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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
collision_cross_section.py
1 ## \example em2d/collision_cross_section.py
2 # Example of how to compute the collision cross section of a molecule.
3 #
4 
5 
6 from __future__ import print_function
7 import IMP
8 import IMP.em2d
9 import IMP.atom
10 import sys
11 
12 IMP.setup_from_argv(sys.argv, "collision cross section")
13 
14 """
15 
16 Example of how to compute the collision cross section of a molecule
17 
18 """
19 
20 
21 IMP.set_log_level(IMP.TERSE)
22 m = IMP.Model()
23 
24 fn = IMP.em2d.get_example_path("1z5s.pdb")
25 prot = IMP.atom.read_pdb(fn, m, IMP.atom.ATOMPDBSelector())
26 IMP.atom.add_radii(prot)
27 
28 
29 projections = 20
30 resolution = 1.0
31 pixel_size = 1.5
32 img_size = 80
33 ccs = IMP.em2d.CollisionCrossSection(projections, resolution, pixel_size,
34  img_size)
35 ccs.set_model_particles(IMP.atom.get_leaves(prot))
36 print("CCS", ccs.get_ccs(), "A**2")
IMP::em2d
Restraints using electron microscopy 2D images (class averages).
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::em2d::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::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::atom::ATOMPDBSelector
Select all non-alternative ATOM records.
Definition: pdb.h:67
IMP::set_log_level
void set_log_level(LogLevel l)
Set the current global log level.
IMP::em2d::CollisionCrossSection
Determine the collision cross section for some projections of particles.
Definition: CollisionCrossSection.h:21
IMP::atom
Functionality for loading, creating, manipulating and scoring atomic structures.
IMP::atom::get_leaves
Hierarchies get_leaves(const Selection &h)