def get_smiles( self, mol):
if not mol.is_connected():
raise oasa_exceptions.oasa_not_implemented_error( "SMILES", "Cannot encode disconnected compounds, such as salts etc. HINT - use molecule.get_disconnected_subgraphs() to divide the molecule to individual parts.")
#mol = molec.copy()
self.molecule = mol
self.ring_joins = []
self._processed_atoms = []
self.branches = {}
self._stereo_bonds_to_code = {} # for bond it will contain character it uses
self._stereo_bonds_to_others = {} # for bond it will contain the other bonds
self._stereo_centers = {}
# at first we mark all the atoms with aromatic bonds
# it is much simple to do it now when all the edges are present
# we can make use of the properties attribute of the vertex
for e in mol.edges:
if e.aromatic:
for v in e.vertices:
v.properties_[ 'aromatic'] = 1
# stereochemistry information preparation
for st in mol.stereochemistry:
if isinstance( st, stereochemistry.cis_trans_stereochemistry):
end1, inside1, inside2, end2 = st.references
e1 = end1.get_edge_leading_to( inside1)
e2 = end2.get_edge_leading_to( inside2)
self._stereo_bonds_to_others[ e1] = self._stereo_bonds_to_others.get( e1, []) + [(e2, st)]
self._stereo_bonds_to_others[ e2] = self._stereo_bonds_to_others.get( e2, []) + [(e1, st)]
elif isinstance( st, stereochemistry.tetrahedral_stereochemistry):
self._stereo_centers[st.center] = st
else:
pass # we cannot handle this
ret = ''.join( [i for i in self._get_smiles( mol)])
mol.reconnect_temporarily_disconnected_edges()
# this is needed because the way temporarily_disconnected edges are handled is not compatible with the way smiles
# generation works - it splits the molecule while reusing the same atoms and bonds and thus disconnected bonds accounting fails
for e in mol.edges:
e.disconnected = False
# here tetrahedral stereochemistry is added
for v, st in self._stereo_centers.iteritems():
processed_neighbors = []
for n in self._processed_atoms:
if n in v.neighbors:
processed_neighbors.append( n)
elif v.explicit_hydrogens and n is v:
processed_neighbors.append( stereochemistry.explicit_hydrogen())
count = match_atom_lists( st.references, processed_neighbors)
clockwise = st.value == st.CLOCKWISE
if count % 2 == 1:
clockwise = not clockwise
ch_symbol = clockwise and "@@" or "@"
ret = ret.replace( "{{stereo%d}}" % mol.vertices.index(v), ch_symbol)
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 get_number_of_hydrogens_in_hydrogen_layer( self):
# version check
layer = self.get_layer( "h")
if not layer:
return 0
# check if we can handle it
if "*" in layer or ";" in layer:
raise oasa_not_implemented_error( "INChI", "multiple compound systems are not supported by the library")
ret = 0
re_for_brackets = "\([H\d,\-]+?\)"
brackets = re.findall( re_for_brackets, layer)
for bracket in brackets:
ret += self._get_hs_in_moving_hydrogen( bracket[1:-1])
layer = re.sub( re_for_brackets, "", layer) # clean the brackets out
for vs, num in self._parse_h_layer( layer):
ret += len( vs) * num
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 get_number_of_hydrogens_in_hydrogen_layer(self):
# version check
layer = self.get_layer("h")
if not layer:
return 0
# check if we can handle it
if "*" in layer or ";" in layer:
raise oasa_not_implemented_error(
"INChI",
"multiple compound systems are not supported by the library")
ret = 0
re_for_brackets = "\([H\d,\-]+?\)"
brackets = re.findall(re_for_brackets, layer)
for bracket in brackets:
ret += self._get_hs_in_moving_hydrogen(bracket[1:-1])
layer = re.sub(re_for_brackets, "", layer) # clean the brackets out
for vs, num in self._parse_h_layer(layer):
ret += len(vs) * num
return ret
