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IMP
2.2.1
The Integrative Modeling Platform
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IMP
2.2.1
The Integrative Modeling Platform
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Storage of proteomics data. More...
#include <IMP/multifit/proteomics_reader.h>
Inheritance diagram for IMP::multifit::ProteomicsData: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. | |
| 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 () |
| virtual void | do_destroy () |
| 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_ |
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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... | |
Definition at line 71 of file proteomics_reader.h.
| 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.