3 __doc__ =
"Generate a Connolly surface for a PDB."
7 from IMP
import OptionParser
11 usage =
"""%prog [options] <pdb file name>
13 This program generates the Connolly surface for a given PDB file."""
15 parser = OptionParser(usage)
16 parser.add_option(
"--density", dest=
"density", default=10.0, type=
"float",
18 help=
"density of probe points, per cubic angstrom "
20 parser.add_option(
"--radius", dest=
"rp", default=1.8, type=
"float",
22 help="probe radius in angstroms (default 1.8)")
24 opts, args = parser.parse_args()
26 parser.error(
"incorrect number of arguments")
27 return args[0], opts.density, opts.rp
31 infile, density, rp = parse_args()
32 outfile = infile +
'.ms'
40 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)