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IMP Reference Guide  2.7.0
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 OptionParser
8 
9 
10 def parse_args():
11  usage = """%prog [options] <pdb file name>
12 
13 This program generates the Connolly surface for a given PDB file."""
14 
15  parser = OptionParser(usage)
16  parser.add_option("--density", dest="density", default=10.0, type="float",
17  metavar="D",
18  help="density of probe points, per cubic angstrom "
19  "(default 10.0)")
20  parser.add_option("--radius", dest="rp", default=1.8, type="float",
21  metavar="R",
22  help="probe radius in angstroms (default 1.8)")
23 
24  opts, args = parser.parse_args()
25  if len(args) != 1:
26  parser.error("incorrect number of arguments")
27  return args[0], opts.density, opts.rp
28 
29 
30 def main():
31  infile, density, rp = parse_args()
32  outfile = infile + '.ms'
33 
34  m = IMP.Model()
35  h = IMP.atom.read_pdb(infile, m,
38  outfile, density, rp)
39 
40 if __name__ == "__main__":
41  main()
Select non water and non hydrogen atoms.
Definition: pdb.h:243
void read_pdb(TextInput input, int model, Hierarchy h)
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:72
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)