def process(pdb_files, nmax, rmax=50.0, fraction=0.9):
pdb_models = []
rmax_over_fraction = rmax / fraction
shift = (rmax_over_fraction, rmax_over_fraction, rmax_over_fraction)
for file in pdb_files:
mom_obj, vox_obj, ipdb = pdb2zernike.zernike_moments(
file, nmax=nmax, coef_out=False, calc_intensity=False)
pdb_rmax = vox_obj.rmax()
if (vox_obj.rmax() < rmax):
mom_obj, vox_obj, ipdb = pdb2zernike.zernike_moments(
file,
nmax=nmax,
external_rmax=rmax,
coef_out=False,
calc_intensity=False)
if (mom_obj is not None):
if (len(pdb_models) == 0):
ref_nlm_array = mom_obj.moments()
pdb_models.append(
pdb_model(mom_obj.moments().coefs(), file, pdb_rmax, ipdb))
ea = (0, 0, 0)
write_pdb(file, vox_obj, ea, shift, ipdb)
else:
mov_nlm_array = mom_obj.moments()
align_obj = fft_align.align(ref_nlm_array,
mov_nlm_array,
nmax=nmax,
refine=True)
pdb_models.append(
pdb_model(align_obj.moving_nlm.coefs(), file, pdb_rmax,
ipdb))
ea = align_obj.best_ea
write_pdb(file, vox_obj, ea, shift, ipdb)
return pdb_models
def run(args, log=sys.stdout):
params = get_input( args, master_params, "fxs_znk", banner, print_help )
if (params is None):
exit()
nmax=params.fxs_znk.nmax
lmax=params.fxs_znk.lmax
if (lmax is None): lmax=nmax
np_on_grid=params.fxs_znk.np_on_grid
filename =params.fxs_znk.pdb
output = params.fxs_znk.output
fix_dx=params.fxs_znk.fix_dx
q_array = None
if q_array is None:
q_array = params.fxs_znk.q_start + \
(params.fxs_znk.q_stop-params.fxs_znk.q_start) \
*flex.double( range(params.fxs_znk.n_step) )/(params.fxs_znk.n_step-1)
mom_obj, vox_obj, pdb = pdb2zernike.zernike_moments( filename, nmax=nmax, \
np=np_on_grid, fix_dx=fix_dx, coef_out=False, calc_intensity=True)
c_nlm = mom_obj.moments()
rmax = vox_obj.rmax()/0.9
znk_mom_variants = zernike_moment_variants( c_nlm, q_array, rmax, nmax, lmax )
out = open(output,'w')
this_blq = znk_mom_variants.get_all_blq2()
blq_data = fxs_tools.blq_data(q_array,this_blq,lmax )
blq_data.print_out(out=out)
out.close()
def run(args):
params = get_input(args, master_params, "db", banner, help)
if params is None:
exit()
path = params.db.path+"/"
nmax=params.db.nmax
np = params.db.np
fix_dx = params.db.fix_dx
prefix = params.db.prefix
files = read(path)
nlm_coefs = []
nn_coefs = []
codes = []
rmax = []
for file in files:
code = file.split('\n')[0].split('.')[0]
file = path+file
mom_obj, vox_obj, pdb = pdb2zernike.zernike_moments( file, nmax=nmax, np=np, fix_dx=fix_dx, coef_out=False, calc_intensity=False )
if(mom_obj is None):
print code, "NOT processed, please check the file"
continue
codes.append( code )
rmax.append( vox_obj.rmax() )
nlm_coefs.append( mom_obj.moments().coefs().deep_copy() )
nn_coefs.append( mom_obj.fnn().coefs().deep_copy() )
print code, "processed."
easy_pickle.dump(prefix+".nlm", nlm_coefs)
easy_pickle.dump(prefix+".nn", nn_coefs)
easy_pickle.dump(prefix+".rmax", rmax)
easy_pickle.dump(prefix+".codes", codes)
def tst(filename):
nmax = 20
np = 30
fix_dx = True
prefix = tst
q_array = flex.double(range(50)) / 100.0
mom_obj, vox_obj, pdb = pdb2zernike.zernike_moments(filename,
nmax=nmax,
np=np,
fix_dx=fix_dx,
coef_out=False,
calc_intensity=True)
c_nlm = mom_obj.moments()
rmax = vox_obj.rmax() / 0.9
znk_mom_variants = zernike_moment_variants(c_nlm, q_array, rmax, nmax)
this_blq = flex.double()
for ii in range(50):
real_coef = znk_mom_variants.get_real_coef(ii)
print q_array[ii],
for cc in real_coef:
print cc,
this_blq.append(cc)
print
def get_results( args ): # args = [path, filename, nmax, np, fix_dx]
code = args[1].split('.')[0]
file = args[0]+args[1]
nmax=args[2]
np = args[3]
fix_dx = args[4]
mom_obj, vox_obj, ipdb = pdb2zernike.zernike_moments( file, nmax=nmax, np=np, fix_dx=fix_dx, coef_out=False, calc_intensity=False )
if( mom_obj is None):
print code, "not processed, check the file"
return None
print code, "processed."
return (mom_obj.moments().coefs(), mom_obj.fnn().coefs(), code, vox_obj.rmax() )
def build_with_pdb(self, pdbfile):
mom_obj, vox_obj, pdb_inp = pdb2zernike.zernike_moments(pdbfile, nmax=self.nmax, fix_dx=True, coef_out=False, calc_intensity=False)
if( mom_obj is None):
print "The file does not have coordinate info, please check", pdbfile
else:
self.nlm_array = mom_obj.moments()
if( self.rmax is None ):
self.rmax = vox_obj.rmax() / self.fraction
self.vox_obj = vox_obj
self.pdb_inp = pdb_inp
oned_np = self.vox_obj.np()*2 + 1
self.volume = self.rmax**3.0*8.0*self.vox_obj.occupied_sites()/( oned_np**3.0 )
self.id = pdbfile.split('.')[0]