allrhos = np.array(
[denss_outputs[i][8] for i in np.arange(superargs.nmaps)])
sides = np.array([denss_outputs[i][9] for i in np.arange(superargs.nmaps)])
if superargs.ref is not None:
#allow input of reference structure
if superargs.ref.endswith('.pdb'):
refside = sides[0]
voxel = (refside / allrhos[0].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(superargs.ref)
if superargs.center:
pdb.coords -= pdb.coords.mean(axis=0)
refrho = saxs.pdb2map_gauss(pdb,
xyz=xyz,
sigma=superargs.resolution)
refrho = refrho * np.sum(allrhos[0]) / np.sum(refrho)
if superargs.ref.endswith('.mrc'):
refrho, refside = saxs.read_mrc(superargs.ref)
if superargs.enan:
print()
print(" Selecting best enantiomers...")
try:
allrhos, scores = saxs.select_best_enantiomers(
allrhos, cores=superargs.cores)
sys.exit(1)
else:
if args.ref.endswith('.pdb'):
logging.info('Center PDB reference: %s', args.center)
logging.info('PDB reference map resolution: %.2f', args.resolution)
refbasename, refext = os.path.splitext(args.ref)
refoutput = refbasename + "_centered.pdb"
refside = side
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)
refrho = saxs.pdb2map_gauss(pdb, xyz=xyz, sigma=args.resolution)
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')
side = args.side
if args.voxel is None:
voxel = side / args.nsamples
else:
voxel = args.voxel
halfside = side / 2
n = int(side / voxel)
#want n to be even for speed/memory optimization with the FFT, ideally a power of 2, but wont enforce that
if n % 2 == 1: n += 1
dx = side / 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.file)
if args.center:
pdboutput = basename + "_centered.pdb"
pdb.coords -= pdb.coords.mean(axis=0)
pdb.write(filename=pdboutput)
if args.mode == "fast":
#rho = saxs.pdb2map_gauss(pdb,xyz=xyz,sigma=args.resolution,mode="fast",eps=1e-6)
rho = saxs.pdb2map_fastgauss(pdb,
x=x,
y=y,
z=z,
sigma=args.resolution,
r=args.resolution * 2)
elif args.mode == "slow":
print("slow mode doesn't exist anymore. Use fast mode.")