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 _process_stereochemistry( self, mol):
## process stereochemistry
## double bonds
def get_stereobond_direction( end_atom, inside_atom, bond, init):
position = mol.vertices.index( end_atom) - mol.vertices.index( inside_atom)
char = bond.properties_['stereo'] == "\\" and 1 or -1
direction = (position * char * init) < 0 and "up" or "down"
return direction
def get_end_and_inside_vertex_from_edge_path( edge, path):
a1,a2 = edge.vertices
if len( [e for e in a1.neighbor_edges if e in path]) == 1:
return a1, a2
return a2, a1
stereo_edges = [e for e in mol.edges if "stereo" in e.properties_]
paths = []
for i,e1 in enumerate( stereo_edges):
for e2 in stereo_edges[i+1:]:
path = mol.get_path_between_edges( e1, e2)
path2 = path[1:-1]
if len( path2)%2 and not [_e for _e in path2 if _e.order != 2]:
# only odd number of double bonds, double bonds only
for _e in path[1:-1]:
if not mol.is_edge_a_bridge_fast_and_dangerous( _e):
break
else:
# only stereo related to non-cyclic bonds
paths.append( path)
for path in paths:
bond1 = path[0]
end_atom1,inside_atom1 = get_end_and_inside_vertex_from_edge_path( bond1, path)
bond2 = path[-1]
end_atom2,inside_atom2 = get_end_and_inside_vertex_from_edge_path( bond2, path)
d1 = get_stereobond_direction( end_atom1, inside_atom1, bond1, -1)
d2 = get_stereobond_direction( end_atom2, inside_atom2, bond2, -1)
if d1 == d2:
value = stereochemistry.cis_trans_stereochemistry.SAME_SIDE
else:
value = stereochemistry.cis_trans_stereochemistry.OPPOSITE_SIDE
if len( path) == 3:
center = path[1]
else:
center = None
refs = [end_atom1,inside_atom1,inside_atom2,end_atom2]
st = stereochemistry.cis_trans_stereochemistry( center=center, value=value, references=refs)
mol.add_stereochemistry( st)
# tetrahedral stereochemistry
for v in mol.vertices:
refs = None
if 'stereo' in v.properties_:
idx = [mol.vertices.index( n) for n in v.neighbors]
idx.sort()
if len( idx) < 3:
pass # no stereochemistry with less then 3 neighbors
elif len( idx) == 3:
if v.explicit_hydrogens == 0:
pass # no stereochemistry without adding hydrogen here
else:
if self.explicit_hydrogens_to_real_atoms:
hs = mol.explicit_hydrogens_to_real_atoms( v)
h = hs.pop()
else:
h = stereochemistry.explicit_hydrogen()
v_idx = mol.vertices.index( v)
idx1 = [i for i in idx if i < v_idx]
idx2 = [i for i in idx if i > v_idx]
refs = [mol.vertices[i] for i in idx1] + [h] + [mol.vertices[i] for i in idx2]
elif len( idx) == 4:
refs = [mol.vertices[i] for i in idx]
else:
pass # unhandled stereochemistry
if refs:
if v.properties_["stereo"] == "@":
direction = stereochemistry.tetrahedral_stereochemistry.ANTICLOCKWISE
elif v.properties_['stereo'] == "@@":
direction = stereochemistry.tetrahedral_stereochemistry.CLOCKWISE
else:
continue # no meaning
st = stereochemistry.tetrahedral_stereochemistry( center=v, value=direction, references=refs)
mol.add_stereochemistry( st)
# delete the data after processing
for e in mol.edges:
if 'stereo' in e.properties_:
del e.properties_['stereo']
for v in mol.vertices:
if 'stereo' in v.properties_:
del v.properties_['stereo']