occ::core::MolecularAxisCalculator Class Reference

Molecular axis calculator class. More...

#include <molecular_axis.h>

Public Member Functions
	MolecularAxisCalculator (const occ::qm::Wavefunction &wfn)
	Construct a molecular axis calculator.
MolecularAxisResult	calculate_neighcrys_axes (const std::vector< int > &axis_atoms) const
	Calculate molecular axes using neighcrys method.
MolecularAxisResult	calculate_pca_axes () const
	Calculate molecular axes using PCA method.
MolecularAxisResult	calculate_moi_axes () const
	Calculate molecular axes using moment of inertia method.
MolecularAxisResult	calculate_axes (AxisMethod method, const std::vector< int > &axis_atoms={}) const
	Calculate molecular axes using specified method.
Vec3	center_of_mass () const
	Get center of mass of the molecule.
std::vector< std::string >	generate_neighcrys_labels () const
	Generate neighcrys-compatible atom labels.
int	calculate_bond_separation (int atom_i, int atom_j) const
	Calculate bond path separation between two atoms.
NeighcrysAxisInfo	generate_neighcrys_info (const std::vector< int > &axis_atoms) const
	Generate neighcrys axis information.

Static Public Member Functions
static void	apply_molecular_transformation (occ::qm::Wavefunction &wfn, const MolecularAxisResult &result)
	Apply molecular transformation to wavefunction.
static void	write_neighcrys_axis_file (const std::string &filename, const NeighcrysAxisInfo &axis_info)
	Write neighcrys-compatible axis file.
static void	write_oriented_xyz (const std::string &filename, const occ::qm::Wavefunction &wfn, const std::string &title="Oriented molecule from OCC")
	Write oriented molecule in XYZ format.
static std::string	axis_method_to_string (AxisMethod method)
	Convert AxisMethod enum to string.
static AxisMethod	string_to_axis_method (const std::string &method_str)
	Convert string to AxisMethod enum.

Detailed Description

Molecular axis calculator class.

Constructor & Destructor Documentation

MolecularAxisCalculator()

occ::core::MolecularAxisCalculator::MolecularAxisCalculator ( const occ::qm::Wavefunction &  wfn )

explicit

Construct a molecular axis calculator.

Parameters

wfn	The wavefunction to analyze

Member Function Documentation

apply_molecular_transformation()

static void occ::core::MolecularAxisCalculator::apply_molecular_transformation ( occ::qm::Wavefunction &  wfn, const MolecularAxisResult &  result  )

static

Apply molecular transformation to wavefunction.

Parameters

wfn	Wavefunction to transform (modified in place)
result	Axis calculation result containing transformation

axis_method_to_string()

static std::string occ::core::MolecularAxisCalculator::axis_method_to_string ( AxisMethod  method )

static

Convert AxisMethod enum to string.

Parameters

method

The axis method

Returns

String representation

calculate_axes()

MolecularAxisResult occ::core::MolecularAxisCalculator::calculate_axes	(	AxisMethod	method,
		const std::vector< int > &	axis_atoms = {}
	)		const

Calculate molecular axes using specified method.

Parameters

method	The axis calculation method to use
axis_atoms	Atom indices for neighcrys method (ignored for other methods)

Returns

MolecularAxisResult containing axes and metadata

calculate_bond_separation()

int occ::core::MolecularAxisCalculator::calculate_bond_separation	(	int	atom_i,
		int	atom_j
	)		const

Calculate bond path separation between two atoms.

Parameters

atom_i	First atom index
atom_j	Second atom index

Returns

Estimated bond path separation

calculate_moi_axes()

MolecularAxisResult occ::core::MolecularAxisCalculator::calculate_moi_axes

(

)

const

Calculate molecular axes using moment of inertia method.

Returns

MolecularAxisResult containing axes and metadata

calculate_neighcrys_axes()

MolecularAxisResult occ::core::MolecularAxisCalculator::calculate_neighcrys_axes

(

const std::vector< int > &

axis_atoms

)

const

Calculate molecular axes using neighcrys method.

Parameters

axis_atoms

Vector of 3 atom indices (0-based) defining the axis system

Returns

MolecularAxisResult containing axes and metadata

calculate_pca_axes()

MolecularAxisResult occ::core::MolecularAxisCalculator::calculate_pca_axes

(

)

const

Calculate molecular axes using PCA method.

Returns

MolecularAxisResult containing axes and metadata

center_of_mass()

Vec3 occ::core::MolecularAxisCalculator::center_of_mass

(

)

const

Get center of mass of the molecule.

Returns

Center of mass position vector

generate_neighcrys_info()

NeighcrysAxisInfo occ::core::MolecularAxisCalculator::generate_neighcrys_info

(

const std::vector< int > &

axis_atoms

)

const

Generate neighcrys axis information.

Parameters

axis_atoms

Atoms defining the axis system

Returns

NeighcrysAxisInfo structure

generate_neighcrys_labels()

std::vector< std::string > occ::core::MolecularAxisCalculator::generate_neighcrys_labels

(

)

const

Generate neighcrys-compatible atom labels.

Returns

Vector of neighcrys-style atom labels

string_to_axis_method()

static AxisMethod occ::core::MolecularAxisCalculator::string_to_axis_method ( const std::string &  method_str )

static

Convert string to AxisMethod enum.

Parameters

method_str

String representation

Returns

AxisMethod enum value

write_neighcrys_axis_file()

static void occ::core::MolecularAxisCalculator::write_neighcrys_axis_file ( const std::string &  filename, const NeighcrysAxisInfo &  axis_info  )

static

Write neighcrys-compatible axis file.

Parameters

filename	Output filename
axis_info	Neighcrys axis information

write_oriented_xyz()

static void occ::core::MolecularAxisCalculator::write_oriented_xyz ( const std::string &  filename, const occ::qm::Wavefunction &  wfn, const std::string &  title = "Oriented molecule from OCC"  )

static

Write oriented molecule in XYZ format.

Parameters

filename	Output filename
wfn	Wavefunction (should be oriented)
title	Optional title for XYZ file

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

• /home/runner/work/occ/occ/include/occ/core/molecular_axis.h