def get_moments_for_scaled_model(map, np_on_grid, grid, nmax, rmax,
external_rmax):
### default params for moments calculation ###
splat_range = 1
uniform = True
fix_dx = False
default_dx = 0.7
fraction = 0.9
### end of default params for moments calculation ###
#threshold = flex.max( map )/3.0
threshold = map.standard_deviation_of_the_sample()
select = flex.bool(map.as_1d() >= threshold)
xyz = grid.select(select)
xyz_norms = xyz.norms()
select = flex.bool(xyz_norms <= rmax)
xyz = xyz.select(select)
density = flex.double(xyz.size(), 1.0)
vox_obj = math.sphere_voxel(np_on_grid, splat_range, uniform, fix_dx,
external_rmax, default_dx, fraction, xyz,
density)
grid_obj = math.sphere_grid(np_on_grid, nmax)
grid_obj.clean_space(vox_obj, False)
grid_obj.construct_space_sum()
moment_obj = math.zernike_moments(grid_obj, nmax)
nlm_array = moment_obj.moments()
return nlm_array.coefs()
def tst_voxel(nmax, np):
splat_range = 1
fraction = 0.9
default_dx = 0.7
external_rmax = -1.0
uniform = True
adjust_dx = False
centering = False
xyz = makexyz()
density=flex.double(xyz.size(),1.0)
voxel_obj = math.sphere_voxel(np,splat_range,uniform,adjust_dx,external_rmax,default_dx, fraction,xyz,density)
assert voxel_obj.np() == np
assert abs(voxel_obj.rmax() - 25)<1e-4
assert voxel_obj.occupied_sites() == 162
info = voxel_obj.status()
expect_info = """number of grid point is: 68921
rmax is : 25.00000000
max fraction one 1-d is: 0.90000000
non-empty grid point is: 162
non-empty grid fract is: 0.00235052
"""
assert info == expect_info
new_xyz = voxel_obj.xyz()
for xxx, yyy in zip(xyz, new_xyz):
for x1, x2 in zip(xxx, yyy):
assert x1 == x2
return voxel_obj
def zernike_moments(pdbfile,
nmax=20,
fix_dx=False,
np_on_grid=15,
shift=False,
buildmap=False,
coef_out=True,
calc_intensity=True,
external_rmax=-1):
base = pdbfile.split('.')[0]
splat_range = 0
fraction = 0.9
default_dx = 0.7
uniform = True
pdbi = pdb.hierarchy.input(file_name=pdbfile)
if (len(pdbi.hierarchy.models()) == 0):
return None, None, None
atoms = pdbi.hierarchy.models()[0].atoms()
# predefine some arrays we will need
atom_types = flex.std_string()
radius = flex.double()
b_values = flex.double()
occs = flex.double()
xyz = flex.vec3_double()
# keep track of the atom types we have encountered
for atom in atoms:
if (not atom.hetero):
xyz.append(atom.xyz)
# b_values.append( atom.b )
# occs.append( atom.occ )
if (xyz.size() == 0):
return None, None, None
density = flex.double(xyz.size(), 1.0)
voxel_obj = math.sphere_voxel(np_on_grid, splat_range, uniform, fix_dx,
external_rmax, default_dx, fraction, xyz,
density)
np = voxel_obj.np()
print 'np', np
rmax = voxel_obj.rmax() / fraction
print 'rmax', rmax
#print base, "RMAX: ", voxel_obj.rmax()
original_map = voxel_obj.map()
rmax = np
#ccp4_map_type( original_map, np, rmax, file_name=base+'_pdb.ccp4')
cube = write_bead(original_map, np)
return cube
####### The following will be optional ###
if (shift):
shift = [rmax, rmax, rmax]
centered_xyz = voxel_obj.xyz() + shift
out_pdb_name = base + '_centered.pdb'
for a, xyz in zip(atoms, centered_xyz):
a.set_xyz(new_xyz=xyz)
pdbi.hierarchy.write_pdb_file(file_name=out_pdb_name,
open_append=False)
def zernike_moments(pdbfile,
nmax=20,
np=50,
fix_dx=False,
np_on_grid=20,
shift=False,
buildmap=False,
coef_out=True,
calc_intensity=True,
external_rmax=-1):
base = pdbfile.split('.')[0]
splat_range = 0
fraction = 0.9
default_dx = 0.7
uniform = True
pdbi = pdb.hierarchy.input(file_name=pdbfile)
# pdbi = iotbx.pdb.hierarchy.input(pdb_string='''ATOM 1 N ASP A 37 10.710 14.456 9.568 1.00 15.78 N''')
if (len(pdbi.hierarchy.models()) == 0):
return None, None, None
atoms = pdbi.hierarchy.models()[0].atoms()
# predefine some arrays we will need
atom_types = flex.std_string()
radius = flex.double()
b_values = flex.double()
occs = flex.double()
# xyz = flex.vec3_double()
xyz = get_xyz_using_split(pdbfile)
# keep track of the atom types we have encountered
# for atom in atoms:
# print"---==================atom=================---",atom.xyz
# if(not atom.hetero):
# xyz.append( atom.xyz )
# b_values.append( atom.b )
# occs.append( atom.occ )
#print time.time()
if (xyz.size() == 0):
return None, None, None
density = flex.double(xyz.size(), 1.0)
voxel_obj = math.sphere_voxel(np, splat_range, uniform, fix_dx,
external_rmax, default_dx, fraction, xyz,
density)
np = voxel_obj.np()
# print "*********************voxel_obj.rmax(): ",voxel_obj.rmax()
rmax = voxel_obj.rmax() / fraction
# print "*********************fraction: ",fraction
# print "*********************rmax=voxel_obj.rmax()/fraction: ",rmax
#print base, "RMAX: ", voxel_obj.rmax()
#print time.time()
grid_obj = math.sphere_grid(np, nmax)
pdb_out = False
grid_obj.clean_space(voxel_obj, pdb_out)
#print time.time(), "END GRID CONST"
grid_obj.construct_space_sum()
#print time.time(), "SS CALC"
mom_obj = math.zernike_moments(grid_obj, nmax)
#print time.time(), "END MOM CALC"
moments = mom_obj.moments()
if (coef_out):
nn = mom_obj.fnn()
easy_pickle.dump(base + '.nlm.pickle', moments.coefs())
easy_pickle.dump(base + '.nn.pickle', nn.coefs())
#
####### The following will be optional ###
if (shift):
shift = [rmax, rmax, rmax]
centered_xyz = voxel_obj.xyz() + shift
out_pdb_name = base + '_centered.pdb'
for a, xyz in zip(atoms, centered_xyz):
a.set_xyz(new_xyz=xyz)
pdbi.hierarchy.write_pdb_file(file_name=out_pdb_name,
open_append=False)
original_map = voxel_obj.map()
xplor_map_type(original_map, np, rmax, file_name=base + '_pdb.xplor')
######## Calculate Intnesity Profile ############
if (calc_intensity):
q_array = flex.double(range(51)) / 100.0
z_model = zm.zernike_model(moments, q_array, rmax, nmax)
nn = mom_obj.fnn()
intensity = z_model.calc_intensity(nn)
#iq_file = open(base+"_"+str(nmax)+"_"+str(int(rmax*fraction))+".zi", 'w')
iq_file = open(base + "_" + str(nmax) + ".zi", 'w')
for qq, ii in zip(q_array, intensity):
print >> iq_file, qq, ii
iq_file.close()
####### END of Intensity Calculation ###########
if (buildmap):
print("grid setting up...")
zga = math.zernike_grid(np_on_grid, nmax, False)
print("grid setting up...Done")
zga.load_coefs(moments.nlm(), moments.coefs())
print("start reconstruction")
map = flex.abs(zga.f())
print("finished reconstruction")
xplor_map_type(map, np_on_grid, rmax, file_name=base + '.xplor')
ccp4_map_type(map, np_on_grid, rmax, file_name=base + '.ccp4')
return mom_obj, voxel_obj, pdbi
def zernike_moments(mol2_file, nmax=20, np=50, uniform=True, fix_dx=False, np_on_grid=20, shift=False, buildmap=False, coef_out=True, calc_intensity=True, external_rmax=-1):
base = mol2_file.split('.')[0]
splat_range = 0
fraction = 0.9
default_dx = 0.5
models = mol2.read_Mol2_file( mol2_file )
if(len( models )== 0):
return None,None,None
## for testing purpose, here only the first model in the mol2 file is converted ##
this_molecule = models[0]
## models should be a list of molecules, same ligand at different conformations ##
all_atoms = this_molecule.atom_list
if(len( all_atoms )== 0):
return None,None,None
# predefine some arrays we will need
xyz = flex.vec3_double()
charges = flex.double()
# keep track of the atom types we have encountered
for atom in all_atoms:
xyz.append( ( atom.X, atom.Y, atom.Z ) )
charges.append( atom.Q )
if(xyz.size() == 0):
return None,None,None
if (uniform):
density=flex.double(xyz.size(),1.0)
else: # use charges
density=charges
voxel_obj = math.sphere_voxel(np,splat_range,uniform,fix_dx,external_rmax, default_dx, fraction,xyz,density)
np = voxel_obj.np()
rmax=voxel_obj.rmax()/fraction
#print base, "RMAX: ", voxel_obj.rmax()
#print time.time()
grid_obj = math.sphere_grid(np, nmax)
pdb_out = False
grid_obj.clean_space(voxel_obj, pdb_out)
#print time.time(), "END GRID CONST"
grid_obj.construct_space_sum()
#print time.time(), "SS CALC"
mom_obj = math.zernike_moments(grid_obj, nmax)
#print time.time(), "END MOM CALC"
moments = mom_obj.moments()
if(coef_out):
nn = mom_obj.fnn()
easy_pickle.dump(base+'.nlm.pickle', moments.coefs() )
easy_pickle.dump(base+'.nn.pickle', nn.coefs() )
#
####### The following will be optional ###
if(shift):
shift = [rmax, rmax, rmax]
centered_xyz = voxel_obj.xyz() + shift
out_mol2_filename =base+'_centered.mol2'
for a,xyz in zip( all_atoms, centered_xyz):
a.X = xyz[0]
a.Y = xyz[1]
a.Z = xyz[2]
mol2.write_mol2( this_molecule, out_mol2_filename )
original_map = voxel_obj.map()
xplor_map_type( original_map, np, rmax, file_name=base+'_pdb.xplor')
######## Calculate Intnesity Profile ############
if(calc_intensity):
q_array = flex.double( range(51) )/100.0
z_model = zm.zernike_model( moments, q_array, rmax, nmax)
nn = mom_obj.fnn()
intensity = z_model.calc_intensity(nn)
#iq_file = open(base+"_"+str(nmax)+"_"+str(int(rmax*fraction))+".zi", 'w')
iq_file = open(base+"_"+str(nmax)+".zi", 'w')
for qq, ii in zip(q_array, intensity):
print>>iq_file, qq,ii
iq_file.close()
####### END of Intensity Calculation ###########
if(buildmap):
print "grid setting up..."
zga = math.zernike_grid(np_on_grid, nmax, False)
print "grid setting up...Done"
zga.load_coefs(moments.nlm(), moments.coefs() )
print "start reconstruction"
map=flex.abs(zga.f() )
print "finished reconstruction"
xplor_map_type( map, np_on_grid, rmax, file_name=base+'.xplor')
ccp4_map_type( map, np_on_grid, rmax, file_name=base+'.ccp4' )
return mom_obj, voxel_obj, models
def calc_mom(self,
np,
splat_range,
uniform,
fix_dx,
default_dx,
fraction,
pdb_out=False):
if (self.xyz.size() == 0):
print "no atom found, double check the model"
return
self.voxel_obj = math.sphere_voxel(np, splat_range + self.layer_thick,
uniform, fix_dx, self.external_rmax,
default_dx, fraction, self.xyz,
self.density)
self.volume_unit = self.default_dx**3.0
self.total_volume = self.voxel_obj.occupied_sites() * self.volume_unit
np = self.voxel_obj.np()
self.rmax = self.voxel_obj.rmax() / fraction
dx_used = self.rmax / np
new_layer_thick = int(self.rmax * (1 - fraction) / dx_used) - 1
if (new_layer_thick < self.layer_thick):
print "solvent layer extended too much, and thickness is reset to ", new_layer_thick
self.layer_thick = new_layer_thick
self.grid_obj = math.sphere_grid(np, self.nmax)
## displaced solvent ##
border_list = self.voxel_obj.border(self.layer_thick -
1) ## only inner section left now
inner_sites = self.voxel_obj.occupied_sites()
self.grid_obj.clean_space(self.voxel_obj, pdb_out)
self.grid_obj.construct_space_sum()
self.mom_obj_s = math.zernike_moments(self.grid_obj, self.nmax)
self.zernike_mom_s = self.mom_obj_s.moments()
## protein ##
self.voxel_obj = math.sphere_voxel(np, splat_range, uniform, fix_dx,
self.external_rmax, default_dx,
fraction, self.xyz, self.density)
real_inner_sites = self.voxel_obj.occupied_sites()
self.grid_obj.clean_space(self.voxel_obj, pdb_out) ## output protein
self.grid_obj.construct_space_sum()
self.mom_obj_p = math.zernike_moments(self.grid_obj, self.nmax)
self.zernike_mom_p = self.mom_obj_p.moments()
## border layer ##
self.inner_volume = inner_sites * self.volume_unit
self.grid_obj.construct_space_sum_via_list(border_list)
self.mom_obj_b = math.zernike_moments(self.grid_obj, self.nmax)
self.zernike_mom_b = self.mom_obj_b.moments()
## scale the densities ##
self.density_scale = self.voxel_obj.weight_sum()
print self.density_scale
#self.density_scale=float(real_inner_sites)/inner_sites
self.sol_layer = self.sol_layer / self.density_scale
#self.solvent = self.solvent*self.density_scale
##self.protein=self.protein*(1.0+0.1*smath.exp(-inner_sites/134000.0) )
### adding moment vectors ##
self.zernike_mom_coef = self.zernike_mom_p.coefs(
) * self.protein #-self.solvent)
self.zernike_mom_coef -= self.zernike_mom_s.coefs() * self.solvent
self.zernike_mom_coef += self.zernike_mom_b.coefs() * self.sol_layer
self.nlm = self.zernike_mom.nlm()
self.zernike_mom.load_coefs(self.nlm, self.zernike_mom_coef)
return