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IMP Reference Guide  develop.ba5ef9f91e,2024/02/26
The Integrative Modeling Platform
IMP::multifit::ProteomicsEMAlignmentAtomic Class Reference

Align proteomics graph to EM density map. More...

#include <IMP/multifit/proteomics_em_alignment_atomic.h>

+ Inheritance diagram for IMP::multifit::ProteomicsEMAlignmentAtomic:

Detailed Description

Align proteomics graph to EM density map.

The alignment is from the em anchors to the proteomics graph

Definition at line 30 of file proteomics_em_alignment_atomic.h.

Public Member Functions

 ProteomicsEMAlignmentAtomic (const ProteinsAnchorsSamplingSpace &mapping_data, multifit::SettingsData *asmb_data, const AlignmentParams &align_param)
 
void add_all_restraints ()
 Set up the restraints that will be used in the alignment. More...
 
void add_states_and_filters ()
 
void align ()
 
domino::Assignments get_combinations (bool uniques=false) const
 
Modelget_model ()
 
atom::Hierarchies get_molecules () const
 
RestraintSetget_restraint_set ()
 Get the restraints set up by add_all_restraints(). More...
 
core::RigidBodies get_rigid_bodies () 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 load_combination_of_states (const Ints &state4particles)
 
void set_density_map (em::DensityMap *dmap, float threshold)
 
void set_fast_scoring (bool state)
 
void show_domino_merge_tree () const
 
void show_scores_header (std::ostream &ous=std::cout) const
 
- Public Member Functions inherited from IMP::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 Member Functions

RestraintsTemp get_alignment_restraints () const
 
void load_atomic_molecules ()
 
domino::ParticleStatesTableset_particle_states_table (domino::SubsetFilterTables &filters)
 
- Protected Member Functions inherited from IMP::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
virtual void do_destroy ()
 

Protected Attributes

PointerMember
< domino::RestraintScoreSubsetFilterTable
all_rs_filt_
 
multifit::SettingsDataasmb_data_
 
std::vector< std::pair< int,
float > > 
cg_sorted_
 
Pointer< RestraintSetconn_rs_
 
Pointer< RestraintSetconn_rs_with_filter_
 
Pointer< em::DensityMapdmap_
 
Pointer< RestraintSetdummy_rs_
 
Pointer< RestraintSetem_rs_
 
Pointer< RestraintSetev_rs_
 
float ev_thr_
 
bool fast_scoring_
 
domino::SubsetFilterTables filters_
 
bool filters_set_
 
IntKey fit_state_key_
 
RestraintsTemp jt_rs_
 
ProteinsAnchorsSamplingSpace mapping_data_
 
Pointer< Modelmdl_
 
atom::Hierarchies mhs_
 
IntKey order_key_
 
AlignmentParams params_
 
IntPairs post_sampling_ev_pairs_
 
PointerMember
< multifit::ProteomicsData
prot_data_
 
PointerMember
< domino::ParticleStatesTable
pst_
 
core::RigidBodies rbs_
 
Pointer< domino::RestraintCacherc_
 
Pointer< RestraintSetrestraint_set_
 
domino::Assignments sampled_assignments_
 
IntsLists sampled_solutions_
 
bool states_set_
 
double threshold_
 
Pointer< RestraintSetxlink_rs_
 
Pointer< RestraintSetxlink_rs_with_filter_
 

Member Function Documentation

void IMP::multifit::ProteomicsEMAlignmentAtomic::add_all_restraints ( )

Set up the restraints that will be used in the alignment.

These restraints are stored internally in a RestraintSet, which can be obtained by calling get_restraint_set(). For example, this allows adding extra restraints to the set.

RestraintSet* IMP::multifit::ProteomicsEMAlignmentAtomic::get_restraint_set ( )

Get the restraints set up by add_all_restraints().

Definition at line 44 of file proteomics_em_alignment_atomic.h.

virtual ::IMP::VersionInfo IMP::multifit::ProteomicsEMAlignmentAtomic::get_version_info ( ) const
overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 71 of file proteomics_em_alignment_atomic.h.

void IMP::multifit::ProteomicsEMAlignmentAtomic::load_combination_of_states ( const Ints state4particles)

load combination of states The order of the states should be the order

void IMP::multifit::ProteomicsEMAlignmentAtomic::set_fast_scoring ( bool  state)

If set to fast EV is calculated as penetration score and Fit restraint is decomposed

Definition at line 69 of file proteomics_em_alignment_atomic.h.


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