3 __doc__ =
"Calculate RMSD between a model and the reference."
6 from IMP
import ArgumentParser
10 desc =
"""%prog [options] <parameter file> <transformations file>
13 This program calculates the RMSD between modeled cyclic symmetric complexes and
14 the reference structure. The RMSD and cross correlation of each complex is
15 written into a file called rmsd.output.
17 Notice: no structural alignment is performed!"""
19 p = ArgumentParser(description=desc)
20 p.add_argument(
"--vec", dest=
"vec", default=
"", metavar=
"FILE",
21 help=
"output the RMSDs as a vector into the named "
23 p.add_argument(
"--start", dest=
"start", default=0, type=int,
24 help=
"first model in transformations file to compare "
25 "with the reference (by default, model 0)")
26 p.add_argument(
"--end", dest=
"end", default=-1, type=int,
27 help=
"last model in transformations file to compare "
28 "with the reference (by default, the final model)")
29 p.add_argument(
"param_file", help=
"parameter file name")
30 p.add_argument(
"trans_file", help=
"transformations file name")
31 p.add_argument(
"ref_pdb", help=
"reference PDB file name")
40 args.trans_file, args.ref_pdb,
43 open(args.vec,
'w').write(
" ".join([
'%f' % x
for x
in rmsds]))
45 if __name__ ==
'__main__':
Floats get_rmsd_for_models(const std::string param_filename, const std::string trans_filename, const std::string ref_filename, int start_model=0, int end_model=-1)
Generate cyclic atomic structures using cryo-electron microscopy data.
void set_log_level(LogLevel l)
Set the current global log level.