doc/ref/generate__density__map__of__fixed__dimension_8py_source.html

 ## \example em/generate_density_map_of_fixed_dimension.py

 # Shows how to generate a density map of fixed dimension and how to sample

 # particles within this density map.


 from __future__ import print_function

 import IMP

 import IMP.atom

 import IMP.em

 import sys


 IMP.setup_from_argv(sys.argv, "generate a density map of fixed dimension")


 m = IMP.Model()

 # 1. read a protein and get its bounding box dimension

 sel = IMP.atom.CAlphaPDBSelector()

 # read protein

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

 apix = 1.

 resolution = 6.

 # compute bbox, and map size in voxels

 bbox = IMP.atom.get_bounding_box(mh)

 #diag            = bbox.get_corner(0) - bbox.get_corner(1)

 #nx              = int(bboxCoverage * diag[0] / apix)

 #ny              = int(bboxCoverage * diag[1] / apix)

 #nz              = int(bboxCoverage * diag[2] / apix)


 # create a density header of the requested size

 dheader = IMP.em.create_density_header(bbox, apix)

 dheader.set_resolution(resolution)

 dmap = IMP.em.SampledDensityMap(dheader)

 ps = IMP.core.get_leaves(mh)

 dmap.set_particles(ps)

 # dmap.get_header_writable().set_number_of_voxels(nx,ny,nz)

 dmap.resample()

 dmap.calcRMS()

              # computes statistic stuff about the map and insert it in the

              # header

 print(dmap.get_header().show(), "\n")

 IMP.em.write_map(dmap, "map.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::get_bounding_box
algebra::BoundingBoxD< 3 > get_bounding_box(const Hierarchy &h)
Get a bounding box for the Hierarchy.

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::em::write_map
void write_map(DensityMap *m, std::string filename)
Write a density map to a file.

IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:72

IMP::em::SampledDensityMap
Class for sampling a density map from particles.
Definition: SampledDensityMap.h:31

IMP::em::create_density_header
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box in 3D.

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::atom::show
void show(Hierarchy h, std::ostream &out=std::cout)
Print out a molecular hierarchy.
Definition: atom/Hierarchy.h:437

IMP::atom::CAlphaPDBSelector
Select all CA ATOM records.
Definition: pdb.h:76

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