Classes
class	Array
	Base class for array containers. More...

class	ArraySet
	Base class for array type containers. More...

class	Atom

class	AtomTemplate

class	AtomTyper
	The AtomTyper class provides a base interface for generating a list of type identifiers describing the atoms in a molecule. More...

class	AvoSpglib
	The AvoSpglib class provides an interface between Avogadro and Spglib. More...

class	BasisSet
	BasisSet contains basis set data. More...

class	Bond

class	BondTemplate

class	Color3f
	Representation of an RGB color using three floats. More...

class	CoordinateBlockGenerator
	The CoordinateBlockGenerator class creates an aligned, formatted block of atomic coordinates. More...

class	CoordinateSet
	Templated class for array type containers. More...

class	CrystalTools
	The CrystalTools class contains a collection of static functions that perform common crystallographic operations on a Core::Molecule. More...

class	Cube
	Provide a data structure for regularly spaced 3D grids. More...

class	Elements
	The Elements class stores basic data about chemical elements. More...

class	GaussianSet
	A container for Gaussian type outputs from QM codes. More...

class	GaussianSetTools
	Provide tools to calculate molecular orbitals, electron densities and other derived data stored in a GaussianSet result. More...

class	Graph
	The Graph class represents a graph data structure. More...

class	Mesh
	Encapsulation of a triangular mesh that makes up a surface. More...

class	Molecule
	The Molecule class represents a chemical molecule. More...

class	MoleculeDeserializer
	Implementation of ProtoCall::Serialization::Deserializer. More...

class	MoleculeSerializer
	Implementation of ProtoCall::Serialization::Serializer. More...

class	Mutex
	The Mutex class provides a simple wrapper for the C++11 or Boost mutex class. More...

class	NameAtomTyper
	The NameAtomTyper class is a simple implementation of AtomTyper that assigns element names to each atom. More...

class	RingPerceiver

class	SlaterSet
	SlaterSet Class. More...

class	SlaterSetTools
	Provide tools to calculate molecular orbitals, electron densities and other derived data stored in a GaussianSet result. More...

class	SpaceGroups
	The Spacegroups class stores basic data about crystal spacegroups. More...

class	SymbolAtomTyper
	The SymbolAtomTyper class is a simple implementation of AtomTyper that assigns element symbols to each atom. More...

class	UnitCell
	The UnitCell class provides a representation of a crystal's unit cell. More...

class	Variant
	The Variant class represents a union of data values. More...

class	VariantMap
	The VariantMap class provides a map between string keys and variant values. More...

Enumerations
enum	AtomHybridization { PerceivedOctaheadral = -6, PerceivedTrigonalBipyramidal = -5, PerceivedSquarePlanar = -4, PerceivedSP3 = -3, PerceivedSP2 = -2, PerceivedSP = -1, HybridizationUnknown = 0, SP = 1, SP2 = 2, SP3 = 3, SquarePlanar = 4, TrigonalBipyramidal = 5, Octahedral = 6 }

enum	ScfType { Rhf, Uhf, Rohf, Unknown }

enum	CrystalSystem { None, Triclinic, Monoclinic, Orthorhombic, Tetragonal, Trigonal, Rhombohedral, Hexagonal, Cubic }

Functions
template<typename T >
bool	operator== (const Array< T > &lhs, const Array< T > &rhs)

template<typename T >
bool	operator!= (const Array< T > &lhs, const Array< T > &rhs)

template<typename T >
bool	operator< (const Array< T > &lhs, const Array< T > &rhs)

template<typename T >
bool	operator> (const Array< T > &lhs, const Array< T > &rhs)

template<typename T >
bool	operator<= (const Array< T > &lhs, const Array< T > &rhs)

template<typename T >
bool	operator>= (const Array< T > &lhs, const Array< T > &rhs)

template<typename T >
void	swap (Array< T > &lhs, Array< T > &rhs)

bool	isCustomElement (unsigned char atomicNumber)

static unsigned int	atomValence (const unsigned char atomicNumber, const int charge, const unsigned int numBonds)

void	swap (UnitCell &lhs, UnitCell &rhs)

std::vector< std::string >	split (const std::string &string, char delimiter, bool skipEmpty=true)
	Split the supplied `string` by the `delimiter`. More...

bool	contains (const std::string &input, const std::string &search)
	Search the input string for the search string. More...

bool	startsWith (const std::string &input, const std::string &search)
	Efficient method to confirm input starts with the search string. More...

std::string	trimmed (const std::string &input)
	Trim a string of whitespace from the left and right.

template<typename T >
T	lexicalCast (const std::string &inputString)
	Cast the inputString to the specified type. More...

template<typename T >
T	lexicalCast (const std::string &inputString, bool &ok)
	Cast the inputString to the specified type. More...

Variables
unsigned char	element_count = 119

const char *	element_symbols []

const char *	element_names []

double	element_masses []

double	element_VDW []

double	element_covalent []

unsigned char	element_color [][3]

const unsigned short	space_group_international_number []

const char *	space_group_schoenflies []

const char *	space_group_hall_symbol []

const char *	space_group_international []

const char *	space_group_international_full []

const char *	space_group_international_short []

const char *	space_group_setting []

const char *	space_group_transforms []

Detailed Description

Returns: True if atomicNumber denotes a custom element type.

Enumeration Type Documentation

◆ ScfType

enum ScfType

Enumeration of the SCF type.

◆ CrystalSystem

enum CrystalSystem

Enumeration of the crystal system.

Function Documentation

◆ atomValence()

static unsigned int Avogadro::Core::atomValence	(	const unsigned char	atomicNumber,
		const int	charge,
		const unsigned int	numBonds
	)

static

Calculate the full valency (e.g. number of expected bonds) for a given atom. This function is adapted from the MDL valence model to indicate when an atom is overbonded.

Parameters

atomicNumber	Atomic number of atom.
charge	Formal charge of atom.
numBonds	Number of existing bonds to atom.

Returns: The total number of expected bonds to the atom to satisfy valency. May be less than numBonds if atom is overbonded.

◆ split()

std::vector<std::string> Avogadro::Core::split	(	const std::string &	string,
		char	delimiter,
		bool	skipEmpty = `true`
	)

Parameters

string	The string to be split up.
delimiter	The delimiter to split the string by.
skipEmpty	If true any empty items will be skipped.

Returns: A vector containing the items.

◆ contains()

bool Avogadro::Core::contains	(	const std::string &	input,
		const std::string &	search
	)

Parameters

input	String to be examined.
search	String that will be searched for.

Returns: True if the string contains search, false otherwise.

◆ startsWith()

bool Avogadro::Core::startsWith	(	const std::string &	input,
		const std::string &	search
	)

Parameters

input	String to be examined.
search	String that will be searched for.

Returns: True if the string starts with search, false otherwise.

◆ lexicalCast() [1/2]

T Avogadro::Core::lexicalCast ( const std::string & inputString )

Parameters

inputString String to cast to the specified type.

◆ lexicalCast() [2/2]

T Avogadro::Core::lexicalCast	(	const std::string &	inputString,
		bool &	ok
	)

Parameters

inputString	String to cast to the specified type.
ok	Set to true on success, and false if the string could not be converted to the specified type.

Variable Documentation

◆ element_symbols

const char* element_symbols[]

Initial value:

= {
  "Xx", "H", "He", "Li", "Be", "B", "C", "N", "O", "F",
  "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K",
  "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu",
  "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y",
  "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In",
  "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr",
  "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm",
  "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au",
  "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac",
  "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es",
  "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt",
  "Ds", "Rg", "Cn", "Nh", "Fl", "Mc", "Lv", "Ts", "Og" }

◆ element_names

const char* element_names[]

Initial value:

= {
  "Dummy", "Hydrogen", "Helium", "Lithium", "Beryllium",
  "Boron", "Carbon", "Nitrogen", "Oxygen", "Fluorine",
  "Neon", "Sodium", "Magnesium", "Aluminium", "Silicon",
  "Phosphorus", "Sulfur", "Chlorine", "Argon", "Potassium",
  "Calcium", "Scandium", "Titanium", "Vanadium", "Chromium",
  "Manganese", "Iron", "Cobalt", "Nickel", "Copper",
  "Zinc", "Gallium", "Germanium", "Arsenic", "Selenium",
  "Bromine", "Krypton", "Rubidium", "Strontium", "Yttrium",
  "Zirconium", "Niobium", "Molybdenum", "Technetium", "Ruthenium",
  "Rhodium", "Palladium", "Silver", "Cadmium", "Indium",
  "Tin", "Antimony", "Tellurium", "Iodine", "Xenon",
  "Caesium", "Barium", "Lanthanum", "Cerium", "Praseodymium",
  "Neodymium", "Promethium", "Samarium", "Europium", "Gadolinium",
  "Terbium", "Dysprosium", "Holmium", "Erbium", "Thulium",
  "Ytterbium", "Lutetium", "Hafnium", "Tantalum", "Tungsten",
  "Rhenium", "Osmium", "Iridium", "Platinum", "Gold",
  "Mercury", "Thallium", "Lead", "Bismuth", "Polonium",
  "Astatine", "Radon", "Francium", "Radium", "Actinium",
  "Thorium", "Protactinium", "Uranium", "Neptunium", "Plutonium",
  "Americium", "Curium", "Berkelium", "Californium", "Einsteinium",
  "Fermium", "Mendelevium", "Nobelium", "Lawrencium", "Rutherfordium",
  "Dubnium", "Seaborgium", "Bohrium", "Hassium", "Meitnerium",
  "Darmstadtium", "Roentgenium", "Copernicium", "Nihonium", "Flerovium",
  "Moscovium", "Livermorium", "Tennessine", "Oganesson" }

◆ element_masses

double element_masses[]

Initial value:

= {
  
  
  0, 1.00784, 4.0026,
  6.938, 9.01218, 10.806, 12.011, 14.006, 15.9994, 18.9984, 20.1797,
  22.9898, 24.305, 26.9815,
  28.0855, 30.9738, 32.065, 35.453, 39.948, 39.0983, 40.078,
  44.9559, 47.867, 50.9415, 51.9961, 54.938, 55.845, 58.9332,
  58.6934, 63.546, 65.38, 69.723, 72.64, 74.9216, 78.971,
  79.904, 83.798, 85.4678, 87.62, 88.9058, 91.224, 92.9064,
  95.95, 97, 101.07, 102.9055, 106.42, 107.8682, 112.414,
  114.818, 118.71, 121.76, 127.6, 126.9045, 131.293, 132.9055,
  137.327, 138.9055, 140.116, 140.9077, 144.242, 145, 150.36,
  151.964, 157.25, 158.9253, 162.5, 164.9303, 167.259, 168.9342,
  173.045, 174.9668, 178.49, 180.9479, 183.84, 186.207, 190.23,
  192.217, 195.084, 196.9666, 200.592, 204.38, 207.2, 208.9804,
  209, 210, 222, 223, 226, 227, 232.0377,
  231.0358, 238.0289, 237, 244, 243, 247, 247,
  251, 252, 257, 258, 259, 262, 267,
  270, 269, 270, 270, 278, 281, 281,
  285, 286, 289, 289, 293, 293, 294 }

Classes

Enumerations

Functions

Variables

Detailed Description

Enumeration Type Documentation

◆ ScfType

◆ CrystalSystem

Function Documentation

◆ atomValence()

◆ split()

◆ contains()

◆ startsWith()

◆ lexicalCast() [1/2]

◆ lexicalCast() [2/2]

Variable Documentation

◆ element_symbols

◆ element_names

◆ element_masses