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

Model *	get_model ()

atom::Hierarchies	get_molecules () const

RestraintSet *	get_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::ParticleStatesTable *	set_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::SettingsData *	asmb_data_

std::vector< std::pair< int, float > >	cg_sorted_

Pointer< RestraintSet >	conn_rs_

Pointer< RestraintSet >	conn_rs_with_filter_

Pointer< em::DensityMap >	dmap_

Pointer< RestraintSet >	dummy_rs_

Pointer< RestraintSet >	em_rs_

Pointer< RestraintSet >	ev_rs_

float	ev_thr_

bool	fast_scoring_

domino::SubsetFilterTables	filters_

bool	filters_set_

IntKey	fit_state_key_

RestraintsTemp	jt_rs_

ProteinsAnchorsSamplingSpace	mapping_data_

Pointer< Model >	mdl_

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::RestraintCache >	rc_

Pointer< RestraintSet >	restraint_set_

domino::Assignments	sampled_assignments_

IntsLists	sampled_solutions_

bool	states_set_

double	threshold_

Pointer< RestraintSet >	xlink_rs_

Pointer< RestraintSet >	xlink_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:

proteomics_em_alignment_atomic.h

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Member Function Documentation