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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
surface.py
1 #!/usr/bin/env python
2 
3 __doc__ = "Generate a Connolly surface for a PDB."
4 
5 import IMP.atom
6 import IMP.multifit
7 from IMP import ArgumentParser
8 
9 
10 def parse_args():
11  desc = """
12 This program generates the Connolly surface for a given PDB file."""
13 
14  p = ArgumentParser(description=desc)
15  p.add_argument("--density", dest="density", default=10.0, type=float,
16  metavar="D",
17  help="density of probe points, per cubic angstrom "
18  "(default 10.0)")
19  p.add_argument("--radius", dest="rp", default=1.8, type=float,
20  metavar="R",
21  help="probe radius in angstroms (default 1.8)")
22  p.add_argument("pdb", help="input PDB file name")
23 
24  args = p.parse_args()
25  return args.pdb, args.density, args.rp
26 
27 
28 def main():
29  infile, density, rp = parse_args()
30  outfile = infile + '.ms'
31 
32  m = IMP.Model()
33  h = IMP.atom.read_pdb(infile, m,
36  outfile, density, rp)
37 
38 if __name__ == "__main__":
39  main()
Select non water and non hydrogen atoms.
Definition: pdb.h:248
void read_pdb(TextInput input, int model, Hierarchy h)
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:86
Fitting atomic structures into a cryo-electron microscopy density map.
void write_connolly_surface(atom::Atoms atoms, TextOutput fn, float density, float probe_radius)
Write the Connolly surface for a set of atoms to a file.
Functionality for loading, creating, manipulating and scoring atomic structures.
Hierarchies get_leaves(const Selection &h)