default=1,
help="Number of cores used for parallel processing. (default: 1)")
parser.set_defaults(enan=True)
parser.set_defaults(center=True)
args = parser.parse_args()
if __name__ == "__main__":
if args.output is None:
fname_nopath = os.path.basename(args.file)
basename, ext = os.path.splitext(fname_nopath)
output = basename + "_enan"
else:
output = args.output
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)
import sys, argparse, os
import logging
parser = argparse.ArgumentParser(
description=
"DENSS: DENsity from Solution Scattering.\n A tool for calculating an electron density map from solution scattering data",
formatter_class=argparse.RawTextHelpFormatter)
args = dopts.parse_arguments(parser)
if args.rho_start is None:
print(
" denss.refine.py requires a .mrc file to be given to the --rho_start option."
)
sys.exit()
args.rho_start, rho_side = saxs.read_mrc(args.rho_start)
rho_nsamples = args.rho_start.shape[0]
rho_voxel = rho_side / rho_nsamples
args.side = args.dmax * args.oversampling
if (not np.isclose(rho_side, args.side)
or not np.isclose(rho_voxel, args.voxel)
or not np.isclose(rho_nsamples, args.nsamples)):
print("rho_start density dimensions do not match given options.")
print(
"Oversampling and voxel size adjusted to match rho_start dimensions.")
args.voxel = rho_voxel
args.oversampling = rho_side / args.dmax
format='%(asctime)s %(message)s',
datefmt='%Y-%m-%d %I:%M:%S %p')
logging.info('BEGIN')
logging.info('Command: %s', ' '.join(sys.argv))
#logging.info('Script name: %s', sys.argv[0])
logging.info('DENSS Version: %s', __version__)
rhosum = None
n = 1
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])
help="Desired number of electrons in map.")
parser.add_argument("-o",
"--output",
default=None,
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 + '_resampled'
else:
output = args.output
rho, (a, b, c) = saxs.read_mrc(args.file, returnABC=True)
ne = np.sum(rho)
vx, vy, vz = np.array((a, b, c)) / np.array(rho.shape)
#print vx, vy, vz
if args.voxel is None:
voxel = min((vx, vy, vz))
else:
voxel = args.voxel
print "prezoom"
print "Shape: ", rho.shape
print "Sides: ", a, b, c
print "Voxels: ", vx, vy, vz
rho = saxs.zoom_rho(rho, (vx, vy, vz), voxel)
#if plotting is enabled, try to import matplotlib
#if import fails, set plotting to false
try:
import matplotlib.pyplot as plt
except ImportError:
args.plot = False
if __name__ == "__main__":
if args.output is None:
basename, ext = os.path.splitext(args.file)
output = basename + '_rho'
else:
output = args.output
rho, side = saxs.read_mrc(args.file)
if rho.shape[0] % 2 == 1:
rho = rho[:-1, :-1, :-1]
#if nstmp%2==1: args.ns+=1
rho = np.copy(rho[::args.ns, ::args.ns, ::args.ns])
if args.threshold is not None:
rho[np.abs(rho) <= args.threshold] = 0
halfside = side / 2
nx, ny, nz = rho.shape[0], rho.shape[1], rho.shape[2]
n = nx
voxel = side / n
#want n to be even for speed/memory optimization with the FFT, ideally a power of 2, but wont enforce that
#store n for later use if needed
n_orig = n
dx = side / n
dV = dx**3
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)
except KeyboardInterrupt:
sys.exit(1)
if superargs.ref is None:
print
print " Generating reference..."
try:
refrho = saxs.binary_average(allrhos, superargs.cores)