#include <indigox/classes/molecule.hpp>

Classes
struct	Impl

Public Types
using	MoleculeAngles = std::vector< Angle >
	Container for storing IXAngle instances. More...

using	MoleculeAtoms = std::vector< Atom >
	Container for storing IXAtom instances. More...

using	MoleculeBonds = std::vector< Bond >
	Container for storing IXBond instances. More...

using	MoleculeDihedrals = std::vector< Dihedral >
	Container for storing IXDihedral instances. More...

using	MoleculeResidues = std::vector< Residue >

Public Member Functions
	Molecule (std::string name)
	Default constructor. More...

	Molecule ()=default

	Molecule (Molecule &&)=default

	Molecule (const Molecule &)=default

	~ Molecule ()=default

Angle	GetAngle (uint32_t pos)
	Get the angle at position `pos`. More...

Angle	GetAngle (const Atom &a, const Atom &b, const Atom &c)
	Get the angle between three atoms, if it exists. More...

Angle	GetAngleID (int64_t id) const
	Get the angle with the given id. More...

const MoleculeAngles &	GetAngles ()

Angle	GetAngleTag (int64_t tag) const
	Get the first angle with the given tag. More...

Atom	GetAtom (uint32_t pos) const
	Get the atom at position `pos`. More...

Atom	GetAtomID (int64_t id) const
	Get the atom with the given id. More...

const MoleculeAtoms &	GetAtoms () const

Atom	GetAtomTag (int64_t tag) const
	Get the first atom with the given tag. More...

Bond	GetBond (uint32_t pos) const
	Get the bond at position `pos`. More...

Bond	GetBond (const Atom &a, const Atom &b) const
	Get the bond between two atoms, if it exists. More...

Bond	GetBondID (int64_t id) const
	Get the bond with the given id. More...

const MoleculeBonds &	GetBonds () const

Bond	GetBondTag (int64_t tag) const
	Get the first bond with the given tag. More...

const graph::CondensedMolecularGraph &	GetCondensedGraph () const

Dihedral	GetDihedral (uint32_t pos)
	Get the angle at position `pos`. More...

Dihedral	GetDihedral (const Atom &a, const Atom &b, const Atom &c, const Atom &d)
	Get the dihedral between four atoms, it if exists. More...

Dihedral	GetDihedralID (int64_t id) const
	Get the dihedral with the given id. More...

const MoleculeDihedrals &	GetDihedrals ()

Dihedral	GetDihedralTag (int64_t tag) const
	Get the first dihedral with the given tag. More...

const Forcefield &	GetForcefield () const

std::string	GetFormula ()
	Get the molecular formula of the molecule. More...

const graph::MolecularGraph &	GetGraph () const
	Get the molecular graph for this molecule. More...

int32_t	GetMolecularCharge () const
	Get the molecular charge of the molecule. More...

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

Residue	GetResidueID (int32_t id)

const MoleculeResidues &	GetResidues ()

bool	HasAngle (const Angle &angle) const
	Check if the angle is owned by this molecule. More...

bool	HasAngle (const Atom &a, const Atom &b, const Atom &c)
	Check if an angle between three atoms exists in this molecule. More...

bool	HasAtom (const Atom &atom) const
	Check if the atom is owned by this molecule. More...

bool	HasBond (const Bond &bond) const
	Check if the bond is owned by this molecule. More...

bool	HasBond (const Atom &a, const Atom &b) const
	Check if a bond between two atoms exists in this molecule. More...

bool	HasDihedral (const Dihedral &dihedral) const
	Check if the dihedral is owned by this molecule. More...

bool	HasDihedral (const Atom &a, const Atom &b, const Atom &c, const Atom &d)
	Check if a dihedral between four atoms exists in this molecule. More...

bool	HasForcefield () const

void	ModificationMade ()

Atom	NewAtom ()
	Create a new atom owned by the molecule. More...

Atom	NewAtom (const Element &element)
	Create a new atom of the given element for the molecule. More...

Atom	NewAtom (const Element &element, double x, double y, double z)
	Create a new named atom of the given element for the molecule. More...

Bond	NewBond (const Atom &a, const Atom &b)
	Create a bond between two atoms. More...

Dihedral	NewDihedral (const Atom &a, const Atom &b, const Atom &c, const Atom &d)
	Create a dihedral between four atoms. More...

int64_t	NumAngles ()
	Get the number of angles in the molecule. More...

int64_t	NumAtoms () const
	Get the number of atoms in the molecule. More...

int64_t	NumBonds () const
	Get the number of bonds in the molecule. More...

int64_t	NumDihedrals ()
	Get the number of dihedrals in the molecule. More...

	operator bool () const

bool	operator!= (const Molecule &mol) const

bool	operator< (const Molecule &mol) const

bool	operator<= (const Molecule &mol) const

Molecule &	operator= (Molecule &&)=default

Molecule &	operator= (const Molecule &)=default

bool	operator== (const Molecule &mol) const

bool	operator> (const Molecule &mol) const

bool	operator>= (const Molecule &mol) const

void	OptimiseChargeGroups ()

int64_t	PerceiveAngles ()
	Determine angles in the molecule. More...

int64_t	PerceiveDihedrals ()
	Determine dihedrals in the molecule. More...

int32_t	PerceiveResidues ()

bool	RemoveAtom (const Atom &atom)
	Remove an atom from the molecule. More...

bool	RemoveBond (const Bond &bond)
	Remove a bond from the molecule. More...

bool	RemoveBond (const Atom &a, const Atom &b)
	Remove a bond between two atoms. More...

void	ReorderAtoms (MoleculeAtoms &new_order)

void	ReserveAtoms (int64_t num)
	Reserve storage space for atoms. More...

void	ReserveBonds (int64_t num)
	Reserve storage space for bonds. More...

void	ResetForcefield (const Forcefield &ff)

void	SetForcefield (const Forcefield &ff)

void	SetMolecularCharge (int32_t q)
	Set the molecular charge of the molecule. More...

void	SetName (std::string name)
	Set the name of the molecule. More...

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

std::ostream &	operator<< (std::ostream &os, const Molecule &mol)

Member Typedef Documentation

◆ MoleculeAngles

using MoleculeAngles = std::vector<Angle>

Container for storing IXAngle instances.

A molecule takes ownership of all angles it contains.

◆ MoleculeAtoms

using MoleculeAtoms = std::vector<Atom>

Container for storing IXAtom instances.

A molecule takes ownership of all atoms it contains.

◆ MoleculeBonds

using MoleculeBonds = std::vector<Bond>

Container for storing IXBond instances.

A molecule takes ownership of all bonds it contains.

◆ MoleculeDihedrals

using MoleculeDihedrals = std::vector<Dihedral>

Container for storing IXDihedral instances.

A molecule takes ownership of all dihedrals it contains.

◆ MoleculeResidues

using MoleculeResidues = std::vector<Residue>

Constructor & Destructor Documentation

◆ Molecule() [1/4]

Molecule ( std::string name )

Default constructor.

Is private to enforce that IXMolecules should only be used via the Molecule shared_ptr.

◆ Molecule() [2/4]

Molecule ( )

default

◆ Molecule() [3/4]

Molecule ( const Molecule & )

default

◆ Molecule() [4/4]

Molecule ( Molecule && )

default

◆ ~ Molecule()

~ Molecule ( )

default

Member Function Documentation

◆ GetAngle() [1/2]

Angle GetAngle ( uint32_t pos )

Get the angle at position pos.

Returns the angle at pos after a range check. If pos is not a valid index, returns an empty shared_ptr. Positioning of angles may change during normal operations. Angles are not re-percieved prior to retrieving the angle.

Parameters

pos	the position of the angle to get.

Returns: the angle at pos or an empty shared_ptr.

◆ GetAngle() [2/2]

Angle GetAngle	(	const Atom &	a,
		const Atom &	b,
		const Atom &	c
	)

Get the angle between three atoms, if it exists.

Searches for an angle between the three atoms and returns it. If no angle is found, the returned shared_ptr is empty. Angles are re-perceived prior to searching.

Parameters

a,b,c the atoms to get the angle between. b is the central atom.

Returns: the angle between a and c centred on b.

◆ GetAngleID()

Angle GetAngleID ( int64_t id ) const

Get the angle with the given id.

Returns the angle with the given unique id. If no such angle is found returns an empty shared_ptr. As the unique id of any created angles will be unknown, angles are not re-percieved prior to searching.

Parameters

id	the unique id of the angle to retrieve.

Returns: the angle with the given id or an empty shared_ptr.

◆ GetAngles()

const MoleculeAngles& GetAngles ( )

◆ GetAngleTag()

Angle GetAngleTag ( int64_t tag ) const

Get the first angle with the given tag.

Returns the first angle with a tag matching that given. If no such angle is found, returns an empty shared_ptr. As tags are not set on creation of angles, angles are not re-percieved prior to searching.

Parameters

tag	the angle tag to search for.

Returns: the first angle with the tag or an empty shared_ptr.

◆ GetAtom()

Atom GetAtom ( uint32_t pos ) const

Get the atom at position pos.

Returns that atom at pos after a range check. If pos is not a valid index, returns an empty shared_ptr. Positioning of atoms may change during normal operations.

Parameters

pos	the position of the atom to get.

Returns: the atom at pos or an empty shared_ptr.

◆ GetAtomID()

Atom GetAtomID ( int64_t id ) const

Get the atom with the given id.

Returns the atom with the given unique id. If no such atom is found returns an empty shared_ptr.

Parameters

id	the unique id of the atom to retrieve.

Returns: the atom with the given id or an empty shared_ptr.

◆ GetAtoms()

const MoleculeAtoms& GetAtoms ( ) const

◆ GetAtomTag()

Atom GetAtomTag ( int64_t tag ) const

Get the first atom with the given tag.

Returns the first atom with a tag matching that given. If no such atom is found, returns an empty shared_ptr.

Parameters

tag	the atom tag to search for.

Returns: the first atom with the tag or an empty shared_ptr.

◆ GetBond() [1/2]

Bond GetBond ( uint32_t pos ) const

Get the bond at position pos.

Returns that bond at pos after a range check. If pos is not a valid index, returns an empty shared_ptr. Positioning of bonds may change during normal operations.

Parameters

pos	the position of the bond to get.

Returns: the bond at pos or an empty shared_ptr.

◆ GetBond() [2/2]

Bond GetBond	(	const Atom &	a,
		const Atom &	b
	)		const

Get the bond between two atoms, if it exists.

Searches for a bond between a and b and returns it. If no bond is found, returns an empty shared_ptr.

Parameters

a,b	the atoms to get the bond between.

Returns: the bond between a and b or an empty shared_ptr.

◆ GetBondID()

Bond GetBondID ( int64_t id ) const

Get the bond with the given id.

Returns the bond with the given unique id. If no such bond is found returns an empty shared_ptr.

Parameters

id	the unique id of the bond to retrieve.

Returns: the bond with the given id or an empty shared_ptr.

◆ GetBonds()

const MoleculeBonds& GetBonds ( ) const

◆ GetBondTag()

Bond GetBondTag ( int64_t tag ) const

Get the first bond with the given tag.

Returns the first bond with a tag matching that given. If no such bond is found, returns an empty shared_ptr.

Parameters

tag	the bond tag to search for.

Returns: the first bond with the tag or an empty shared_ptr.

◆ GetCondensedGraph()

const graph::CondensedMolecularGraph& GetCondensedGraph ( ) const

◆ GetDihedral() [1/2]

Dihedral GetDihedral ( uint32_t pos )

Get the angle at position pos.

Returns the dihedral at pos after a range check. If pos is not a valid index, returns an empty shared_ptr. Positioning of dihedrals may change during normal operations. Dihedrals are not re-perceived prior to retrieving the dihedral.

Parameters

pos	the position of the dihedral to get.

Returns: the dihedral at pos or an empty shared_ptr.

◆ GetDihedral() [2/2]

Dihedral GetDihedral	(	const Atom &	a,
		const Atom &	b,
		const Atom &	c,
		const Atom &	d
	)

Get the dihedral between four atoms, it if exists.

Searches for a dihedral between the four atoms and returns it. If no dihedral is found, the returned shared_ptr is empty. Dihedrals are re-perceived prior to searching.

Parameters

a,b,c,d the atoms to get the dihedral between.

Returns: the dihedral between a, b, c and d.

◆ GetDihedralID()

Dihedral GetDihedralID ( int64_t id ) const

Get the dihedral with the given id.

Returns the dihedral with the given unique id. If no such dihedral is found returns an empty shared_ptr. As the unique id of any created dihedrals will be unknown, dihedrals are not re-perceived prior to searching.

Parameters

id	the unique id of the dihedral to retrieve.

Returns: the dihedral with the given id or an empty shared_ptr.

◆ GetDihedrals()

const MoleculeDihedrals& GetDihedrals ( )

◆ GetDihedralTag()

Dihedral GetDihedralTag ( int64_t tag ) const

Get the first dihedral with the given tag.

Returns the first dihedral with a tag matching that given. If no such dihedral is found, returns an empty shared_ptr. As tags are not set on creation of dihedrals, dihedrals are not re-perceived prior to searching.

Parameters

tag	the dihedral tag to search for.

Returns: the first dihedral with the tag or an empty shraed_ptr.

◆ GetForcefield()

const Forcefield& GetForcefield ( ) const

◆ GetFormula()

std::string GetFormula ( )

Get the molecular formula of the molecule.

Determines the molecular formula of the molecule. The elements of the formula are arranged in the order: carbon, hydrogen and then alphabetically by atomic symbol. The resultant formula is cached and recalculated only when the IXMolecule::ATOM_ELEMENTS property has been modified.

Returns: the molecular formula of the molecule.

◆ GetGraph()

const graph::MolecularGraph& GetGraph ( ) const

Get the molecular graph for this molecule.

Returns: the molecular graph of this molecule.

◆ GetMolecularCharge()

int32_t GetMolecularCharge ( ) const

Get the molecular charge of the molecule.

Returns: the molecular charge of the molecule.

◆ GetName()

const std::string& GetName ( ) const

Get the name of the molecule.

Returns: the name of the molecule.

◆ GetResidueID()

Residue GetResidueID ( int32_t id )

◆ GetResidues()

const MoleculeResidues& GetResidues ( )

◆ HasAngle() [1/2]

bool HasAngle ( const Angle & angle ) const

Check if the angle is owned by this molecule.

Parameters

angle the angle to check for.

Returns: if the angle is owned by this molecule.

◆ HasAngle() [2/2]

bool HasAngle	(	const Atom &	a,
		const Atom &	b,
		const Atom &	c
	)

Check if an angle between three atoms exists in this molecule.

If the Emergent::ANGLE_PERCEPTION property is set, angles are re-percieved prior to check for the existance of the angle. b is the central atom of the angle.

Parameters

a,b,c the atoms the angle should be between.

Returns: if there is an angle between the three atoms.

◆ HasAtom()

bool HasAtom ( const Atom & atom ) const

Check if the atom is owned by this molecule.

Parameters

atom	the atom to check for.

Returns: if the atom is owned by this molecule.

◆ HasBond() [1/2]

bool HasBond ( const Bond & bond ) const

Check if the bond is owned by this molecule.

Parameters

bond	the bond to check for.

Returns: if the bond is owned by this molecule.

◆ HasBond() [2/2]

bool HasBond	(	const Atom &	a,
		const Atom &	b
	)		const

Check if a bond between two atoms exists in this molecule.

Parameters

a,b	the atoms the bond should be between.

Returns: if there is a bond between the two atoms.

◆ HasDihedral() [1/2]

bool HasDihedral ( const Dihedral & dihedral ) const

Check if the dihedral is owned by this molecule.

Parameters

dihedral the dihedral to check for.

Returns: if the dihedral is owned by this molecule.

◆ HasDihedral() [2/2]

bool HasDihedral	(	const Atom &	a,
		const Atom &	b,
		const Atom &	c,
		const Atom &	d
	)

Check if a dihedral between four atoms exists in this molecule.

If the Emergent::DIHEDRAL_PERCEPTION property is set, dihedrals are re-perceived prior to checking for the existance of the dihedral.

Parameters

a,b,c,d the atoms the dihedral should be between.

Returns: if there is a dihedral between the four atoms.

◆ HasForcefield()

bool HasForcefield ( ) const

◆ ModificationMade()

void ModificationMade ( )

◆ NewAtom() [1/3]

Atom NewAtom ( )

Create a new atom owned by the molecule.

Returns: the new atom.

◆ NewAtom() [2/3]

Atom NewAtom ( const Element & element )

Create a new atom of the given element for the molecule.

Parameters

element the element of the new atom.

Returns: the new atom.

◆ NewAtom() [3/3]

Atom NewAtom	(	const Element &	element,
		double	x,
		double	y,
		double	z
	)

Create a new named atom of the given element for the molecule.

Parameters

name	the name of the new atom.
element	the element of the new atom.

Returns: the new atom.

◆ NewBond()

Bond NewBond	(	const Atom &	a,
		const Atom &	b
	)

Create a bond between two atoms.

To create a bond, both atoms need to be owned by the molecule and there cannot be an existing bond between the atoms. If either condition is not met, the returned shared_ptr is empty.

Parameters

a,b	the atoms to create a bond between.

Returns: the new bond.

◆ NewDihedral()

Dihedral NewDihedral	(	const Atom &	a,
		const Atom &	b,
		const Atom &	c,
		const Atom &	d
	)

Create a dihedral between four atoms.

Parameters

a,b,c,d the atoms to create the dihedral between.

Returns: the new dihedral.

◆ NumAngles()

int64_t NumAngles ( )

Get the number of angles in the molecule.

If the Emergent::ANGLE_PERCEPTION property is set, angles are re-calculated prior to determining how many there are in the molecule.

Returns: the number of angles in the molecule.

◆ NumAtoms()

int64_t NumAtoms ( ) const

Get the number of atoms in the molecule.

Returns: the number of atoms in the molecule.

◆ NumBonds()

int64_t NumBonds ( ) const

Get the number of bonds in the molecule.

Returns: the number of bonds in the molecule.

◆ NumDihedrals()

int64_t NumDihedrals ( )

Get the number of dihedrals in the molecule.

If the CONNECTIVITY property has been modified, dihedrals are re-calculated prior to determining how many there are in the molecule.

Returns: the number of dihedrals in the molecule.

◆ operator bool()

operator bool ( ) const

inline

◆ operator!=()

bool operator!= ( const Molecule & mol ) const

inline

◆ operator<()

bool operator< ( const Molecule & mol ) const

◆ operator<=()

bool operator<= ( const Molecule & mol ) const

inline

◆ operator=() [1/2]

Molecule& operator= ( Molecule && )

default

◆ operator=() [2/2]

Molecule& operator= ( const Molecule & )

default

◆ operator==()

bool operator== ( const Molecule & mol ) const

◆ operator>()

bool operator> ( const Molecule & mol ) const

◆ operator>=()

bool operator>= ( const Molecule & mol ) const

inline

◆ OptimiseChargeGroups()

void OptimiseChargeGroups ( )

◆ PerceiveAngles()

int64_t PerceiveAngles ( )

Determine angles in the molecule.

An angle is defined for each group of three connected atoms within a molecule. Subsequent calls to this method will only generate angles which have not been previously generated. Additionally, angles can only be removed by removing an atom or a bond.

Returns: the number of angles added.

◆ PerceiveDihedrals()

int64_t PerceiveDihedrals ( )

Determine dihedrals in the molecule.

A dihedral is defined for each group of four connected atoms within a molecule. Subsequent calls to this method will only generate dihedrals which have not been previously generated. Additionally, dihedrals can only be removed by removing an atom or bond.

Returns: the number of dihedrals added.

◆ PerceiveResidues()

int32_t PerceiveResidues ( )

◆ RemoveAtom()

bool RemoveAtom ( const Atom & atom )

Remove an atom from the molecule.

In addition to removing the atom, any bonds to the atom are also removed. A removal will not occur if the atom is not owned by the molecule it is being removed from.

Parameters

atom	the atom to remove.

Returns: if a removal occured.

◆ RemoveBond() [1/2]

bool RemoveBond ( const Bond & bond )

Remove a bond from the molecule.

A removal will not occur if the bond is not owned by the molecule it is being removed from. Reference to the bond is removed from both of the atoms of the bond.

Parameters

bond	the bond to remove.

Returns: if a removal occured.

◆ RemoveBond() [2/2]

bool RemoveBond	(	const Atom &	a,
		const Atom &	b
	)

Remove a bond between two atoms.

Parameters

a,b	the atoms to remove a bond between.

Returns: if removal occured.

◆ ReorderAtoms()

void ReorderAtoms ( MoleculeAtoms & new_order )

◆ ReserveAtoms()

void ReserveAtoms ( int64_t num )

Reserve storage space for atoms.

Reserves storage space for a minimum of num IXAtom instances. This is more efficient when building large molecules as the vector will not need to grow as more atoms are added.

Parameters

num	the number of IXAtoms to reserve space for.

◆ ReserveBonds()

void ReserveBonds ( int64_t num )

Reserve storage space for bonds.

Reserves storage space for a minimum of num IXBond instances. This is more efficient when building large molecules as the vector will not need to grow as more bonds are added.

Parameters

num	the number of IXBonds to reserve space for.

◆ ResetForcefield()

void ResetForcefield ( const Forcefield & ff )

◆ SetForcefield()

void SetForcefield ( const Forcefield & ff )

◆ SetMolecularCharge()

void SetMolecularCharge ( int32_t q )

Set the molecular charge of the molecule.

Sets the IXMolecule::ELECTRON_COUNT property as modified.

Parameters

q	the new charge to set.

◆ SetName()

void SetName ( std::string name )

Set the name of the molecule.

Parameters

name	the new to set.

Friends And Related Function Documentation

◆ cereal::access

friend class cereal::access

friend

Friendship allows serialisation.

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		const Molecule &	mol
	)

friend

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

include/indigox/classes/molecule.hpp

Classes

Public Types

Public Member Functions

Friends

Member Typedef Documentation

◆ MoleculeAngles

◆ MoleculeAtoms

◆ MoleculeBonds

◆ MoleculeDihedrals

◆ MoleculeResidues

Constructor & Destructor Documentation

◆ Molecule() [1/4]

◆ Molecule() [2/4]

◆ Molecule() [3/4]

◆ Molecule() [4/4]

◆ ~ Molecule()

Member Function Documentation

◆ GetAngle() [1/2]

◆ GetAngle() [2/2]

◆ GetAngleID()

◆ GetAngles()

◆ GetAngleTag()

◆ GetAtom()

◆ GetAtomID()

◆ GetAtoms()

◆ GetAtomTag()

◆ GetBond() [1/2]

◆ GetBond() [2/2]

◆ GetBondID()

◆ GetBonds()

◆ GetBondTag()

◆ GetCondensedGraph()

◆ GetDihedral() [1/2]

◆ GetDihedral() [2/2]

◆ GetDihedralID()

◆ GetDihedrals()

◆ GetDihedralTag()

◆ GetForcefield()

◆ GetFormula()

◆ GetGraph()

◆ GetMolecularCharge()

◆ GetName()

◆ GetResidueID()

◆ GetResidues()

◆ HasAngle() [1/2]

◆ HasAngle() [2/2]

◆ HasAtom()

◆ HasBond() [1/2]

◆ HasBond() [2/2]

◆ HasDihedral() [1/2]

◆ HasDihedral() [2/2]

◆ HasForcefield()

◆ ModificationMade()

◆ NewAtom() [1/3]

◆ NewAtom() [2/3]

◆ NewAtom() [3/3]

◆ NewBond()

◆ NewDihedral()

◆ NumAngles()

◆ NumAtoms()

◆ NumBonds()

◆ NumDihedrals()

◆ operator bool()

◆ operator!=()

◆ operator<()

◆ operator<=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ operator>()

◆ operator>=()

◆ OptimiseChargeGroups()

◆ PerceiveAngles()

◆ PerceiveDihedrals()

◆ PerceiveResidues()

◆ RemoveAtom()

◆ RemoveBond() [1/2]

◆ RemoveBond() [2/2]

◆ ReorderAtoms()

◆ ReserveAtoms()