type=str,
help="output filename prefix")
args = parser.parse_args()
if __name__ == "__main__":
if args.output is None:
basename, ext = os.path.splitext(args.file)
output = basename + "_aligned2xyz"
else:
output = args.output
logging.basicConfig(filename=output + '.log',
level=logging.INFO,
filemode='w',
format='%(asctime)s %(message)s',
datefmt='%Y-%m-%d %I:%M:%S %p')
logging.info('BEGIN')
logging.info('Script name: %s', sys.argv[0])
logging.info('DENSS Version: %s', __version__)
logging.info('Map filename(s): %s', args.file)
rho, side = saxs.read_mrc(args.file)
aligned = saxs.align2xyz(rho)
saxs.write_mrc(aligned, side, output + '.mrc')
print "%s.mrc written. " % (output, )
logging.info('END')
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')
print "%s.mrc written. " % (output, )
logging.info('END')
if superargs.enan:
print()
print(" Selecting best enantiomers...")
try:
allrhos, scores = saxs.select_best_enantiomers(
allrhos, cores=superargs.cores)
except KeyboardInterrupt:
sys.exit(1)
if superargs.ref is None:
print()
print(" Generating reference...")
try:
refrho = saxs.binary_average(allrhos, superargs.cores)
saxs.write_mrc(refrho, sides[0], output + "_reference.mrc")
except KeyboardInterrupt:
sys.exit(1)
print()
print(" Aligning all maps to reference...")
try:
aligned, scores = saxs.align_multiple(refrho, allrhos, superargs.cores)
except KeyboardInterrupt:
sys.exit(1)
#filter rhos with scores below the mean - 2*standard deviation.
mean = np.mean(scores)
std = np.std(scores)
threshold = mean - 2 * std
filtered = np.empty(len(scores), dtype=str)
nmaps = len(args.files)
rhos = []
for file in args.files:
sys.stdout.write("\r% 5i / % 5i" % (n, nmaps))
sys.stdout.flush()
n += 1
rho, side = saxs.read_mrc(file)
rhos.append(rho)
if rhosum is None:
rhosum = rho
else:
rhosum += rho
print()
rhos = np.array(rhos)
average_rho = rhosum / nmaps
saxs.write_mrc(average_rho, side, output + "_avg.mrc")
print("%s_avg.mrc written." % output)
"""
#split maps into 2 halves--> enan, align, average independently with same refrho
avg_rho1 = np.mean(aligned[::2],axis=0)
avg_rho2 = np.mean(aligned[1::2],axis=0)
fsc = saxs.calc_fsc(avg_rho1,avg_rho2,sides[0])
np.savetxt(args.output+'_fsc.dat',fsc,delimiter=" ",fmt="%.5e",header="qbins, FSC")
"""
#rather than compare two halves, average all fsc's to the reference
fscs = []
for map in range(nmaps):
fscs.append(saxs.calc_fsc(rhos[map], average_rho, side))
fscs = np.array(fscs)
fsc = np.mean(fscs, axis=0)
np.savetxt(args.output + '_fsc.dat',
else:
n = max((int(newside / vx), int(newside / vy), int(newside / vz)))
if n % 2 == 1: n += 1
newshape = (n, n, n)
rho = saxs.pad_rho(rho, newshape)
a, b, c = vx * newshape[0], vy * newshape[1], vz * newshape[2]
print "postpad"
print "Shape: ", rho.shape
print "Sides: ", a, b, c
print "Voxels: ", vx, vy, vz
#rescale map after interpolation
if args.ne is not None:
ne = args.ne
rho *= ne / np.sum(rho)
#convert to density in e-/A^3 for thresholding
rho /= vx * vy * vz
if args.threshold is not None:
rho[rho < args.threshold] = 0
rho *= ne / np.sum(rho) #rescale to the total number of electrons
rho /= vx * vy * vz #now divide by total volume to convert to electron density
print rho.sum() * vx * vy * vz
saxs.write_mrc(rho, (a, b, c), filename=output + '.mrc')
rho, side = saxs.read_mrc(args.file)
if args.ref is not None:
#allow input of reference for enantiomer selection
if args.ref.endswith('.mrc'):
refrho, refside = saxs.read_mrc(args.ref)
else:
print("Invalid reference filename given. .mrc file required")
sys.exit(1)
rho_nsamples = rho.shape[0]
rho_voxel = side / rho_nsamples
ref_nsamples = refrho.shape[0]
ref_voxel = refside / ref_nsamples
if (not np.isclose(side, refside)
or not np.isclose(rho_voxel, ref_voxel)
or not np.isclose(rho_nsamples, ref_nsamples)):
print("reference density dimensions do not match given options.")
sys.exit()
else:
print("reference file required")
sys.exit(1)
print(" Selecting best enantiomer...")
try:
best_enan, score = saxs.select_best_enantiomer(refrho=refrho, rho=rho)
saxs.write_mrc(best_enan, side, output + '.mrc')
except KeyboardInterrupt:
sys.exit(1)
F = np.fft.fftn(rho)
I3D = np.abs(F)**2
Imean = ndimage.mean(I3D,
labels=qbin_labels,
index=np.arange(0,
qbin_labels.max() + 1))
qmax_to_use = np.max(qx_)
print("qmax to use: %f" % qmax_to_use)
qbinsc_to_use = qbinsc[qbinsc < qmax_to_use]
Imean_to_use = Imean[qbinsc < qmax_to_use]
qbinsc = np.copy(qbinsc_to_use)
Imean = np.copy(Imean_to_use)
Iq = np.vstack((qbinsc, Imean, Imean * .03)).T
np.savetxt(output + '.dat', Iq, delimiter=' ', fmt='% .16e')
if args.save_mrc:
saxs.write_mrc(rho, side, output + '_mod.mrc')
if args.plot:
print('Actual dq = %.4f' % (2 * np.pi / side))
plt.plot(qbinsc_to_use,
Imean_to_use,
label='Actual dq = %.4f' % (2 * np.pi / side))
plt.semilogy()
plt.legend()
plt.show()
sides.append(side)
allrhos = np.array(allrhos)
sides = np.array(sides)
if args.ref is not None:
#allow input of reference for enantiomer selection
if args.ref.endswith('.mrc'):
refrho, refside = saxs.read_mrc(args.ref)
if (not args.ref.endswith('.mrc')):
print("Invalid reference filename given. .mrc file required")
sys.exit(1)
print(" Selecting best enantiomers...")
try:
if args.ref:
allrhos, scores = saxs.select_best_enantiomers(allrhos,
refrho=refrho,
cores=args.cores)
else:
allrhos, scores = saxs.select_best_enantiomers(allrhos,
refrho=allrhos[0],
cores=args.cores)
except KeyboardInterrupt:
sys.exit(1)
#save each selected enantiomer
for i in range(nmaps):
basename, ext = os.path.splitext(args.files[i])
ioutput = basename + "_enan"
saxs.write_mrc(allrhos[i], sides[0], ioutput + '.mrc')
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(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(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 enantiomers...")
try:
if args.ref:
allrhos, scores = saxs.select_best_enantiomers(allrhos, refrho=refrho, cores=args.cores)
else:
allrhos, scores = saxs.select_best_enantiomers(allrhos, refrho=allrhos[0], cores=args.cores)
except KeyboardInterrupt:
sys.exit(1)
basename, ext = os.path.splitext(args.files[0])
output = basename
else:
output = args.output
nmaps = len(args.files)
allrhos = []
sides = []
for file in args.files:
rho, side = saxs.read_mrc(file)
allrhos.append(rho)
sides.append(side)
allrhos = np.array(allrhos)
sides = np.array(sides)
if nmaps<2:
print("Not enough maps to generate reference. Please input more maps again...")
sys.exit(1)
print(" Generating reference...")
try:
refrho = saxs.binary_average(allrhos, args.cores)
saxs.write_mrc(refrho, sides[0], output+"_reference.mrc")
except KeyboardInterrupt:
sys.exit(1)
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.")
#not even going to bother with this version anymore. fastgauss is the
#same function as slow, so just as accurate, but it way, way faster
#rho = saxs.pdb2map_gauss(pdb,xyz=xyz,sigma=args.resolution,mode="slow")
else:
print(
"Note: Using FFT method results in severe truncation ripples in map."
)
print(
"This will also run a quick refinement of phases to attempt to clean this up."
)
rho, pdbidx = saxs.pdb2map_FFT(pdb, x=x, y=y, z=z, radii=None)
rho = saxs.denss_3DFs(rho_start=rho,
dmax=side,
voxel=dx,
oversampling=1.,
shrinkwrap=False,
support=pdbidx)
print()
saxs.write_mrc(rho, side, output + ".mrc")
