Detailed Description

Align proteomics graph to EM density map.

The alignment is from the em anchors to the proteomics graph

Public Member Functions
	ProteomicsEMAlignmentAtomic (const ProteinsAnchorsSamplingSpace &mapping_data, multifit::SettingsData *asmb_data, const AlignmentParams &align_param)

void	add_all_restraints ()

void	add_states_and_filters ()

void	align ()

domino::Assignments	get_combinations (bool uniques=false) const

kernel::Model *	get_model ()

atom::Hierarchies	get_molecules () const

core::RigidBodies	get_rigid_bodies () 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	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::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 Member Functions
kernel::RestraintsTemp	get_alignment_restraints () const

void	load_atomic_molecules ()

domino::ParticleStatesTable *	set_particle_states_table (domino::SubsetFilterTables &filters)

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

virtual void	do_destroy ()

Protected Attributes
base::PointerMember < domino::RestraintScoreSubsetFilterTable >	all_rs_filt_

multifit::SettingsData *	asmb_data_

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

base::Pointer < kernel::RestraintSet >	conn_rs_

base::Pointer < kernel::RestraintSet >	conn_rs_with_filter_

base::Pointer< em::DensityMap >	dmap_

base::Pointer < kernel::RestraintSet >	dummy_rs_

base::Pointer < kernel::RestraintSet >	em_rs_

base::Pointer < kernel::RestraintSet >	ev_rs_

float	ev_thr_

bool	fast_scoring_

domino::SubsetFilterTables	filters_

bool	filters_set_

IntKey	fit_state_key_

kernel::RestraintsTemp	jt_rs_

ProteinsAnchorsSamplingSpace	mapping_data_

base::Pointer< Model >	mdl_

atom::Hierarchies	mhs_

IntKey	order_key_

AlignmentParams	params_

IntPairs	post_sampling_ev_pairs_

base::PointerMember < multifit::ProteomicsData >	prot_data_

base::PointerMember < domino::ParticleStatesTable >	pst_

core::RigidBodies	rbs_

base::Pointer < domino::RestraintCache >	rc_

bool	restraints_set_

domino::Assignments	sampled_assignments_

IntsLists	sampled_solutions_

bool	states_set_

double	threshold_

base::Pointer < kernel::RestraintSet >	xlink_rs_

base::Pointer < kernel::RestraintSet >	xlink_rs_with_filter_

Member Function Documentation

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

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

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

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