3 from __future__
import print_function
5 from IMP
import OptionParser
7 __doc__ =
"Show the DOMINO merge tree to be used in alignment."
10 usage =
"""%prog [options] <asmb> <asmb.proteomics> <asmb.mapping>
13 Show the DOMINO merge tree to be used in the alignment procedure
15 parser = OptionParser(usage)
17 options, args = parser.parse_args()
19 parser.error(
"incorrect number of arguments")
23 def run(asmb_fn, proteomics_fn, mapping_fn, params_fn):
25 asmb.set_was_used(
True)
26 dmap = IMP.em.read_map(asmb.get_assembly_header().get_dens_fn())
27 dmap.get_header().set_resolution(
29 threshold = asmb.get_assembly_header().get_threshold()
30 dmap.update_voxel_size(asmb.get_assembly_header().get_spacing())
31 dmap.set_origin(asmb.get_assembly_header().get_origin())
33 alignment_params = IMP.multifit.AlignmentParams(params_fn)
34 alignment_params.show()
41 em_anchors = mapping_data.get_anchors()
47 align.set_fast_scoring(
False)
48 align.set_density_map(dmap, threshold)
49 align.add_states_and_filters()
50 align.add_all_restraints()
51 print(
"\n\n\nDOMINO MERGE TREE\n\n")
52 align.show_domino_merge_tree()
56 options, args = parse_args()
57 run(args[0], args[1], args[2], args[3])
59 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.