Storage class for relevant information of a Molecule. More...

#include <molecule.h>

Public Types
enum	Origin { Cartesian , Centroid , CenterOfMass }
	An enum to specify the origin used in some calculations on the Molecule object. More...

Public Member Functions
	Molecule ()

	Molecule (const IVec &nums, const Mat3N &pos)
	Construct a Molecule from a vector of atomic numbers and positions.

	Molecule (const std::vector< core::Atom > &atoms)
	Construct a Molecule from a vector of Atom objects.

	Molecule (const std::vector< Element > &els, const std::vector< std::array< double, 3 > > &pos)
	Construct a Molecule from a vector of Element objects, and std::array<double, 3> positions.

template<typename N , typename D >
	Molecule (const std::vector< N > &nums, const std::vector< std::array< D, 3 > > &pos)
	Construct a Molecule from a vector of atomic numbers a vector arrays of positions.

size_t	size () const
	The number of atoms in this molecule.

void	set_name (const std::string &name)
	Set the name for this molecule.

const std::string &	name () const
	Get the name for this molecule.

Vec	interatomic_distances () const
	A vector representing the compressed distance matrix for this Molecule.

const auto &	elements () const
	The Element objects for the atoms in this Molecule.

const Mat3N &	positions () const
	The positions of the atoms in this Molecule.

const IVec &	atomic_numbers () const
	The atomic numbers for the atoms in this Molecule.

Vec	vdw_radii () const
	The van der Waals radii for the atoms in this Molecule.

Vec	covalent_radii () const
	The van der Waals radii for the atoms in this Molecule.

Vec	atomic_masses () const
	The atomic masses of the atoms in this Molecule.

double	molar_mass () const
	The total molecular mass.

std::vector< core::Atom >	atoms () const
	Convert the atoms represented by this molecule to a std:vector<Atom>

void	set_cell_shift (const IVec3 &shift, bool update_atoms=true)
	Set the unit cell offset for this Molecule (default 000)

const IVec3 &	cell_shift () const
	Get the unit cell offset for this Molecule (default 000)

Vec3	centroid () const
	The geometric centre of this molecule.

Vec3	center_of_mass () const
	The mass-weighted geometric centre of this molecule.

Mat3	inertia_tensor () const
	The tensor of inertia (in matrix form).

Vec3	principal_moments_of_inertia () const
	The principal moments of inertia, derived from the intertia tensor.

Vec3	rotational_constants () const
	The rotational constants of this Molecule in GHz.

double	rotational_free_energy (double T) const
	The rotational component of the entropic free energy of this Molecule (rigid molecule, ideal gas approximation), units are kJ/mol.

double	translational_free_energy (double T) const
	The translational component of the entropic free energy of this Molecule (rigid molecule, ideal gas approximation), units are kJ/mol.

std::tuple< size_t, size_t, double >	nearest_atom (const Molecule &rhs) const
	The nearest atom-atom pair between atoms in this Molecule and atoms in another.

void	add_bond (size_t l, size_t r)
	Manually add a bond connection between two atoms in this Molecule.

void	set_bonds (const std::vector< std::pair< size_t, size_t > > &bonds)
	Set the known bond connections in this Molecule.

const std::vector< std::pair< size_t, size_t > > &	bonds () const
	Get the list of bonds in this Molecule.

int	charge () const
	The net charge of this Molecule.

void	set_charge (int c)
	Set the net charge of this Molecule.

int	multiplicity () const
	Get the spin multiplicity of this molecule.

void	set_multiplicity (int m)
	Set the spin multiplicity of this molecule.

int	num_electrons () const
	The number of electrons in this molecule.

int	asymmetric_molecule_idx () const
	Get the index into Crystal::symmetry_unique_molecules for this Molecule.

void	set_asymmetric_molecule_idx (size_t idx)
	Set the index into Crystal::symmetry_unique_molecules for this Molecule.

int	unit_cell_molecule_idx () const
	Get the index into Crystal::unit_cell_molecules for this Molecule.

void	set_unit_cell_molecule_idx (size_t idx)
	Set the index into Crystal::unit_cell_molecules for this Molecule.

void	set_asymmetric_unit_transformation (const Mat3 &rot, const Vec3 &trans)
	Set the transformation from the corresponding molecule in the asymmetric unit of a Crystal to this geometry.

std::pair< Mat3, Vec3 >	asymmetric_unit_transformation () const
	Get the transformation from the corresponding molecule in the asymmetric unit of a Crystal to this geometry.

void	set_unit_cell_idx (const IVec &idx)
	Set the unit cell atom indices for all atoms in this Molecule.

void	set_unit_cell_shift (const IMat3N &shifts)
	Set the unit cell atom shifts for all atoms in this Molecule.

void	set_asymmetric_unit_idx (const IVec &idx)
	Set the asymmetric unit atom indices for all atoms in this Molecule.

void	set_asymmetric_unit_symop (const IVec &symop)
	Set the associated SymmetryOperation for all all atoms in from their asymmetric unit counterpart (encoded as an int).

const auto &	unit_cell_idx () const
	Get the unit cell atom indices for all atoms in this Molecule.

const auto &	unit_cell_shift () const
	Get the unit cell atom shifts for all atoms in this Molecule.

const auto &	asymmetric_unit_idx () const
	Get the asymmetric unit atom indices for all atoms in this Molecule.

const auto &	asymmetric_unit_symop () const
	Get the set of SymmetryOperation for all atoms in this Molecule (i.e.

void	rotate (const Eigen::Affine3d &r, Origin o=Cartesian)
	Rotate this Molecule by the given rotation, about the specified origin.

void	rotate (const Mat3 &r, Origin o=Cartesian)
	Rotate this Molecule by the given rotation, about the specified origin.

void	rotate (const Mat3 &r, const Vec3 &o)
	Rotate this Molecule by the given rotation, about the specified origin.

void	transform (const Mat4 &t, Origin o=Cartesian)
	Transform this Molecule by the given homogeneous transformation matrix, with rotation performed about the specified origin.

void	transform (const Mat4 &t, const Vec3 &o)
	Transform this Molecule by the given homogeneous transformation matrix, with rotation performed about the specified origin.

void	translate (const Vec3 &t)
	Translate this Molecule by the given vector.

Molecule	rotated (const Eigen::Affine3d &r, Origin o=Cartesian) const
	A copy of this Molecule transformed by the given rotation, about the specified origin.

Molecule	rotated (const Mat3 &r, Origin o=Cartesian) const
	A copy of this Molecule transformed by the given rotation, about the specified origin.

Molecule	rotated (const Mat3 &r, const Vec3 &o) const
	A copy of this Molecule transformed by the given rotation, about the specified origin.

Molecule	transformed (const Mat4 &t, Origin o=Cartesian) const
	A copy of this Molecule transformed by the given homogeneous transformation matrix, with rotation performed about the specified origin.

Molecule	transformed (const Mat4 &t, const Vec3 &o) const
	A copy of this Molecule transformed by the given homogeneous transformation matrix, with rotation performed about the specified origin.

Molecule	translated (const Vec3 &t) const
	A copy of this Molecule translated by the given vector.

bool	is_comparable_to (const Molecule &rhs) const
	Determine whether this Molecule and another can be sensibly compared.

bool	is_equivalent_to (const Molecule &rhs) const
	Determine whether this Molecule and another are equivalent.

void	set_partial_charges (const Vec &v)

const auto &	partial_charges ()

Vec	esp_partial_charges (const occ::Mat3N &positions) const

Detailed Description

Storage class for relevant information of a Molecule.

The role of the Molecule class is to store basic information about atoms which are bonded, and to facilitate convenient calculations of properties of these atoms.

Member Enumeration Documentation

◆ Origin

enum occ::core::Molecule::Origin

An enum to specify the origin used in some calculations on the Molecule object.

Enumerator

Cartesian

The Cartesian origin i.e.

(0, 0, 0) in R3

Centroid

The molecular centroid i.e.

average position of atoms (ignoring mass)

CenterOfMass

The centre of mass i.e.

the weighted average positon

Constructor & Destructor Documentation

◆ Molecule() [1/5]

occ::core::Molecule::Molecule ( )

inlineexplicit

◆ Molecule() [2/5]

occ::core::Molecule::Molecule	(	const IVec &	nums,
		const Mat3N &	pos
	)

Construct a Molecule from a vector of atomic numbers and positions.

Parameters

nums	Vector of length N atomic numbers
pos	Matrix (3, N) of atomic positions (Angstroms)

◆ Molecule() [3/5]

occ::core::Molecule::Molecule ( const std::vector< core::Atom > & atoms )

Construct a Molecule from a vector of Atom objects.

Parameters

atoms std::vector<Atom> of length N atoms.

Will convert from the expected Bohr unit of the Atom objects internally to Angstroms.

◆ Molecule() [4/5]

occ::core::Molecule::Molecule	(	const std::vector< Element > &	els,
		const std::vector< std::array< double, 3 > > &	pos
	)

Construct a Molecule from a vector of Element objects, and std::array<double, 3> positions.

Parameters

els	std::vector<Element> of length N Element objects.
pos	std::vector<std::array<double, 3> > of length N of atomic positions.

Positions are assumed to be in Angstroms.

◆ Molecule() [5/5]

template<typename N , typename D >

occ::core::Molecule::Molecule	(	const std::vector< N > &	nums,
		const std::vector< std::array< D, 3 > > &	pos
	)

inline

Construct a Molecule from a vector of atomic numbers a vector arrays of positions.

Parameters

nums	std::vector<N> of atomic numbers, convertible to int
pos	std::vector<std::array<D, 3> > of atomic positions, convertible to double.

Positions are assumed to be in Angstroms.

Member Function Documentation

◆ add_bond()

void occ::core::Molecule::add_bond	(	size_t	l,
		size_t	r
	)

inline

Manually add a bond connection between two atoms in this Molecule.

Parameters

l	the first index of an atom into this Molecule.
r	the second index of an atom into this Molecule.

Internally, the set of bonds in this Molecule will be updated.

◆ asymmetric_molecule_idx()

int occ::core::Molecule::asymmetric_molecule_idx ( ) const

inline

Get the index into Crystal::symmetry_unique_molecules for this Molecule.

Returns: an integer representing the index (default is -1)

Warning: This will return an invalid index (-1) by default, and should be checked or ensured to have a value before use.

◆ asymmetric_unit_idx()

const auto & occ::core::Molecule::asymmetric_unit_idx ( ) const

inline

Get the asymmetric unit atom indices for all atoms in this Molecule.

Returns: a const ref to the internal IVec containing the relevant indices into the set of asymmetric unit atoms for the Crystal associated with this Molecule.

See also Molecule::asymmetric_molecule_idx if you wish to get the mapping for the molecule index rather than atom indices.

◆ asymmetric_unit_symop()

const auto & occ::core::Molecule::asymmetric_unit_symop ( ) const

inline

Get the set of SymmetryOperation for all atoms in this Molecule (i.e.

mapping from their corresponding asymmetric unit atom to their position here).

Returns: a const ref to the internal IVec containing the relevant integer encoded SymmeteryOperations for the mapping from asymmetric unit atoms for the Crystal associated with this Molecule.

See also Molecule::asymmetric_unit_transformation if you wish to get the mapping for the molecule index rather than atom indices.

◆ asymmetric_unit_transformation()

std::pair< Mat3, Vec3 > occ::core::Molecule::asymmetric_unit_transformation ( ) const

inline

Get the transformation from the corresponding molecule in the asymmetric unit of a Crystal to this geometry.

Returns: a std::pair<Mat3, Vec3> representing the rotation part of the transform. and the translation part of the transform.

By default the rotation is the identity matrix, and the translation is the zero vector.

◆ atomic_masses()

Vec occ::core::Molecule::atomic_masses ( ) const

The atomic masses of the atoms in this Molecule.

Returns: a newly constructed Vec containing the masses.

Creates a vector, they are not stored internally to the Molecule object.

◆ atomic_numbers()

const IVec & occ::core::Molecule::atomic_numbers ( ) const

inline

The atomic numbers for the atoms in this Molecule.

Returns: a const ref to the internal vector of atomic numbers.

◆ atoms()

std::vector< core::Atom > occ::core::Molecule::atoms ( ) const

Convert the atoms represented by this molecule to a std:vector<Atom>

Returns: a vector of Atom objects (positions in Bohr).

◆ bonds()

const std::vector< std::pair< size_t, size_t > > & occ::core::Molecule::bonds ( ) const

inline

Get the list of bonds in this Molecule.

Returns: a std::vector<std::pair<size_t, size_t>> i.e. list of the bond edges that have been set in this Molecule.

◆ cell_shift()

const IVec3 & occ::core::Molecule::cell_shift ( ) const

Get the unit cell offset for this Molecule (default 000)

Returns: the CellShift stored in this Molecule

See Molecule::set_cell_shift

◆ center_of_mass()

Vec3 occ::core::Molecule::center_of_mass ( ) const

The mass-weighted geometric centre of this molecule.

Returns: a Vec3 representing the average atomic position (including masses)

See Molecule::centroid if you don't need to incorporate masses

◆ centroid()

Vec3 occ::core::Molecule::centroid ( ) const

The geometric centre of this molecule.

Returns: a Vec3 representing the average atomic position (ignoring masses)

See Molecule::center_of_mass if you need to incorporate masses

◆ charge()

int occ::core::Molecule::charge ( ) const

inline

The net charge of this Molecule.

Returns: an integer representing the net charge. Default is neutral (0)

◆ covalent_radii()

Vec occ::core::Molecule::covalent_radii ( ) const

The van der Waals radii for the atoms in this Molecule.

Returns: a newly constructed Vec containing van der Waals radii

Creates a vector, they are not stored internally to the Molecule object.

◆ elements()

const auto & occ::core::Molecule::elements ( ) const

inline

The Element objects for the atoms in this Molecule.

Returns: a const std::vector<Element>& to the internal vector of elements

◆ esp_partial_charges()

Vec occ::core::Molecule::esp_partial_charges ( const occ::Mat3N & positions ) const

◆ inertia_tensor()

Mat3 occ::core::Molecule::inertia_tensor ( ) const

The tensor of inertia (in matrix form).

Returns: a Mat3 representing the distribution of mass about the Molecule::center_of_mass of this Molecule.

◆ interatomic_distances()

Vec occ::core::Molecule::interatomic_distances ( ) const

A vector representing the compressed distance matrix for this Molecule.

Returns: distances a Vec object representing the distances

Since the NxN distance matrix for all atoms in this molecule is by definition symmetric, and the diagonals would be 0, this will return a N * (N - 1) / 2 length vector where the distance for atom i to atom j can be calculated in the following loop:

for (size_t i = 0; i < N; i++) {
    for (size_t j = i + 1; j < N; j++) {
     // distance
    }
}

◆ is_comparable_to()

bool occ::core::Molecule::is_comparable_to ( const Molecule & rhs ) const

Determine whether this Molecule and another can be sensibly compared.

Returns: true if they are comparable Molecules per the definition, false otherwise.

The working definition here of whether two molecules are comparable is whether they have the exact same IVec of atomic numbers, in the same order (i.e. the same chemical composition, and the order of atoms is not permuted.

◆ is_equivalent_to()

bool occ::core::Molecule::is_equivalent_to ( const Molecule & rhs ) const

Determine whether this Molecule and another are equivalent.

Parameters

rhs	The other Molecule object to check equivalence

Returns: true if they are comparable Molecules per the definition, false otherwise.

The working definition here of whether two molecules are equivalent if a) they are comparable (i.e. all atomic numbers are the same) and b) all interatomic distances are the same.

◆ molar_mass()

double occ::core::Molecule::molar_mass ( ) const

The total molecular mass.

Returns: a double representing the sum of atomic masses in this molecule

◆ multiplicity()

int occ::core::Molecule::multiplicity ( ) const

inline

Get the spin multiplicity of this molecule.

Returns: an integer representing the spin multiplicity of this molecule (default 1)

◆ name()

const std::string & occ::core::Molecule::name ( ) const

inline

Get the name for this molecule.

Returns: name std::string representing the name/identifier for this Molecule.

See Molecule::set_name

◆ nearest_atom()

std::tuple< size_t, size_t, double > occ::core::Molecule::nearest_atom ( const Molecule & rhs ) const

The nearest atom-atom pair between atoms in this Molecule and atoms in another.

Parameters

rhs	The other Molecule object to find distances.

Returns: a std::tuple<size_t, size_t, double> consisting of the index into atoms in this Molecule, the index into the atoms of the Molecule rhs, and the distance in Angstroms.

See Molecule::nearest_atom_distance if you only need the distance

◆ num_electrons()

int occ::core::Molecule::num_electrons ( ) const

inline

The number of electrons in this molecule.

Returns: an integer representing total number of electrons.

Molecule::charge is incorporated, so the result should be the sum of atomic numbers - net charge (as electrons have -ve charge).

◆ partial_charges()

const auto & occ::core::Molecule::partial_charges ( )

inline

◆ positions()

const Mat3N & occ::core::Molecule::positions ( ) const

inline

The positions of the atoms in this Molecule.

Returns: a const ref to the internal matrix of positions (Angstroms).

◆ principal_moments_of_inertia()

Vec3 occ::core::Molecule::principal_moments_of_inertia ( ) const

The principal moments of inertia, derived from the intertia tensor.

Returns: a Vec3 representing the three moments of inertia. Eigenvalues calculated using Eigen::SelfAdjointEigenSolver.

◆ rotate() [1/3]

void occ::core::Molecule::rotate	(	const Eigen::Affine3d &	r,
		Origin	o = `Cartesian`
	)

Rotate this Molecule by the given rotation, about the specified origin.

Parameters

r	The rotation.
o	The desired Origin about which to rotate.

All rotations will be in the Cartesian axis frame (though not necessarily about the Cartesian origin)

See Molecule::rotated if you wish to return a copy of this Molecule.

◆ rotate() [2/3]

void occ::core::Molecule::rotate	(	const Mat3 &	r,
		const Vec3 &	o
	)

Rotate this Molecule by the given rotation, about the specified origin.

Overload for any Mat3.

Parameters

r	The rotation.
o	The desired position about which to rotate (Angstroms).

All rotations will be in the Cartesian axis frame (though not necessarily about the Cartesian origin).

Warning: The provided Mat3 is not checked to be a valid rotation matrix.

See Molecule::rotated if you wish to return a copy of this Molecule.

◆ rotate() [3/3]

void occ::core::Molecule::rotate	(	const Mat3 &	r,
		Origin	o = `Cartesian`
	)

Rotate this Molecule by the given rotation, about the specified origin.

Overload for any Mat3.

Parameters

r	The rotation.
o	The desired Origin about which to rotate.

All rotations will be in the Cartesian axis frame (though not necessarily about the Cartesian origin).

Warning: The provided Mat3 is not checked to be a valid rotation matrix.

See Molecule::rotated if you wish to return a copy of this Molecule.

◆ rotated() [1/3]

Molecule occ::core::Molecule::rotated	(	const Eigen::Affine3d &	r,
		Origin	o = `Cartesian`
	)		const

A copy of this Molecule transformed by the given rotation, about the specified origin.

Parameters

r	The rotation.
o	The desired Origin about which to rotate.

Returns: a rotated copy of this Molecule.

All rotations will be in the Cartesian axis frame (though not necessarily about the Cartesian origin)

See Molecule::rotate if you wish to modify this Molecule.

◆ rotated() [2/3]

Molecule occ::core::Molecule::rotated	(	const Mat3 &	r,
		const Vec3 &	o
	)		const

A copy of this Molecule transformed by the given rotation, about the specified origin.

Parameters

r	The rotation.
o	The desired position about which to rotate (Angstroms).

Returns: a rotated copy of this Molecule.

All rotations will be in the Cartesian axis frame (though not necessarily about the Cartesian origin)

Warning: The provided Mat3 is not checked to be a valid rotation matrix.

See Molecule::rotate if you wish to modify this Molecule.

◆ rotated() [3/3]

Molecule occ::core::Molecule::rotated	(	const Mat3 &	r,
		Origin	o = `Cartesian`
	)		const

A copy of this Molecule transformed by the given rotation, about the specified origin.

Parameters

r	The rotation.
o	The desired Origin about which to rotate.

Returns: a rotated copy of this Molecule.

All rotations will be in the Cartesian axis frame (though not necessarily about the Cartesian origin)

Warning: The provided Mat3 is not checked to be a valid rotation matrix.

See Molecule::rotate if you wish to modify this Molecule.

◆ rotational_constants()

Vec3 occ::core::Molecule::rotational_constants ( ) const

The rotational constants of this Molecule in GHz.

Returns: a Vec3 representing the three rotational constants. Calculated directly from Molecule::principal_moments_of_inertia.

◆ rotational_free_energy()

double occ::core::Molecule::rotational_free_energy ( double T ) const

The rotational component of the entropic free energy of this Molecule (rigid molecule, ideal gas approximation), units are kJ/mol.

Parameters

T	the temperature (K).

Returns: a double representing the rotational free energy for this Molecule at the given temperature in kJ/mol

◆ set_asymmetric_molecule_idx()

void occ::core::Molecule::set_asymmetric_molecule_idx ( size_t idx )

inline

Set the index into Crystal::symmetry_unique_molecules for this Molecule.

Parameters

idx	an integer representing the index.

Warning: No check is performed to ensure this is a sensible value.

◆ set_asymmetric_unit_idx()

void occ::core::Molecule::set_asymmetric_unit_idx ( const IVec & idx )

inline

Set the asymmetric unit atom indices for all atoms in this Molecule.

Parameters

idx	an IVec containing the relevant indices into the set of asymmetric unit atoms for the Crystal associated with this Molecule.

See also Molecule::set_asymmetric_molecule_idx if you wish to set the molecule index rather than atom indices.

◆ set_asymmetric_unit_symop()

void occ::core::Molecule::set_asymmetric_unit_symop ( const IVec & symop )

Set the associated SymmetryOperation for all all atoms in from their asymmetric unit counterpart (encoded as an int).

Parameters

symop an IVec containing the integer encoded SymmetryOperation from the corresponding asymmetric unit atoms in the Crystal for all atoms in.

See also Molecule::set_asymmetric_unit_transformation if you wish to set the transformation from the molecule. And note that these are not the same thing.

◆ set_asymmetric_unit_transformation()

void occ::core::Molecule::set_asymmetric_unit_transformation	(	const Mat3 &	rot,
		const Vec3 &	trans
	)

inline

Set the transformation from the corresponding molecule in the asymmetric unit of a Crystal to this geometry.

Parameters

rot	A Mat3 representing the rotation part of the transform.
trans	A Vec3 representing the translation part of the transform.

By default the rotation is the identity matrix, and the translation is the zero vector. Molecule::set_asymmetric_molecule_index should also be set for this to make sense. It is the responsibility of the caller to ensure these values correspond.

◆ set_bonds()

void occ::core::Molecule::set_bonds ( const std::vector< std::pair< size_t, size_t > > & bonds )

inline

Set the known bond connections in this Molecule.

Parameters

bonds a std::vector<std::pair<size_t, size_t>> i.e. list of the bond edges to set in this Molecule.

Warning: Existing bonds will be removed, this method will overwrite bonds already stored.

◆ set_cell_shift()

void occ::core::Molecule::set_cell_shift	(	const IVec3 &	shift,
		bool	update_atoms = `true`
	)

Set the unit cell offset for this Molecule (default 000)

Parameters

shift the desired CellShift

See Molecule::cell_shift

◆ set_charge()

void occ::core::Molecule::set_charge ( int c )

inline

Set the net charge of this Molecule.

Parameters

c	an integer representing the net charge.

No checks are performed to ensure this charge is sensible.

◆ set_multiplicity()

void occ::core::Molecule::set_multiplicity ( int m )

inline

Set the spin multiplicity of this molecule.

Parameters

m	an integer representing the spin multiplicity of this molecule.

No checks are performed to ensure this is a sensible value.

◆ set_name()

void occ::core::Molecule::set_name ( const std::string & name )

inline

Set the name for this molecule.

Parameters

name	std::string representing the name/identifier for this Molecule.

See Molecule::name

◆ set_partial_charges()

void occ::core::Molecule::set_partial_charges ( const Vec & v )

inline

◆ set_unit_cell_idx()

void occ::core::Molecule::set_unit_cell_idx ( const IVec & idx )

inline

Set the unit cell atom indices for all atoms in this Molecule.

Parameters

idx	an IVec containing the relevant indices into the set of unit cell atoms for the Crystal associated with this Molecule.

See also Molecule::set_unit_cell_molecule_idx if you wish to set the molecule index rather than atom indices.

◆ set_unit_cell_molecule_idx()

void occ::core::Molecule::set_unit_cell_molecule_idx ( size_t idx )

inline

Set the index into Crystal::unit_cell_molecules for this Molecule.

Parameters

idx	an integer representing the index.

Warning: No check is performed to ensure this is a sensible value.

◆ set_unit_cell_shift()

void occ::core::Molecule::set_unit_cell_shift ( const IMat3N & shifts )

inline

Set the unit cell atom shifts for all atoms in this Molecule.

Parameters

shifts an IMat3N containing the relevant shifts to generate the atoms of this molecule from the unit cell atoms of the Crystal associated with this Molecule.

See also Molecule::set_cell_shift if you wish to set the unit cell molecule shift rather than atom indices.

◆ size()

size_t occ::core::Molecule::size ( ) const

inline

The number of atoms in this molecule.

Returns: size size_t representing the number of atoms in this Molecule.

Calculated based on the internal IVec of atomic numbers.

◆ transform() [1/2]

void occ::core::Molecule::transform	(	const Mat4 &	t,
		const Vec3 &	o
	)

Transform this Molecule by the given homogeneous transformation matrix, with rotation performed about the specified origin.

Parameters

t	The homogeneous transformation matrix.
o	The desired position about which to rotate (Angstroms).

All rotations will be in the Cartesian axis frame (though not necessarily about the Cartesian origin)

See Molecule::transformed if you wish to return a copy of this Molecule.

◆ transform() [2/2]

void occ::core::Molecule::transform	(	const Mat4 &	t,
		Origin	o = `Cartesian`
	)

Transform this Molecule by the given homogeneous transformation matrix, with rotation performed about the specified origin.

Parameters

t	The homogeneous transformation matrix.
o	The desired Origin about which to rotate.

All rotations will be in the Cartesian axis frame (though not necessarily about the Cartesian origin)

See Molecule::transformed if you wish to return a copy of this Molecule.

◆ transformed() [1/2]

Molecule occ::core::Molecule::transformed	(	const Mat4 &	t,
		const Vec3 &	o
	)		const

A copy of this Molecule transformed by the given homogeneous transformation matrix, with rotation performed about the specified origin.

Parameters

t	The homogeneous transformation matrix.
o	The desired position about which to rotate (Angstroms).

Returns: transformed copy of this Molecule.

All rotations will be in the Cartesian axis frame (though not necessarily about the Cartesian origin)

See Molecule::transforme if you wish to modify this Molecule.

◆ transformed() [2/2]

Molecule occ::core::Molecule::transformed	(	const Mat4 &	t,
		Origin	o = `Cartesian`
	)		const

A copy of this Molecule transformed by the given homogeneous transformation matrix, with rotation performed about the specified origin.

Parameters

t	The homogeneous transformation matrix.
o	The desired origin about which to rotate.

Returns: transformed copy of this Molecule.

All rotations will be in the Cartesian axis frame (though not necessarily about the Cartesian origin)

See Molecule::transform if you wish to modify this Molecule.

◆ translate()

void occ::core::Molecule::translate ( const Vec3 & t )

Translate this Molecule by the given vector.

Parameters

t	translation vector (Angstroms).

See Molecule::translated if you wish to return a copy of this Molecule.

◆ translated()

Molecule occ::core::Molecule::translated ( const Vec3 & t ) const

A copy of this Molecule translated by the given vector.

Parameters

t	translation vector (Angstroms).

Returns: a translated copy of this Molecule.

See Molecule::translate if you wish to modify this Molecule.

◆ translational_free_energy()

double occ::core::Molecule::translational_free_energy ( double T ) const

The translational component of the entropic free energy of this Molecule (rigid molecule, ideal gas approximation), units are kJ/mol.

Parameters

T	the temperature (K).

Returns: a double representing the translational component of the free energy for this Molecule at the given temperature in kJ/mol

◆ unit_cell_idx()

const auto & occ::core::Molecule::unit_cell_idx ( ) const

inline

Get the unit cell atom indices for all atoms in this Molecule.

Returns: a const ref to the internal IVec containing the relevant indices into the set of unit cell atoms for the Crystal associated with this Molecule.

See also Molecule::unit_cell_molecule_idx if you wish to get the mapping for the molecule index rather than atom indices.

◆ unit_cell_molecule_idx()

int occ::core::Molecule::unit_cell_molecule_idx ( ) const

inline

Get the index into Crystal::unit_cell_molecules for this Molecule.

Returns: an integer representing the index (default is -1)

Warning: This will return an invalid index (-1) by default, and should be checked or ensured to have a value before use.

◆ unit_cell_shift()

const auto & occ::core::Molecule::unit_cell_shift ( ) const

inline

Get the unit cell atom shifts for all atoms in this Molecule.

Returns: an IMat3N containing the relevant shifts to generate the atoms of this molecule from the unit cell atoms of the Crystal associated with this Molecule.

See also Molecule::cell_shift if you wish to get the unit cell molecule shift rather than atom indices.

◆ vdw_radii()

Vec occ::core::Molecule::vdw_radii ( ) const

The van der Waals radii for the atoms in this Molecule.

Returns: a newly constructed Vec containing van der Waals radii

Creates a vector, they are not stored internally to the Molecule object.

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

/home/runner/work/occ/occ/include/occ/core/molecule.h

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ Origin

Constructor & Destructor Documentation

◆ Molecule() [1/5]

◆ Molecule() [2/5]

◆ Molecule() [3/5]

◆ Molecule() [4/5]

◆ Molecule() [5/5]

Member Function Documentation

◆ add_bond()

◆ asymmetric_molecule_idx()

◆ asymmetric_unit_idx()

◆ asymmetric_unit_symop()

◆ asymmetric_unit_transformation()

◆ atomic_masses()

◆ atomic_numbers()

◆ atoms()

◆ bonds()

◆ cell_shift()

◆ center_of_mass()

◆ centroid()

◆ charge()

◆ covalent_radii()

◆ elements()

◆ esp_partial_charges()

◆ inertia_tensor()

◆ interatomic_distances()

◆ is_comparable_to()

◆ is_equivalent_to()

◆ molar_mass()

◆ multiplicity()

◆ name()

◆ nearest_atom()

◆ num_electrons()

◆ partial_charges()

◆ positions()

◆ principal_moments_of_inertia()

◆ rotate() [1/3]

◆ rotate() [2/3]

◆ rotate() [3/3]

◆ rotated() [1/3]

◆ rotated() [2/3]

◆ rotated() [3/3]

◆ rotational_constants()

◆ rotational_free_energy()

◆ set_asymmetric_molecule_idx()

◆ set_asymmetric_unit_idx()

◆ set_asymmetric_unit_symop()

◆ set_asymmetric_unit_transformation()

◆ set_bonds()

◆ set_cell_shift()

◆ set_charge()

◆ set_multiplicity()

◆ set_name()

◆ set_partial_charges()

◆ set_unit_cell_idx()

◆ set_unit_cell_molecule_idx()

◆ set_unit_cell_shift()

◆ size()

◆ transform() [1/2]

◆ transform() [2/2]

◆ transformed() [1/2]

◆ transformed() [2/2]

◆ translate()

◆ translated()

◆ translational_free_energy()

◆ unit_cell_idx()

◆ unit_cell_molecule_idx()

◆ unit_cell_shift()

◆ vdw_radii()