T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ > Class Template Reference

Loader for covalent structures from PDB / mmCIF files. More...

#include <Molecular_covalent_structure_loader.hpp>

Public Member Functions
virtual boost::program_options::options_description	add_options (void) override
	Virtual method for adding options to the module.
virtual bool	check_options (std::string &message) const override
	Checks that the input options' values are coherent.
bool	load (unsigned verbose=false, std::ostream &out=std::cout) override
	Load function.
std::string	get_name (void) const override
	Return the name of the class itself.
std::string	get_output_prefix (void) const override
	Returns a prefix that concatains the input line options used when running the module.
const std::vector< Molecular_covalent_structure > &	get_molecular_covalent_structures (void) const
	Retrieves the molecular covalent structures loaded from PDB / mmCIF file(s).
std::vector< Molecular_covalent_structure > &	get_molecular_covalent_structures (void)
	Retrieves the molecular covalent structures loaded from PDB / mmCIF file(s).
const std::vector< bool > &	are_files_valid () const
	Tells whether a loaded file led to the construction of a Molecular_covalent_structure.
void	statistics (std::ostream &out)
	Prints statistics about the loaded PDB files.
	SET_AND_GET (allow_incomplete_chains, bool)
	By default, set to false, incomplete chains are not allowed, forbidding the construction of incomplete chains and Molecular_covalent_structures.
	SET_AND_GET (coarse_level, unsigned)
	By default set to 0, loading every single atom as a particle in the Molecular_covalent_structure.
	SET_AND_GET (max_bond_distance, double)
	By default set to 3 angstom.
	SET_AND_GET (ss_bond_search, bool)
	By default set to false.
void	transfer_options (void)
const std::vector< std::shared_ptr< Molecular_system > > &	get_molecular_systems (void) const
	Retrieves the molecular systems loaded from the PDB / mmCIF file(s). This function returns a constant reference to the vector containing the molecular systems loaded from the PDB file(s).
void	statistics (std::ostream &out) const
	Prints statistics about the loaded PDB files. This function prints statistics about the loaded PDB files, including the number of files, their details, and various counts related to the loaded molecular systems.
void	check_validity (void) const
	Performs validity / sanity checks on the loaded PDB file. It notably controls that each residue as a Calpha, and identify missing residues in the sequence. As it returns void, it is only interesting as an informational purpose.
	SET_AND_GET (loaded_file_paths, std::vector< std::string >)
	Provide a list of file paths to load, pdb and cif formats and are accepted, as well as these format compressed to gz / tar.gz.

Static Public Member Functions
static boost::program_options::options_description *&	get_options (void)
	Access to the options' description of the module.

Protected Member Functions
void	load_molecular_covalent_structures (void)
	Loads the Molecular_covalent_structures.
void	load_molecular_systems (void)
	Loads the molecular systems from the specified files taking into account all the provided options.
void	delete_molecular_systems (void)
	Deletes instances of molecular systems allocated by the loader.
void	add_cif_atom_to_sbl_residue (const cif::mm::atom &cif_atom, typename Molecular_system::Residue &sbl_residue, bool is_hetatm)
	Adds a CIF atom or hetatom to a SBL residue. This function adds a CIF atom or hetatom to a SBL residue.

Protected Attributes
std::vector< std::size_t >	m_atm_discarded
	Number of actually discarded atoms for each loaded PDB file (not the sum of all discarded atoms in each category).
std::vector< std::size_t >	m_model_discarded
	Number of discarded atom for not beeing in loaded models.
std::vector< std::size_t >	m_chain_discarded
	Number of discarded atom for not beeing in loaded chains.
std::vector< std::size_t >	m_temp_discarded
	Number of discarded atom for having a too great B factor for each loaded PDB file.
std::vector< std::size_t >	m_htm_discarded
	Number of discarded hetero-atoms for each loaded PDB file.
std::vector< std::size_t >	m_hoh_discarded
	Number of discarded water atoms for each loaded PDB file.
std::vector< std::size_t >	m_h_discarded
	Number of discarded hydrogens for each loaded PDB file.
std::vector< std::size_t >	m_alt_discarded
	Number of discarded alternate location atoms for each loaded PDB file.

Detailed Description

template<class Molecular_covalent_structure_builder_>
class SBL::IO::T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >

Loader for covalent structures from PDB / mmCIF files.

Loader for covalent structures from PDB / mmCIF files.

Template Parameters

MolecularCovalentStructureBuilder

Builder of the covalent structure.

Member Function Documentation

add_cif_atom_to_sbl_residue()

void add_cif_atom_to_sbl_residue ( const cif::mm::atom & cif_atom, typename Molecular_system::Residue & sbl_residue, bool is_hetatm )

protectedinherited

Adds a CIF atom or hetatom to a SBL residue. This function adds a CIF atom or hetatom to a SBL residue.

Parameters

cif_atom	The CIF atom to be added.
sbl_residue	The SBL residue to which the CIF atom / hetatom will be added.
is_hetatm	flag indicating whether the atom is a heteroatom.

add_options()

template<class Molecular_covalent_structure_builder_>

boost::program_options::options_description add_options ( void )

overridevirtual

Virtual method for adding options to the module.

Adds options specific to the "Covalent structures loader" to the option parser and also as command line arguments.

Reimplemented from T_Molecular_system_loader< Molecular_covalent_structure_builder_::Molecular_covalent_structure::Particle_info::Particle_traits::Molecular_system >.

are_files_valid()

template<typename Molecular_covalent_structure_builder_>

const std::vector< bool > & are_files_valid

(

)

const

Tells whether a loaded file led to the construction of a Molecular_covalent_structure.

To be accessed after load is called.

Returns

A constant reference to the vector of booleans

check_options()

template<class Molecular_covalent_structure_builder_>

bool check_options ( std::string & message ) const

overridevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Molecular_system_loader< Molecular_covalent_structure_builder_::Molecular_covalent_structure::Particle_info::Particle_traits::Molecular_system >.

check_validity()

void check_validity ( void ) const

inherited

Performs validity / sanity checks on the loaded PDB file. It notably controls that each residue as a Calpha, and identify missing residues in the sequence. As it returns void, it is only interesting as an informational purpose.

delete_molecular_systems()

void delete_molecular_systems ( void )

protectedinherited

Deletes instances of molecular systems allocated by the loader.

get_molecular_covalent_structures() [1/2]

template<class Molecular_covalent_structure_builder_>

std::vector< typename Molecular_covalent_structure_builder_::Molecular_covalent_structure > & get_molecular_covalent_structures

(

void

)

Retrieves the molecular covalent structures loaded from PDB / mmCIF file(s).

This function returns a reference to the vector containing the molecular covalent structures loaded from the PDB / mmCIF file(s).

Returns

A reference to the vector of molecular covalent structures

get_molecular_covalent_structures() [2/2]

template<class Molecular_covalent_structure_builder_>

const std::vector< typename Molecular_covalent_structure_builder_::Molecular_covalent_structure > & get_molecular_covalent_structures

(

void

)

const

Retrieves the molecular covalent structures loaded from PDB / mmCIF file(s).

This function returns a constant reference to the vector containing the molecular covalent structures loaded from the PDB / mmCIF file(s).

Returns

A constant reference to the vector of molecular covalent structures

get_molecular_systems()

const std::vector< std::shared_ptr< Molecular_covalent_structure_builder_::Molecular_covalent_structure::Particle_info::Particle_traits::Molecular_system > > & get_molecular_systems ( void ) const

inlineinherited

Retrieves the molecular systems loaded from the PDB / mmCIF file(s). This function returns a constant reference to the vector containing the molecular systems loaded from the PDB file(s).

Returns

A constant reference to the vector of booleans

get_name()

template<class Molecular_covalent_structure_builder_>

std::string get_name ( void ) const

overridevirtual

Return the name of the class itself.

Reimplemented from Loader_base.

get_options()

template<class Dummy = void>

boost::program_options::options_description *& get_options ( void )

inlinestaticinherited

Access to the options' description of the module.

get_output_prefix()

template<class Molecular_covalent_structure_builder_>

std::string get_output_prefix ( void ) const

overridevirtual

Returns a prefix that concatains the input line options used when running the module.

Reimplemented from T_Module_option_description< Dummy >.

load()

template<class Molecular_covalent_structure_builder_>

bool load ( unsigned verbose = false, std::ostream & out = std::cout )

overridevirtual

Load function.

Parameters

	verbose	Verbosity level.
[out]	out	Output stream.

Returns

True if loading is successful, false otherwise. Function to call to execute the main function of a Loader This function loads the molecular covalent structures based on the specified options.

Reimplemented from Loader_base.

load_molecular_covalent_structures()

template<class Molecular_covalent_structure_builder_>

void load_molecular_covalent_structures ( void )

protected

Loads the Molecular_covalent_structures.

Retrieve the sequences of residues from the files, then builds as many Molecular_covalent_structure based on these sequences of residues. Incomplete chains can be allowed (missing residues), in which case, parts of the chains will be isolated and the number of components will therefore be increased. The Molecular_covalent_structures are then updated : terminal residues can be ionised–one proton added, water molecules can be added, disulfide bonds can be added from file information and geometrical search.

Returns

nothing

load_molecular_systems()

void load_molecular_systems ( void )

protectedinherited

Loads the molecular systems from the specified files taking into account all the provided options.

SET_AND_GET() [1/5]

template<class Molecular_covalent_structure_builder_>

SET_AND_GET	(	allow_incomplete_chains	,
		bool	)

By default, set to false, incomplete chains are not allowed, forbidding the construction of incomplete chains and Molecular_covalent_structures.

SET_AND_GET() [2/5]

template<class Molecular_covalent_structure_builder_>

SET_AND_GET	(	coarse_level	,
		unsigned	)

By default set to 0, loading every single atom as a particle in the Molecular_covalent_structure.

1 for loading heavy atoms only as particles, and 2 for loading residues as particles

SET_AND_GET() [3/5]

template<class Molecular_covalent_structure_builder_>

SET_AND_GET	(	max_bond_distance	,
		double	)

By default set to 3 angstom.

Controls the maximum distance between two bond atoms that is tolerated upon checking for incomplete chains

SET_AND_GET() [4/5]

template<class Molecular_covalent_structure_builder_>

SET_AND_GET	(	ss_bond_search	,
		bool	)

By default set to false.

If true, a geometrical search, based on the positions of sulfur atoms of cysteins will be conducted. Close enough sulfur atoms will be bond.

SET_AND_GET() [5/5]

SET_AND_GET ( loaded_file_paths , std::vector< std::string >  )

inherited

Provide a list of file paths to load, pdb and cif formats and are accepted, as well as these format compressed to gz / tar.gz.

statistics() [1/2]

template<class Molecular_covalent_structure_builder_>

void statistics ( std::ostream & out )

inline

Prints statistics about the loaded PDB files.

This function prints statistics about the loaded covalent structures.

Parameters

out	The output stream to which the statistics will be printed.

statistics() [2/2]

void statistics ( std::ostream & out ) const

inherited

Prints statistics about the loaded PDB files. This function prints statistics about the loaded PDB files, including the number of files, their details, and various counts related to the loaded molecular systems.

Parameters

out	The output stream to which the statistics will be printed.

transfer_options()

void transfer_options ( void )

inherited

Member Data Documentation

m_alt_discarded

std::vector<std::size_t> m_alt_discarded

protectedinherited

Number of discarded alternate location atoms for each loaded PDB file.

m_atm_discarded

std::vector<std::size_t> m_atm_discarded

protectedinherited

Number of actually discarded atoms for each loaded PDB file (not the sum of all discarded atoms in each category).

m_chain_discarded

std::vector<std::size_t> m_chain_discarded

protectedinherited

Number of discarded atom for not beeing in loaded chains.

m_h_discarded

std::vector<std::size_t> m_h_discarded

protectedinherited

Number of discarded hydrogens for each loaded PDB file.

m_hoh_discarded

std::vector<std::size_t> m_hoh_discarded

protectedinherited

Number of discarded water atoms for each loaded PDB file.

m_htm_discarded

std::vector<std::size_t> m_htm_discarded

protectedinherited

Number of discarded hetero-atoms for each loaded PDB file.

m_model_discarded

std::vector<std::size_t> m_model_discarded

protectedinherited

Number of discarded atom for not beeing in loaded models.

m_temp_discarded

std::vector<std::size_t> m_temp_discarded

protectedinherited

Number of discarded atom for having a too great B factor for each loaded PDB file.