3 from __future__
import print_function
5 from IMP
import ArgumentParser
7 __doc__ =
"Show the DOMINO merge tree to be used in alignment."
11 Show the DOMINO merge tree to be used in the alignment procedure
13 p = ArgumentParser(description=desc)
14 p.add_argument(
"assembly_file", help=
"assembly file name")
15 p.add_argument(
"proteomics_file", help=
"proteomics file name")
16 p.add_argument(
"mapping_file", help=
"mapping file name")
17 p.add_argument(
"param_file", help=
"parameter file name")
21 def run(asmb_fn, proteomics_fn, mapping_fn, params_fn):
23 asmb.set_was_used(
True)
24 dmap = IMP.em.read_map(asmb.get_assembly_header().get_dens_fn())
25 dmap.get_header().set_resolution(
27 threshold = asmb.get_assembly_header().get_threshold()
28 dmap.update_voxel_size(asmb.get_assembly_header().get_spacing())
29 dmap.set_origin(asmb.get_assembly_header().get_origin())
31 alignment_params = IMP.multifit.AlignmentParams(params_fn)
32 alignment_params.show()
39 em_anchors = mapping_data.get_anchors()
45 align.set_fast_scoring(
False)
46 align.set_density_map(dmap, threshold)
47 align.add_states_and_filters()
48 align.add_all_restraints()
49 print(
"\n\n\nDOMINO MERGE TREE\n\n")
50 align.show_domino_merge_tree()
55 run(args.assembly_file, args.proteomics_file, args.mapping_file,
58 if __name__ ==
"__main__":
SettingsData * read_settings(const char *filename)
ProteinsAnchorsSamplingSpace read_protein_anchors_mapping(multifit::ProteomicsData *prots, const std::string &anchors_prot_map_fn, int max_paths=INT_MAX)
Align proteomics graph to EM density map.
Fitting atomic structures into a cryo-electron microscopy density map.
ProteomicsData * read_proteomics_data(const char *proteomics_fn)
Proteomics reader.
void set_log_level(LogLevel l)
Set the current global log level.
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.