import IMP
import IMP.em2d as em2d
import os
"""
Conversion of Electron Microscopy Images.
"""
# Read images
fn_selection=em2d.get_example_path("all-1z5s-projections.sel")
srw = em2d.SpiderImageReaderWriter()
trw = em2d.TIFFImageReaderWriter()
fn_images=em2d.read_selection_file(fn_selection)
fn_images = [em2d.get_example_path(x) for x in fn_images]
images = em2d.read_images(fn_images,srw)
# write
fn_saved=em2d.create_filenames(3,"1z5s-projection","tif")
em2d.save_images(images,fn_saved,trw)
## \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"
self.count=0
o=self.get_optimizer()
m=o.get_model()
m.show_restraint_score_statistics()
m.show_all_statistics()
#for i in range(0,m.get_number_of_restraints()):
# r=m.get_restraint(i)
# print "restraint",r.get_name(),"value",r.evaluate(False)
def do_show(self, stream):
print >> stream, ps
# Get model from PDB file
IMP.base.set_log_level(IMP.base.TERSE)
m = IMP.Model()
prot = atom.read_pdb(em2d.get_example_path("1z5s.pdb"),m,atom.ATOMPDBSelector())
atom.add_radii(prot)
# get the chains
chains = atom.get_by_type(prot,atom.CHAIN_TYPE)
print "there are",len(chains),"chains in 1z5s.pdb"
# set the chains as rigid bodies
native_chain_centers = []
rigid_bodies= []
for c in chains:
atoms=core.get_leaves(c)
rbd=core.RigidBody.setup_particle(c,atoms)
rigid_bodies.append(rbd)
print "chain has",rbd.get_number_of_members(), \
"atoms","coordinates: ",rbd.get_coordinates()
where min_index is the index of the minimum value
"""
min_value = sequence[0]
min_index = 0
for i in range(0,len(sequence)):
# print "argmin - checking ",sequence[i]
if(sequence[i]<min_value):
min_value = sequence[i]
min_index =i
# print "argmin - selecting ",min_value,min_index
return min_value,min_index
#***************************
fn_selection = em2d.get_example_path("all-models-1z5s.sel")
fn_em2d_scores = em2d.get_example_path("em2d_scores_for_clustering.data")
# Load models
print "Reading models ..."
model = IMP.Model()
ssel = atom.ATOMPDBSelector()
coords =[]
fn_models = em2d.read_selection_file(fn_selection)
n_models = len(fn_models)
hierarchies=[]
for fn in fn_models:
fn_model=em2d.get_example_path(fn)
h=atom.read_pdb(fn_model,model,ssel,True)
hierarchies.append(h)
xyz=core.XYZs(atom.get_leaves(h))
coords.append( [x.get_coordinates() for x in xyz])
## \example em2d/em_images_conversion.py
# Conversion of Electron Microscopy Images.
#
import IMP
import IMP.em2d as em2d
import os
"""
Conversion of Electron Microscopy Images.
"""
# Read images
fn_selection = em2d.get_example_path("all-1z5s-projections.sel")
srw = em2d.SpiderImageReaderWriter()
trw = em2d.TIFFImageReaderWriter()
fn_images = em2d.read_selection_file(fn_selection)
fn_images = [em2d.get_example_path(x) for x in fn_images]
images = em2d.read_images(fn_images, srw)
# write
fn_saved = em2d.create_filenames(3, "1z5s-projection", "tif")
em2d.save_images(images, fn_saved, trw)
