def get_formula_dict(self):
"""returns formula as dictionary that can
be passed to functions in periodic_table"""
ret = PT.formula_dict(self.symbol)
if self.free_valency + self.explicit_hydrogens > 0:
ret['H'] = self.free_valency + self.explicit_hydrogens
return ret
def get_formula_dict( self):
"""returns formula as dictionary that can
be passed to functions in periodic_table"""
ret = PT.formula_dict( self.symbol)
if self.free_valency + self.explicit_hydrogens > 0:
ret['H'] = self.free_valency + self.explicit_hydrogens
return ret
def read_sum_layer( self):
if "." in self.layers[1]:
raise oasa_not_implemented_error( "INChI", "multiple compound systems are not supported by the library")
form = pt.formula_dict( self.layers[1])
processed_hs = 0 #for diborane and similar compounds we must process some Hs here
j = 0
for k in form.sorted_keys():
for i in range( form[k]):
if k == 'H':
# we want to process only the Hs that are not in the h-layer
if processed_hs >= form[k] - self.hs_in_hydrogen_layer:
continue
else:
processed_hs += 1
j += 1
a = self.structure.create_vertex()
a.symbol = k
self.structure.add_vertex( a)
a.properties_['inchi_number'] = j
def read_sum_layer(self):
if "." in self.layers[1]:
raise oasa_not_implemented_error(
"INChI",
"multiple compound systems are not supported by the library")
form = pt.formula_dict(self.layers[1])
processed_hs = 0 #for diborane and similar compounds we must process some Hs here
j = 0
for k in form.sorted_keys():
for i in range(form[k]):
if k == 'H':
# we want to process only the Hs that are not in the h-layer
if processed_hs >= form[k] - self.hs_in_hydrogen_layer:
continue
else:
processed_hs += 1
j += 1
a = self.structure.create_vertex()
a.symbol = k
self.structure.add_vertex(a)
a.properties_['inchi_number'] = j
def get_formula_dict(self):
"""returns a formula dict as defined in the periodic_table.py::formula_dict"""
comp = PT.formula_dict()
for a in self.atoms:
comp += a.get_formula_dict()
return comp
def get_formula_dict( self):
"""returns a formula dict as defined in the periodic_table.py::formula_dict"""
comp = PT.formula_dict()
for a in self.atoms:
comp += a.get_formula_dict()
return comp
