def test_ccs_value(self):
"""Test the calculation of the collision cross section of a complex"""
IMP.base.set_log_level(IMP.base.TERSE)
m = IMP.kernel.Model()
fn = self.get_input_file_name("1z5s.pdb")
prot = atom.read_pdb(fn, m, atom.ATOMPDBSelector())
atom.add_radii(prot)
projections = 20
resolution = 1.0
pixel_size = 1.5
img_size = 80
ccs = em2d.CollisionCrossSection(
projections,
resolution,
pixel_size,
img_size)
ccs.set_model_particles(IMP.atom.get_leaves(prot))
ccs_calculated = ccs.get_ccs()
ccs_value = 3838 # A**2
# good within 2%
self.assertAlmostEqual(
ccs_calculated,
ccs_value,
delta=ccs_value * 0.02)
def read_component(model,fn_pdb, name=False):
""" Read a PDB molecule, add atoms, and set a name
"""
log.debug("reading component %s from %s", name, fn_pdb)
hierarchy = atom.read_pdb(fn_pdb, model,
atom.NonWaterNonHydrogenPDBSelector())
if(name):
hierarchy.set_name(name)
atom.add_radii(hierarchy)
return hierarchy
def read_component(model, fn_pdb, name=False):
""" Read a PDB molecule, add atoms, and set a name
"""
if name:
log.debug("reading component %s from %s", name, fn_pdb)
else:
log.debug("reading component from %s", fn_pdb)
hierarchy = atom.read_pdb(fn_pdb, model,
atom.NonWaterNonHydrogenPDBSelector())
if name:
hierarchy.set_name(name)
atom.add_radii(hierarchy)
return hierarchy
def create_assembly_from_pdb(model, fn_pdb, names=False):
"""
Builds the assembly setting the chains in the PDB file as components
"""
temp = read_component(model, fn_pdb)
hchains = atom.get_by_type(temp, atom.CHAIN_TYPE)
ids = [atom.Chain(h).get_id() for h in hchains]
log.debug("Creating assembly from pdb %s,names: %s. Chains %s",
fn_pdb, names, ids)
atom.add_radii(temp)
if(names):
for i, h in enumerate(hchains):
h.set_name(names[i])
assembly = IMP.atom.Molecule.setup_particle(temp)
return assembly
def create_assembly_from_pdb(model, fn_pdb, names=False):
"""
Builds the assembly setting the chains in the PDB file as components
"""
temp = read_component(model, fn_pdb)
hchains = atom.get_by_type(temp, atom.CHAIN_TYPE)
ids = [atom.Chain(h).get_id() for h in hchains]
log.debug("Creating assembly from pdb %s,names: %s. Chains %s", fn_pdb,
names, ids)
atom.add_radii(temp)
if (names):
for i, h in enumerate(hchains):
h.set_name(names[i])
assembly = IMP.atom.Molecule.setup_particle(temp)
return assembly
def test_ccs_value(self):
"""Test the calculation of the collision cross section of a complex"""
IMP.set_log_level(IMP.TERSE)
m = IMP.Model()
fn = self.get_input_file_name("1z5s.pdb")
prot = atom.read_pdb(fn, m, atom.ATOMPDBSelector())
atom.add_radii(prot)
projections = 20
resolution = 7.0
pixel_size = 1.5
img_size = 80
ccs = em2d.CollisionCrossSection(projections, resolution, pixel_size,
img_size)
ccs.set_model_particles(IMP.atom.get_leaves(prot))
ccs_calculated = ccs.get_ccs()
ccs_value = 3838 # A**2
# good within 2%
self.assertAlmostEqual(ccs_calculated,
ccs_value,
delta=ccs_value * 0.02)
## \example em2d/collision_cross_section.py
# Example of how to compute the collision cross section of a molecule.
#
import IMP
import IMP.em2d as em2d
import IMP.atom as atom
"""
Example of how to compute the collision cross section of a molecule
"""
IMP.base.set_log_level(IMP.base.TERSE)
m = IMP.kernel.Model()
fn = em2d.get_example_path("1z5s.pdb")
prot = atom.read_pdb(fn, m, atom.ATOMPDBSelector())
atom.add_radii(prot)
projections = 20
resolution = 1.0
pixel_size = 1.5
img_size = 80
ccs = em2d.CollisionCrossSection(projections, resolution, pixel_size, img_size)
ccs.set_model_particles(IMP.atom.get_leaves(prot))
print "CCS", ccs.get_ccs(), "A**2"
## Example of how to compute the collision cross section of a molecule.
##
import IMP
import IMP.em2d as em2d
import IMP.atom as atom
"""
Example of how to compute the collision cross section of a molecule
"""
IMP.base.set_log_level(IMP.base.TERSE)
m = IMP.Model()
fn = em2d.get_example_path("1z5s.pdb")
prot = atom.read_pdb(fn, m ,atom.ATOMPDBSelector())
atom.add_radii(prot)
projections = 20
resolution = 1.0
pixel_size = 1.5
img_size = 80
ccs = em2d.CollisionCrossSection(projections, resolution, pixel_size, img_size)
ccs.set_model_particles(IMP.atom.get_leaves(prot))
print "CCS",ccs.get_ccs(),"A**2"