def xds_to_mtz(self):
"""Use pointless to convert XDS file to MTZ."""
if not self._xdsin:
raise RuntimeError("XDSIN not set")
self.check_hklout()
# -c for copy - just convert the file to MTZ multirecord
self.add_command_line("-c")
self.start()
if self._pname and self._xname and self._dname:
self.input(
"name project %s crystal %s dataset %s"
% (self._pname, self._xname, self._dname)
)
self.input("xdsin %s" % self._xdsin)
if self._scale_factor:
Debug.write("Scaling intensities by factor %e" % self._scale_factor)
self.input("multiply %e" % self._scale_factor)
self.close_wait()
# FIXME need to check the status and so on here
if self._xdsin:
from xia2.Wrappers.XDS import XDS
XDS.add_xds_version_to_mtz_history(self.get_hklout())
def add_xds_version_to_mtz_history(mtz_file):
import time
from iotbx.reflection_file_reader import any_reflection_file
from xia2.Wrappers.XDS import XDS
reader = any_reflection_file(mtz_file)
assert reader.file_type() == 'ccp4_mtz'
mtz_object = reader.file_content()
date_str = time.strftime('%d/%m/%Y at %H:%M:%S', time.gmtime())
mtz_object.add_history('From XDS %s, run on %s' %
(XDS.get_xds_version(), date_str))
mtz_object.write(mtz_file)
def decide_spacegroup(self):
"""Given data indexed in the correct pointgroup, have a
guess at the spacegroup."""
if not self._xdsin:
self.check_hklin()
self.set_task(
"Computing the correct spacegroup for %s" % self.get_hklin()
)
else:
Debug.write("Pointless using XDS input file %s" % self._xdsin)
self.set_task(
"Computing the correct spacegroup for %s" % self.get_xdsin()
)
# FIXME this should probably be a standard CCP4 keyword
if self._xdsin:
self.add_command_line("xdsin")
self.add_command_line(self._xdsin)
self.add_command_line("xmlout")
self.add_command_line("%d_pointless.xml" % self.get_xpid())
self.add_command_line("hklout")
self.add_command_line("pointless.mtz")
self.start()
self.input("lauegroup hklin")
self.input("setting symmetry-based")
if PhilIndex.params.xia2.settings.symmetry.chirality is not None:
self.input(
"chirality %s" % PhilIndex.params.xia2.settings.symmetry.chirality
)
self.close_wait()
# check for errors
self.check_for_errors()
xml_file = os.path.join(
self.get_working_directory(), "%d_pointless.xml" % self.get_xpid()
)
mend_pointless_xml(xml_file)
if not os.path.exists(xml_file) and os.path.exists("%s.xml" % xml_file):
xml_file = "%s.xml" % xml_file
dom = xml.dom.minidom.parse(xml_file)
sg_list = dom.getElementsByTagName("SpacegroupList")[0]
sg_node = sg_list.getElementsByTagName("Spacegroup")[0]
best_prob = float(
sg_node.getElementsByTagName("TotalProb")[0].childNodes[0].data.strip()
)
# FIXME 21/NOV/06 in here record a list of valid spacegroups
# (that is, those which are as likely as the most likely)
# for later use...
self._spacegroup = (
sg_node.getElementsByTagName("SpacegroupName")[0]
.childNodes[0]
.data.strip()
)
self._spacegroup_reindex_operator = (
sg_node.getElementsByTagName("ReindexOperator")[0]
.childNodes[0]
.data.strip()
)
self._spacegroup_reindex_matrix = tuple(
map(
float,
sg_node.getElementsByTagName("ReindexMatrix")[0]
.childNodes[0]
.data.split(),
)
)
# get a list of "equally likely" spacegroups
for node in sg_list.getElementsByTagName("Spacegroup"):
prob = float(
node.getElementsByTagName("TotalProb")[0].childNodes[0].data.strip()
)
name = (
node.getElementsByTagName("SpacegroupName")[0]
.childNodes[0]
.data.strip()
)
if math.fabs(prob - best_prob) < 0.01:
# this is jolly likely!
self._likely_spacegroups.append(name)
# now parse the output looking for the unit cell information -
# this should look familiar from mtzdump
output = self.get_all_output()
length = len(output)
a = 0.0
b = 0.0
c = 0.0
alpha = 0.0
beta = 0.0
gamma = 0.0
self._cell_info["datasets"] = []
self._cell_info["dataset_info"] = {}
for i in range(length):
line = output[i][:-1]
if "Dataset ID, " in line:
block = 0
while output[block * 5 + i + 2].strip():
dataset_number = int(output[5 * block + i + 2].split()[0])
project = output[5 * block + i + 2][10:].strip()
crystal = output[5 * block + i + 3][10:].strip()
dataset = output[5 * block + i + 4][10:].strip()
cell = map(float, output[5 * block + i + 5].strip().split())
wavelength = float(output[5 * block + i + 6].strip())
dataset_id = "%s/%s/%s" % (project, crystal, dataset)
self._cell_info["datasets"].append(dataset_id)
self._cell_info["dataset_info"][dataset_id] = {}
self._cell_info["dataset_info"][dataset_id][
"wavelength"
] = wavelength
self._cell_info["dataset_info"][dataset_id]["cell"] = cell
self._cell_info["dataset_info"][dataset_id][
"id"
] = dataset_number
block += 1
for dataset in self._cell_info["datasets"]:
cell = self._cell_info["dataset_info"][dataset]["cell"]
a += cell[0]
b += cell[1]
c += cell[2]
alpha += cell[3]
beta += cell[4]
gamma += cell[5]
n = len(self._cell_info["datasets"])
self._cell = (a / n, b / n, c / n, alpha / n, beta / n, gamma / n)
if self._xdsin:
from xia2.Wrappers.XDS import XDS
XDS.add_xds_version_to_mtz_history(self.get_hklout())
return "ok"