AvogadroLibs
1.90.0
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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... | |
enum ScfType |
Enumeration of the SCF type.
enum CrystalSystem |
Enumeration of the crystal system.
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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.
atomicNumber | Atomic number of atom. |
charge | Formal charge of atom. |
numBonds | Number of existing bonds to atom. |
std::vector<std::string> Avogadro::Core::split | ( | const std::string & | string, |
char | delimiter, | ||
bool | skipEmpty = true |
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) |
string | The string to be split up. |
delimiter | The delimiter to split the string by. |
skipEmpty | If true any empty items will be skipped. |
bool Avogadro::Core::contains | ( | const std::string & | input, |
const std::string & | search | ||
) |
input | String to be examined. |
search | String that will be searched for. |
bool Avogadro::Core::startsWith | ( | const std::string & | input, |
const std::string & | search | ||
) |
input | String to be examined. |
search | String that will be searched for. |
T Avogadro::Core::lexicalCast | ( | const std::string & | inputString | ) |
inputString | String to cast to the specified type. |
T Avogadro::Core::lexicalCast | ( | const std::string & | inputString, |
bool & | ok | ||
) |
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. |
const char* element_symbols[] |
const char* element_names[] |
double element_masses[] |