atom/cg_pdb.py

This example shows how to properly write out a pdb of the structure results when using coarse grained rigid bodies.

## \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.

from __future__ import print_function
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)