IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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Align proteomics graph to EM density map. More...
#include <IMP/multifit/proteomics_em_alignment_atomic.h>
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 |
virtual ::IMP::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::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_ |
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.
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virtual |
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.