngleTypes()

◆ ReserveAtomTypes()

◆ ReserveBondTypes()

◆ ReserveDihedralTypes()

Friends And Related Function Documentation

◆ cereal::access

◆ operator<<