voxel = (refside / movrho.shape)[0]
halfside = refside / 2
n = int(refside / voxel)
dx = refside / n
x_ = np.linspace(-halfside, halfside, n)
x, y, z = np.meshgrid(x_, x_, x_, indexing='ij')
xyz = np.column_stack((x.ravel(), y.ravel(), z.ravel()))
pdb = saxs.PDB(args.ref)
if args.center:
pdb.coords -= pdb.coords.mean(axis=0)
pdb.write(filename=refoutput)
#use the new fastgauss function
#refrho = saxs.pdb2map_gauss(pdb,xyz=xyz,sigma=args.resolution)
refrho = saxs.pdb2map_fastgauss(pdb,
x=x,
y=y,
z=z,
sigma=args.resolution,
r=args.resolution * 2)
refrho = refrho * np.sum(movrho) / np.sum(refrho)
saxs.write_mrc(refrho, side, filename=refbasename + '_pdb.mrc')
if args.ref.endswith('.mrc'):
refrho, refside = saxs.read_mrc(args.ref)
if (not args.ref.endswith('.mrc')) and (not args.ref.endswith('.pdb')):
print(
"Invalid reference filename given. .mrc or .pdb file required")
sys.exit(1)
aligned = saxs.principal_axis_alignment(refrho, rho)
saxs.write_mrc(aligned, side, output + '.mrc')
print("%s.mrc written. " % (output, ))
halfside = refside / 2
n = int(refside / voxel)
dx = refside / n
x_ = np.linspace(-halfside, halfside, n)
x, y, z = np.meshgrid(x_, x_, x_, indexing='ij')
xyz = np.column_stack((x.ravel(), y.ravel(), z.ravel()))
pdb = saxs.PDB(args.ref)
if args.center:
pdb.coords -= pdb.coords.mean(axis=0)
pdb.write(filename=refoutput)
#use the new fastgauss function
#refrho = saxs.pdb2map_gauss(pdb,xyz=xyz,sigma=args.resolution)
refrho = saxs.pdb2map_fastgauss(pdb,
x=x,
y=y,
z=z,
sigma=args.resolution,
r=args.resolution * 2,
ignore_waters=args.ignore_waters)
refrho = refrho * np.sum(allrhos[0]) / np.sum(refrho)
saxs.write_mrc(refrho, sides[0], filename=refbasename + '_pdb.mrc')
if args.ref.endswith('.mrc'):
refrho, refside = saxs.read_mrc(args.ref)
if (not args.ref.endswith('.mrc')) and (not args.ref.endswith('.pdb')):
print(
"Invalid reference filename given. .mrc or .pdb file required")
sys.exit(1)
if args.enan:
print(" Selecting best enantiomer(s)...")
try:
