doc/ref/fit__restraint_8py_source.html

 ## \example em/fit_restraint.py

 # A simple example showing how to set up a fit restraint. The number of

 # spheres and resolution are randomly chosen and so should not be

 # considered significant.


 from __future__ import print_function

 import IMP.em

 import IMP.core

 import IMP.atom

 import sys


 IMP.setup_from_argv(sys.argv, "fit restraint")


 IMP.set_log_level(IMP.SILENT)

 m = IMP.Model()

 # 1. setup the input protein

 # 1.1 select a selector.

 sel = IMP.atom.NonWaterPDBSelector()

 # 1.2 read the protein

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

 ps = IMP.core.get_leaves(mh)

 IMP.atom.add_radii(mh)

 # 2. read the density map

 resolution = 8.

 voxel_size = 1.5

 dmap = IMP.em.read_map(

     IMP.em.get_example_path("input.mrc"), IMP.em.MRCReaderWriter())

 dmap.get_header_writable().set_resolution(resolution)

 # 3. calculate the cross correlation between the density and the map

 print("The cross-correlation score is:", 1. - IMP.em.compute_fitting_score(ps, dmap))

 # 4. add a fitting restraint

 r = IMP.em.FitRestraint(ps, dmap)

 print("The fit of the particles in the density is:", r.evaluate(False))

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"))

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

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:72

IMP::em::compute_fitting_score
Float compute_fitting_score(const ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key())
Compute fitting scores for a given set of rigid transformations.

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

IMP::em::read_map
DensityMap * read_map(std::string filename)
Read a density map from a file and return it.

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::set_log_level
void set_log_level(LogLevel l)
Set the current global log level.

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

IMP::em::FitRestraint
Calculate score based on fit to EM map.
Definition: FitRestraint.h:32

IMP::atom::NonWaterPDBSelector
Select all non-water non-alternative ATOM and HETATM records.
Definition: pdb.h:219

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