def main():
from argparse import ArgumentParser, RawDescriptionHelpFormatter
headerhelp = \
'''
MTZ2NPY converts an mtz-file to numpy readable npy file.
'''
parser = ArgumentParser(formatter_class=RawDescriptionHelpFormatter,
description=headerhelp)
parser.add_argument('inpath', help='The input MTZ file.')
parser.add_argument('outpath', help='The output NPY file.')
parser.add_argument('-z',
'--gzipped',
action='store_true',
help='Compress the output.')
parser.add_argument('-f',
'--overwrite',
action='store_true',
help='Overwirte existing files.')
args = parser.parse_args()
from pymtz import read_mtz_file
print("Reading ", args.inpath, end='...', flush=True)
dataset = read_mtz_file(args.inpath)
print("done")
print("Writing ", args.outpath, end='...', flush=True)
dataset.savenpy(args.outpath,
fOverwrite=args.overwrite,
fCompressed=args.gzipped)
print("done")
def rotate_freeflag(args):
mtz = read_mtz_file(args.mtzin)
avlabels = mtz.GetLabels()
if args.free not in avlabels:
print('Column '+args.free+' not found. Check input mtz-file and test set label selection.')
print('Available columns:')
print(' '.join(avlabels))
return False
sys.stdout.write('Rotating the free flag column by %d... ' % (args.free_shift))
mtz.RotateFreeFlag(args.free, args.free_shift)
sys.stdout.write('done\n')
utils.mtzsave(mtz, args)
def rcompute(args):
mtz = read_mtz_file(args.mtzin)
if not args.dhigh:
args.dhigh = mtz.GetHighD()
avlabels = mtz.GetLabels()
if args.free not in avlabels:
print('Column '+args.free+' not found. Check input mtz-file and test set label selection.')
print('Available columns:')
print(' '.join(avlabels))
if args.fobs not in avlabels:
print('Column '+args.fobs+' not found. Check input mtz-file and Fobs label selection.')
print('Available columns:')
print(' '.join(avlabels))
if args.fcalc not in avlabels:
print('Column '+args.fcalc+' not found. Check input mtz-file and Fcalc label selection.')
print('Available columns:')
print(' '.join(avlabels))
else:
d = array(mtz.GetResolutionColumn())
fp, fc, sigf = mtz.GetReflectionColumns([args.fobs, args.fcalc, args.sigfobs])
test_index = mtz.GetTestIndex(args.free, True)
work_index = mtz.GetWorkIndex(args.free, True)
ind = (d >= args.dhigh) * isfinite(fp)
test_index = test_index[ind]
work_index = work_index[ind]
fp, fc, sigf = fp[ind], fc[ind], sigf[ind]
fpfc = fp-fc
sys.stdout.write('%9s %9s %9s %9s\n' % ('R','RWORK','RFREE','REXP'))
sys.stdout.write('%9.3f ' % (100*abs(fpfc).sum()/fp.sum()))
sys.stdout.write('%9.3f ' % (100*abs(fpfc[work_index]).sum()/fp[work_index].sum()))
sys.stdout.write('%9.3f ' % (100*abs(fpfc[test_index]).sum()/fp[test_index].sum()))
sys.stdout.write('%9.3f\n ' % (79.8*sigf.sum()/fp.sum()))
dR=(abs(fpfc)*fp.sum()-abs(fpfc).sum()*fp)/((fp.sum())**2-fp*fp.sum())
indr = argsort(dR)
Rc = 100*cumsum(abs(fpfc[indr]))/cumsum(fp[indr])
Rce = 79.8*cumsum(sigf[indr])/cumsum(fp[indr])
plot(Rc-Rce,'r')
grid()
show()
def scale_columns(args):
mtz = read_mtz_file(args.mtzin)
for label in args.cols.split(','):
mtz.ScaleColumn(label, args.scale)
utils.mtzsave(mtz, args)
def info(args):
mtz = read_mtz_file(args.mtzin)
print("Columns: "+','.join(mtz.GetLabels()))
print("Resolution range: ",mtz.GetLowD(),mtz.GetHighD())
def filter_columns(args):
mtz = read_mtz_file(args.mtzin)
for label in set(mtz.GetLabels()).difference(args.cols.split(','), ['H','K','L']):
mtz.DeleteColumn(label)
utils.mtzsave(mtz, args)
def testset(args):
mtz = read_mtz_file(args.mtzin)
sys.stdout.write('Generating the free flag column (%.1f%%)... ' % (100*args.free_fraction))
mtz.GenerateFreeFlag(args.free, args.free_fraction)
sys.stdout.write('done\n')
utils.mtzsave(mtz, args)
def main():
from argparse import ArgumentParser, RawDescriptionHelpFormatter
headerhelp = \
'''
'''
parser = ArgumentParser(formatter_class=RawDescriptionHelpFormatter,
description=headerhelp)
parser.add_argument('inpath', help='The input mTZ file.')
parser.add_argument('-n',
'--nobs-per-shell',
type=int,
default=1000,
help='Number of observations per shaell target.')
args = parser.parse_args()
from pymtz import read_mtz_file
from scipy import random, corrcoef, array, nonzero, zeros, ones
from scipy.stats import spearmanr
from matplotlib.pyplot import figure, show
print("Reading ", args.inpath, end='...', flush=True)
dataset = read_mtz_file(args.inpath)
print("done")
Nmeas = dataset.GetReflectionNumber()
print("Found %d measurements" % Nmeas)
ashes = dataset.GetHKLhash()
uniqhkl = set(ashes)
Nunq = len(uniqhkl)
Nshells = int(Nunq / args.nobs_per_shell)
Ihl, shl = array(dataset.reflections).T[nonzero([
(t in ['I', 'SIGI']) for t in dataset.GetLabels()
])[0]]
whl = 1 / shl**2
hkldict = dict.fromkeys(uniqhkl)
for (i, ash) in enumerate(ashes):
if hkldict[ash]:
hkldict[ash].append(i)
else:
hkldict[ash] = [i]
print("Found %d unique reflections" % (Nunq))
print("Will subdivide data into %d resolution shells" % Nshells)
edges = dataset.GetResolutionShells(Nshells)
shell_column = dataset.GetShellColumn(edges)
d12, cc12, sp12, p12, Ish = [], [], [], [], []
for i in range(Nshells):
Ish1, Ish2, shkl = [], [], []
shind = (shell_column == i)
for ash in set(ashes[shind]):
mcity = len(hkldict[ash])
if mcity > 1:
Nhalf = int(mcity / 2)
wr = list(ones(Nhalf)) + list(zeros(Nhalf))
if len(wr) < mcity:
wr.append(random.random_integers(0, 1))
wr = random.permutation(wr)
Ish1.append(
sum(wr * Ihl[hkldict[ash]] * whl[hkldict[ash]]) /
sum(wr * whl[hkldict[ash]]))
Ish2.append(
sum((1 - wr) * Ihl[hkldict[ash]] * whl[hkldict[ash]]) /
sum((1 - wr) * whl[hkldict[ash]]))
shkl.append(dataset.hash2hkl(ash))
cc12.append(corrcoef(Ish1, Ish2)[0][1])
sp12t, p12t = spearmanr(Ish1, Ish2)
sp12.append(sp12t)
p12.append(p12t)
Ish.append([Ish1, Ish2, shkl])
d12.append(dataset.GetResolutionColumn()[shind].mean())
print("%4d %7.2f %7.2f %7.2f %8d %5.3f %5.3f %6.3g" %
(i + 1, edges[i], edges[i + 1], d12[-1], sum(shind), cc12[-1],
sp12t, p12t))
Ish_fig = figure(FigureClass=KDWindow)
Ish_fig.set_data([Ish, array(d12), cc12, sp12])
Ish_fig.plot()
Ish_fig.canvas.mpl_connect('key_press_event', Ish_fig.onkeypress)
show()