doc/ref/pdb2density_8py_source.html

 ## \example em/pdb2density.py

 # A simple example showing how to simulate density from a protein.

 # IMP uses a Gaussian smoothing kernel. see SampledDensityMap::resample

 # for documentation.

 #


 import IMP.em

 import IMP.core

 import IMP.atom

 import sys


 IMP.setup_from_argv(sys.argv, "pdb2density")


 m = IMP.Model()

 # read protein

 sel = IMP.atom.NonWaterPDBSelector()

 mh = IMP.atom.read_pdb(IMP.em.get_example_path("input.pdb"), m, sel)

 # add radius info to each atom, otherwise the resampling would fail.

 IMP.atom.add_radii(mh)

 ps = IMP.core.get_leaves(mh)

 # decide on resolution and spacing you would like to simulate to

 resolution = 10.

 apix = 1.5

 dmap = IMP.em.particles2density(ps, resolution, apix)

 # write out the map in the favorite format (xplor, mrc, em and spider are

 # supported)

 IMP.em.write_map(dmap, "example.mrc", IMP.em.MRCReaderWriter())

IMP::setup_from_argv
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)

IMP::atom::add_radii
void add_radii(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
Add vdW radius from given force field.

IMP::em::MRCReaderWriter
Definition: MRCReaderWriter.h:20

IMP::em::particles2density
SampledDensityMap * particles2density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key())
Resample a set of particles into a density grid.

IMP::core::get_leaves
GenericHierarchies get_leaves(Hierarchy mhd)
Get all the leaves of the bit of hierarchy.

IMP::atom::read_pdb
void read_pdb(TextInput input, int model, Hierarchy h)

IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:86

IMP::em
Basic utilities for handling cryo-electron microscopy 3D density maps.

IMP::em::get_example_path
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.

IMP::core
Basic functionality that is expected to be used by a wide variety of IMP users.

IMP::atom::NonWaterPDBSelector
Select all non-water non-alternative ATOM and HETATM records.
Definition: pdb.h:356

IMP::atom
Functionality for loading, creating, manipulating and scoring atomic structures.