IMP  2.3.1
The Integrative Modeling Platform
IMP::multifit::ProteomicsData Class Reference

Storage of proteomics data. More...

#include <IMP/multifit/proteomics_reader.h>

+ Inheritance diagram for IMP::multifit::ProteomicsData:

Detailed Description

Storage of proteomics data.

Definition at line 71 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
 
virtual ::IMP::base::VersionInfo get_version_info () const
 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::base::Object
virtual void clear_caches ()
 
CheckLevel get_check_level () const
 
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::base::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 77 of file proteomics_reader.h.

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

return the assigned index

Definition at line 87 of file proteomics_reader.h.

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

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 189 of file proteomics_reader.h.


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