doc/ref/cg__pdb_8py_source.html

 ## \example atom/cg_pdb.py

 # This example shows how to properly write out a pdb of the structure

 # results when using coarse grained rigid bodies.


 import IMP.atom

 import sys


 IMP.setup_from_argv(sys.argv, "CG pdb")


 m = IMP.Model()

 full = IMP.atom.read_pdb(IMP.atom.get_example_path("example_protein.pdb"), m)

 chain = IMP.atom.get_by_type(full, IMP.atom.CHAIN_TYPE)[0]

 print(chain)

 # for some reason the Python wrapper won't make the implicit conversion to

 # Chain

 simplified = IMP.atom.create_simplified_along_backbone(

     IMP.atom.Chain(chain), 3)

 IMP.atom.destroy(full)

 rb = IMP.atom.create_rigid_body(simplified)

 original_transform = rb.get_reference_frame().get_transformation_to()


 # fake optimization, just move the rigid body

 tr = IMP.algebra.get_random_rotation_3d()

 rb.set_reference_frame(IMP.algebra.ReferenceFrame3D(

     IMP.algebra.Transformation3D(tr, IMP.algebra.Vector3D(0, 0, 0))))


 # extract the difference

 diff = rb.get_reference_frame().get_transformation_to() / original_transform

 reload = IMP.atom.read_pdb(IMP.atom.get_example_path("example_protein.pdb"), m)

 IMP.atom.transform(reload, diff)

 name = IMP.create_temporary_file("out", ".pdb")

 IMP.atom.write_pdb(reload, name)

IMP::algebra::Transformation3D
Simple 3D transformation class.
Definition: Transformation3D.h:37

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

IMP::algebra::get_random_rotation_3d
Rotation3D get_random_rotation_3d(const Rotation3D &center, double distance)
Pick a rotation at random near the provided one.

IMP::atom::write_pdb
void write_pdb(const Selection &mhd, TextOutput out, unsigned int model=1)

IMP::atom::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::create_temporary_file
TextOutput create_temporary_file(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file. The path can be extracted from the TextOutput.

IMP::algebra::ReferenceFrame3D
A reference frame in 3D.
Definition: ReferenceFrame3D.h:22

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

IMP::atom::transform
void transform(Hierarchy h, const algebra::Transformation3D &tr)
Transform a hierarchy. This is aware of rigid bodies.

IMP::atom::create_simplified_along_backbone
Hierarchy create_simplified_along_backbone(Chain input, const IntRanges &residue_segments, bool keep_detailed=false)

IMP::algebra::Vector3D
VectorD< 3 > Vector3D
Definition: VectorD.h:408

IMP::atom::create_rigid_body
IMP::core::RigidBody create_rigid_body(Hierarchy h)

IMP::atom::Chain
Store info for a chain of a protein.
Definition: Chain.h:61

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