def __init__(self, list_cif=None, another_list_cif=None, verbose=False):
if (list_cif is None):
list_cif = mon_lib_list_cif()
if (another_list_cif is None):
# get the geostd CIF links object and merge
geostd_list_cif_obj = geostd_list_cif()
list_cif = merge_and_overwrite_cifs(
geostd_list_cif_obj,
list_cif,
)
self.root_path = os.path.dirname(os.path.dirname(list_cif.path))
self.geostd_path = os.path.join(os.path.dirname(self.root_path),
"geostd")
self.deriv_list_dict = {}
self.comp_synonym_list_dict = {}
self.comp_synonym_atom_list_dict = dicts.with_default_factory(dict)
self.comp_comp_id_dict = {}
self.link_link_id_list = []
self.link_link_id_dict = {}
self.mod_mod_id_list = []
self.mod_mod_id_dict = {}
self.convert_all(source_info="file: " + list_cif.path,
cif_object=list_cif.cif,
skip_comp_list=True)
self.comp_comp_id_mod_dict = {}
self.process_geostd_rna_dna()
def analyze_redundancies(asu, n, redundancies, verbose=1):
if (len(redundancies) == 0): return
print("Overview:")
for symop, pairs in redundancies:
print(symop, ": number of redundancies:", len(pairs))
print(" ", rt_mx_analysis(sgtbx.rt_mx(symop)))
print("Details:")
for symop, pairs in redundancies:
print(symop, ": number of redundancies:", len(pairs))
print(" ", rt_mx_analysis(sgtbx.rt_mx(symop)))
all_cuts = dicts.with_default_factory(dict)
not_in_cuts = {}
for pair in pairs:
for point in pair:
cuts = asu.in_which_cuts(rational.vector(point, n))
if (len(cuts) == 0):
not_in_cuts[point] = 1
all_cuts[tuple(cuts)][point] = 1
print(" In cuts:")
for cuts, points in all_cuts.items():
print(" ", end=' ')
show_amp = False
for cut in cuts:
if (show_amp): print("&", end=' ')
print(cut, end=' ')
show_amp = True
print("#points: %d:" % len(points), end=' ')
# FIXME : ordering of keys in py2/3 is different
print(str(list(points.keys())[:4]).replace(" ", ""))
if (verbose):
print(" Pairs:")
for pair in pairs:
print(" ", pair)
if (len(not_in_cuts) > 0):
print(" Not in cuts:")
for point in not_in_cuts.keys():
print(" ", point)
raise AssertionError("Some redundant points not in any cuts.")
print()
def analyze_redundancies(asu, n, redundancies, verbose=1):
if (len(redundancies) == 0): return
print "Overview:"
for symop, pairs in redundancies:
print symop, ": number of redundancies:", len(pairs)
print " ", rt_mx_analysis(sgtbx.rt_mx(symop))
print "Details:"
for symop, pairs in redundancies:
print symop, ": number of redundancies:", len(pairs)
print " ", rt_mx_analysis(sgtbx.rt_mx(symop))
all_cuts = dicts.with_default_factory(dict)
not_in_cuts = {}
for pair in pairs:
for point in pair:
cuts = asu.in_which_cuts(rational.vector(point, n))
if (len(cuts) == 0):
not_in_cuts[point] = 1
all_cuts[tuple(cuts)][point] = 1
print " In cuts:"
for cuts, points in all_cuts.items():
print " ",
show_amp = False
for cut in cuts:
if (show_amp): print "&",
print cut,
show_amp = True
print "#points: %d:" % len(points),
print str(points.keys()[:4]).replace(" ", "")
if (verbose):
print " Pairs:"
for pair in pairs:
print " ", pair
if (len(not_in_cuts) > 0):
print " Not in cuts:"
for point in not_in_cuts.keys():
print " ", point
raise AssertionError, "Some redundant points not in any cuts."
print
def __init__(self, list_cif=None, another_list_cif=None, verbose=False):
if (list_cif is None):
list_cif = mon_lib_list_cif()
if (another_list_cif is None):
# get the geostd CIF links object and merge
geostd_list_cif_obj = geostd_list_cif()
list_cif = merge_and_overwrite_cifs(geostd_list_cif_obj,
list_cif,
)
self.root_path = os.path.dirname(os.path.dirname(list_cif.path))
self.geostd_path = os.path.join(os.path.dirname(self.root_path), "geostd")
self.deriv_list_dict = {}
self.comp_synonym_list_dict = {}
self.comp_synonym_atom_list_dict = dicts.with_default_factory(dict)
self.comp_comp_id_dict = {}
self.link_link_id_list = []
self.link_link_id_dict = {}
self.mod_mod_id_list = []
self.mod_mod_id_dict = {}
self.convert_all(
source_info="file: "+list_cif.path,
cif_object=list_cif.cif, skip_comp_list=True)
self.comp_comp_id_mod_dict = {}
self.process_geostd_rna_dna()
