Detailed Description

Storage of proteomics data.

Definition at line 81 of file proteomics_reader.h.

Public Member Functions
void	add_cross_link_interaction (Int prot1, Int res1, Int prot2, Int res2, bool used_in_filter, Float linker_len)

void	add_ev_pair (Int prot1, Int prot2)

void	add_interaction (const Ints &ii, bool used_for_filter, float linker_len)

int	add_protein (std::string name, int start_res, int end_res, const std::string &mol_fn, const std::string &surface_fn, const std::string &ref_fn)

int	add_protein (const ProteinRecordData &rec)

int	find (const std::string &name) const

std::pair< IntPair, IntPair >	get_cross_link (int xlink_ind) const

float	get_cross_link_length (int xlink_ind) const

bool	get_cross_link_part_of_filter (int xlink_ind) const

int	get_end_res (int protein_ind) const

IntPair	get_ev_pair (int ev_ind) const

Ints	get_interaction (int interaction_ind) const

int	get_interaction_linker_length (int interaction_ind) const

bool	get_interaction_part_of_filter (int interaction_ind) const

int	get_num_allowed_violated_cross_links () const

int	get_num_allowed_violated_ev () const

int	get_num_allowed_violated_interactions () const

int	get_number_of_cross_links () const

int	get_number_of_ev_pairs () const

int	get_number_of_interactions () const

int	get_number_of_proteins () const

ProteinRecordData	get_protein_data (int protein_ind) const

std::string	get_protein_filename (int protein_ind) const

std::string	get_protein_name (int protein_ind) const

std::string	get_reference_filename (int protein_ind) const

int	get_start_res (int protein_ind) const

std::string	get_surface_filename (int protein_ind) const

virtual std::string	get_type_name () const override

virtual ::IMP::VersionInfo	get_version_info () const override
	Get information about the module and version of the object. More...

void	set_num_allowed_violated_cross_links (int n)

void	set_num_allowed_violated_ev (int n)

void	set_num_allowed_violated_interactions (int n)

Public Member Functions inherited from IMP::Object
virtual void	clear_caches ()

CheckLevel	get_check_level () const

def	get_derived_object
	Return this object cast to the most derived subclass. More...

LogLevel	get_log_level () const

void	set_check_level (CheckLevel l)

void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...

void	set_was_used (bool tf) const

void	show (std::ostream &out=std::cout) const

const std::string &	get_name () const

void	set_name (std::string name)

Protected Attributes
IntPairs	ev_

std::vector< bool >	interaction_in_filter_

Floats	interaction_linker_len_

IntsList	interactions_

int	num_allowed_violated_ev_

int	num_allowed_violated_interactions_

int	num_allowed_violated_xlinks_

std::vector< ProteinRecordData >	prot_data_

std::map< std::string, int >	prot_map_

std::vector< bool >	xlink_in_filter_

Floats	xlink_len_

std::vector< std::pair < IntPair, IntPair > >	xlinks_

Additional Inherited Members
Protected Member Functions inherited from IMP::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Member Function Documentation

int IMP::multifit::ProteomicsData::add_protein	(	std::string	name,
		int	start_res,
		int	end_res,
		const std::string &	mol_fn,
		const std::string &	surface_fn,
		const std::string &	ref_fn
	)

return the assigned index

Definition at line 87 of file proteomics_reader.h.

int IMP::multifit::ProteomicsData::add_protein ( const ProteinRecordData & rec )

return the assigned index

Definition at line 97 of file proteomics_reader.h.

virtual ::IMP::VersionInfo IMP::multifit::ProteomicsData::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 199 of file proteomics_reader.h.

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

proteomics_reader.h

Detailed Description

Public Member Functions

Protected Attributes

Additional Inherited Members

Member Function Documentation