def determine_extent(numpy_in, tolerance):
"""Reads numpy array, determines the extent of the electron density
Parameters:
numpy_in -- a numpy array containing grid points
tolerance -- number of points in a plane with value greater than 1 sigma
Returns:
a vector of grid indices: (min_u, max_u, min_v, max_v, min_w, max_w)"""
log_string = ''
min = clipper.Coord_orth()
max = clipper.Coord_orth()
map_mean = numpy.mean(map_numpy)
map_std = numpy.std(map_numpy)
mask = map_numpy > map_mean + map_std
sum_u = sum(sum(mask))
sum_w = sum(sum(numpy.transpose(mask)))
sum_v = sum(numpy.transpose(sum(mask)))
log_string += '\n >> dumping 1D summaries of the map\'s content:\n\n >> U:\n %s\n' % sum_u
log_string += '\n >> V:\n %s\n' % sum_v
log_string += '\n >> W:\n %s\n' % sum_w
point_list = []
for idx_u, val_u in enumerate(sum_u):
if val_u > tolerance:
point_list.append(idx_u)
min_u = point_list[0]
max_u = point_list[-1]
log_string += '\n >> First meaningful U: %i ; Last meaningful U: %i' % (
min_u, max_u)
point_list = []
for idx_v, val_v in enumerate(sum_v):
if val_v > tolerance:
point_list.append(idx_v)
min_v = point_list[0]
max_v = point_list[-1]
log_string += '\n >> First meaningful V: %i ; Last meaningful V: %i' % (
min_v, max_v)
point_list = []
for idx_w, val_w in enumerate(sum_w):
if val_w > tolerance:
point_list.append(idx_w)
min_w = point_list[0]
max_w = point_list[-1]
log_string += '\n >> First meaningful W: %i ; Last meaningful W: %i\n' % (
min_w, max_w)
extent = [min_u, max_u, min_v, max_v, min_w, max_w]
return extent, log_string
def atom_kicks(mmol=None, amplitude=0.0, frequency=0.0):
log_string = "\n >> clipper_tools: atom_kicks"
log_string += "\n amplitude: %f" % amplitude
log_string += "\n frequency: %f" % frequency
xml_root = etree.Element('atom_kicks')
xml_root.attrib['amplitude'] = str(amplitude)
xml_root.attrib['frequency'] = str(frequency)
if mmol is None:
log_string += "\n ERROR: no valid molecule object supplied\n\n"
log_string += "\n << atom_kicks has finished\n"
xml_root.attrib['ok'] = 'no'
return log_string, xml_root
if amplitude == 0.0 or frequency == 0.0:
log_string += "\n ERROR: cannot compute kicks with zero amplitude and/or frequency\n\n"
log_string += "\n << atom_kicks has finished\n"
xml_root.attrib['ok'] = 'no'
return log_string, xml_root
if frequency < 0.0 or frequency > 100.0:
log_string += "\n ERROR: frequency is not in the (0,100] range\n\n"
log_string += "\n << atom_kicks has finished\n"
xml_root.attrib['ok'] = 'no'
return log_string, xml_root
import random
model = mmol.model()
kicked = not_kicked = 0
for chain in model:
for residue in chain:
for atom in residue:
if random.uniform(0.0, 100.0) < frequency:
sign = random.choice([-1, 1])
x = atom.coord_orth().x() + sign * random.uniform(
0.01, amplitude)
sign = random.choice([-1, 1])
y = atom.coord_orth().y() + sign * random.uniform(
0.01, amplitude)
sign = random.choice([-1, 1])
z = atom.coord_orth().z() + sign * random.uniform(
0.01, amplitude)
coords = clipper.Coord_orth(x, y, z)
atom.set_coord_orth(coords)
kicked += 1
else:
not_kicked += 1
log_string += "\n %i atoms have been kicked, while %i remain in their original positions" % (
kicked, not_kicked)
log_string += "\n That means %f percent of the atoms have been kicked" % (
(kicked / (kicked + not_kicked)) * 100.0)
log_string += "\n << atom_kicks has finished\n"
xml_root.attrib['ok'] = 'yes'
return log_string, xml_root
at = clipper.Atom()
at.set_element("H")
# Do not know why this is necessary.
print clipper.ClipperStringAsString(at.element())
stats = clipper.Map_stats(xmap)
print stats.mean(), stats.min(), stats.max(), stats.std_dev()
# Range is unwrapped memory leak, but Range<double> and Range<float> are OK, but require specialized methods.
# There may be a better way, but this works!
print stats.range_double().max()
print stats.range_double().min()
print stats.range_double().contains(0)
print stats.range_double().contains(100)
c1 = clipper.Coord_orth(1, 2, 3)
c2 = clipper.Coord_orth(10, 10, 10)
c = c1 + c2
cm = -c
print c.x(), c.y(), c.z()
print cm.x(), cm.y(), cm.z()
cif = clipper.CIFfile()
mydata = clipper.HKL_info()
if len(sys.argv) > 2:
cif.open_read(sys.argv[2])
cif.import_hkl_info(mydata)
print dir(mydata)
stats = clipper._clipper.Map_stats(xmap)
print ('Stats from clipper::Map_stats:')
print (stats.mean(), stats.min(),stats.max(),stats.std_dev())
print ('Stats from Xmap.stats:')
print (xmap.mean, xmap.min, xmap.max, xmap.sigma)
# Range is unwrapped memory leak, but Range<double> and Range<float> are OK, but require specialized methods.
# There may be a better way, but this works!
print (stats.range().max())
print (stats.range().min())
print (0 in stats.range())
print (100 in stats.range())
c1 = clipper.Coord_orth([1,2,3])
c2 = clipper.Coord_orth([10,10,10])
c = c1+c2
cm = -c
print c.xyz
print cm.xyz
cif = clipper.CIFfile()
mydata = clipper.HKL_info()
fphi1 = clipper._clipper.HKL_data_F_phi_double(mydata)
fphi2 = clipper._clipper.HKL_data_F_phi_double(mydata)
fphi3 = fphi1.copy()