def copy_cifs(self, target_folder):
"""Copy cif files from their existing location to the specified
target_folder.
:param target_folder: Path of folder to copy collection CIF files to.
"""
if target_folder is None:
return
tf_abspath = os.path.abspath(target_folder)
Helper.make_folder(tf_abspath)
print(self.separator)
print('The cif files for this collection will be copied to'
' the specified folder:\n\"{}\"'.format(tf_abspath))
print('The cif paths will be updated.')
for i, mi in enumerate(list(self.mof_coll)):
destination_path = "{}/{}.cif".format(tf_abspath, mi['mof_name'])
self.mof_coll[i] = {
"mof_name": mi['mof_name'],
"mof_file": destination_path,
"checksum": mi['checksum']
}
if not os.path.isfile(destination_path):
shutil.copyfile(mi['mof_file'], destination_path)
print(self.separator)
def summarize_tfactors(self):
"""Summarize the t-factor information and make histograms for all the
MOFs in the collection.
"""
tfac_analysis_folder = self.summary_folder + '/tfac_analysis'
Helper.make_folder(self.summary_folder)
Helper.make_folder(tfac_analysis_folder)
df = self.metal_site_df.copy()
sites_u = df[df['unique']]
for n in range(4, 7):
self._write_t_factors(sites_u, n, tfac_analysis_folder)
def _load_mofs(self):
"""Add MOfs to collection, use CIF file checksum as an identifier."""
print('Loading CIF files...')
li = max(int(len(self.path_list) / 1000), 1)
lm = len(self.path_list) / 100.0
for i, mof_file in enumerate(self.path_list):
if i % li == 0:
print("{:4.1f} %".format((i + 1) / lm), end="\r", flush=True)
checksum = Helper.get_checksum(mof_file)
mof_name = os.path.splitext(os.path.basename(mof_file))[0]
mof_info = {
"mof_name": mof_name,
"mof_file": mof_file,
"checksum": checksum
}
self.mof_coll.append(mof_info)
if checksum not in self.properties:
self.properties[checksum] = {"mof_name": mof_name}
else:
if self.properties[checksum]["mof_name"] != mof_name:
exit("MOF name and CIF checksum mismatch for {}.cif "
"{}.cif. Either the CIF files has already been "
"processed with a different name, or the CIF file "
"has changed since it was processed."
"".format(mof_name,
self.properties[checksum]['mof_name']))
if self._check_if_results_exist(mof_name):
self._compare_checksums(mof_file, mof_name, checksum)
print("\nAll Done.")
self._store_properties()
def copy_results(self, target_folder):
"""Copy OMS result files from their existing location to the specified
target_folder.
:param target_folder: Path of folder to copy collection OMS result
files to.
"""
if target_folder is None:
return
print(self.separator)
tf_abspath = os.path.abspath(target_folder)
destination_path = tf_abspath + '/oms_results'
print('The result files for this collection will be copied to the '
'specified folder:\n{}\nThe analysis folder will be updated.'
''.format(tf_abspath))
Helper.make_folder(tf_abspath)
Helper.make_folder(destination_path)
for i, mi in enumerate(self.mof_coll):
mof_name = mi['mof_name']
if self._check_if_results_exist(mof_name):
source_path = "{}/{}".format(self.oms_results_folder, mof_name)
Helper.copy_folder(destination_path, source_path)
self.analysis_folder = tf_abspath
self._validate_properties(['has_oms'])
print(self.separator)
def summary_folder(self):
"""Get value of the summary folder."""
sf = self.analysis_folder + '/summary'
Helper.make_folder(sf)
return sf
def oms_results_folder(self):
"""Get value of the OMS results folder."""
orf = self.analysis_folder + '/oms_results'
Helper.make_folder(orf)
return orf
def analysis_folder(self):
"""Get value of the analysis folder."""
Helper.make_folder(self._analysis_folder)
return self._analysis_folder