9 #ifndef IMPMULTIFIT_PROTEOMICS_EM_ALIGNMENT_ATOMIC_H
10 #define IMPMULTIFIT_PROTEOMICS_EM_ALIGNMENT_ATOMIC_H
22 #include <IMP/multifit/multifit_config.h>
24 #include <boost/scoped_ptr.hpp>
26 IMPMULTIFIT_BEGIN_NAMESPACE
31 class IMPMULTIFITEXPORT ProteomicsEMAlignmentAtomic :
public base::Object {
33 ProteomicsEMAlignmentAtomic(
34 const ProteinsAnchorsSamplingSpace &mapping_data,
35 multifit::SettingsData *asmb_data,
36 const AlignmentParams &align_param);
38 void add_all_restraints();
39 void add_states_and_filters();
40 void show_domino_merge_tree()
const;
42 void set_density_map(em::DensityMap *dmap,
float threshold) {
43 dmap_=dmap;threshold_=threshold;
45 atom::Hierarchies get_molecules()
const {
return mhs_;}
46 core::RigidBodies get_rigid_bodies()
const {
return rbs_;}
53 void load_combination_of_states(
const Ints &state4particles);
54 void show_scores_header(std::ostream& ous=std::cout)
const;
58 Model * get_model() {
return mdl_;}
61 void set_fast_scoring(
bool state) {
68 RestraintsTemp get_alignment_restraints()
const;
69 Pointer<domino::RestraintCache> rc_;
71 domino::ParticleStatesTable*
73 void load_atomic_molecules();
75 ProteinsAnchorsSamplingSpace mapping_data_;
76 OwnerPointer<multifit::ProteomicsData> prot_data_;
77 Pointer<em::DensityMap> dmap_;
79 atom::Hierarchies mhs_;
80 core::RigidBodies rbs_;
82 AlignmentParams params_;
86 std::vector<std::pair<int,float> >cg_sorted_;
87 Pointer<RestraintSet> conn_rs_;
88 Pointer<RestraintSet> conn_rs_with_filter_;
89 Pointer<RestraintSet> xlink_rs_;
90 Pointer<RestraintSet> xlink_rs_with_filter_;
91 Pointer<RestraintSet> dummy_rs_;
92 Pointer<RestraintSet> em_rs_;
93 Pointer<RestraintSet> ev_rs_;
94 RestraintsTemp jt_rs_;
99 OwnerPointer<domino::RestraintScoreSubsetFilterTable> all_rs_filt_;
100 IntKey fit_state_key_,order_key_;
101 bool restraints_set_,states_set_,filters_set_;
102 OwnerPointer<domino::ParticleStatesTable> pst_;
104 multifit::SettingsData *asmb_data_;
110 IMPMULTIFIT_END_NAMESPACE