File database.hpp

This file contains the interface for the application wide database, which, among other things, defines physical constants and atom name mapping.

Author

Benjamin Lindner ben@benlabs.net

Version

See VERSION in CMakeLists.txt

Copyright

GNU General Public License

class DatabaseExlusionParameters

#include <database.hpp>

Implements a mapping between integer based atom IDs and exclusion factors. Exclusion factors are a means to scale atomic volumes.

Public Functions

inline DatabaseExlusionParameters()

void reg(size_t ID, std::vector<double> constants, size_t function_type)

double get(size_t ID, double effvolume, double q)

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

void add_quicklookup(size_t ID, double value)

void clear_quicklookup()

Private Members

std::map<size_t, size_t> m_functiontypes

std::map<size_t, std::vector<double>> m_constants

std::map<size_t, double> m_quicklookup

size_t quicklookup_counter

Friends

friend class Database

friend class boost::serialization::access

class DatabaseVolumesParameters

#include <database.hpp>

Implements a mapping between integer based atom IDs and their associated volume.

Public Functions

inline DatabaseVolumesParameters()

void reg(size_t ID, std::vector<double> constants, size_t function_type)

double get(size_t ID)

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

void add_quicklookup(size_t ID, double value)

void clear_quicklookup()

Private Members

std::map<size_t, size_t> m_functiontypes

std::map<size_t, std::vector<double>> m_constants

std::map<size_t, double> m_quicklookup

size_t quicklookup_counter

Friends

friend class Database

friend class boost::serialization::access

class DatabaseSFactorsParameters

#include <database.hpp>

Implements a mapping between integer based atom IDs and their potentially q dependent scattering factors.

Public Functions

inline DatabaseSFactorsParameters()

void reg(size_t ID, std::vector<double> constants, size_t function_type)

double get(size_t ID, double q)

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

void add_quicklookup(size_t ID, double q, double value)

void clear_quicklookup()

Private Members

std::map<size_t, size_t> m_functiontypes

std::map<size_t, std::vector<double>> m_constants

std::map<double, std::map<size_t, double>> m_quicklookup

size_t quicklookup_counter

Friends

friend class Database

friend class boost::serialization::access

class DatabaseMassesParameters

#include <database.hpp>

Implements a mapping between integer based atom IDs and their masses.

Public Functions

void reg(size_t ID, double)

double get(size_t ID)

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

Private Members

std::map<size_t, double> m_masses

Friends

friend class Database

friend class boost::serialization::access

class DatabaseAtomIDsParameters

#include <database.hpp>

Implements a mapping between integer based atom IDs and string labels. For efficency, internally all physical constants are associated with integer based atom IDs.

Public Functions

inline DatabaseAtomIDsParameters()

void reg(std::string label)

size_t get(std::string label)

std::string rget(size_t ID)

inline size_t size()

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

Private Members

std::map<std::string, size_t> m_IDs

std::map<size_t, std::string> m_rIDs

size_t nextID

Friends

friend class Database

friend class boost::serialization::access

class DatabaseNamesPDBParameters

#include <database.hpp>

Support for PDB style atom names

Public Functions

inline DatabaseNamesPDBParameters()

void reg(std::string label, std::string regexp)

std::string get(std::string testlabel)

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

void add_quicklookup(std::string testlabel, std::string label)

void clear_quicklookup()

Private Members

std::map<std::string, std::string> m_label2regexp

std::map<std::string, std::string> m_quicklookup

size_t quicklookup_counter

Friends

friend class Database

friend class boost::serialization::access

class DatabaseNamesParameters

#include <database.hpp>

Implements the name mapping facility of the database

Public Members

DatabaseNamesPDBParameters pdb

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class Database

friend class boost::serialization::access

class Database

#include <database.hpp>

This singleton class is the root of a strong class hierarchy which implements a software wide database for physical constants and atom labeling. It also performs required computation, e.g. when the scattering factor for an atom is q vector length dependent.

Public Functions

void init()

inline void get_rawconfig(std::vector<char> &rc)

inline void get_config(std::vector<char> &c)

~Database() = default

void write(std::string filename, std::string format = "")

Public Members

DatabaseNamesParameters names

DatabaseMassesParameters masses

DatabaseVolumesParameters volumes

DatabaseExlusionParameters exclusionfactors

DatabaseSFactorsParameters sfactors

DatabaseAtomIDsParameters atomIDs

Public Static Functions

static inline Database *Inst()

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

inline Database()

Database(const Database&)

Database &operator=(const Database&)

void read_xml(std::string filename)

std::string guessformat(std::string filename)

bool check()

Private Members

std::vector<char> rawconfig

std::vector<char> config

Friends

friend class boost::serialization::access