3 __doc__ =
"Generate a Connolly surface for a PDB."
7 from IMP
import ArgumentParser
12 This program generates the Connolly surface for a given PDB file."""
14 p = ArgumentParser(description=desc)
15 p.add_argument(
"--density", dest=
"density", default=10.0, type=float,
17 help=
"density of probe points, per cubic angstrom "
19 p.add_argument(
"--radius", dest=
"rp", default=1.8, type=float,
21 help="probe radius in angstroms (default 1.8)")
22 p.add_argument(
"pdb", help=
"input PDB file name")
25 return args.pdb, args.density, args.rp
29 infile, density, rp = parse_args()
30 outfile = infile +
'.ms'
39 if __name__ ==
"__main__":
Select non water and non hydrogen atoms.
void read_pdb(TextInput input, int model, Hierarchy h)
Class for storing model, its restraints, constraints, and particles.
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)