def read_double_bond_stereo_layer( self):
def get_lowest_numbered_neighbor( atom, verbotten_atom):
neighs = [(n.properties_.get('inchi_number',1000000), n)
for n in atom.neighbors
if n is not verbotten_atom and "inchi_number" in n.properties_]
if neighs:
neighs.sort( reverse=True)
return neighs[0][1]
else:
# we take the only one that is there (if any)
neighs = [n for n in atom.neighbors if n is not verbotten_atom]
if neighs:
return neighs[0]
else:
raise oasa_inchi_error( "No neigbors on atom with stereo information!")
layer = self.get_layer( "b")
if not layer:
return
for a1,a2,sign in re.findall( "(\d+)-(\d+)([-+?u])", layer):
atom1 = self.get_atom_with_inchi_number( int( a1))
atom2 = self.get_atom_with_inchi_number( int( a2))
bond = self.structure.get_edge_between( atom1, atom2)
# we need neighbors with lowest inchi_number
neigh1 = get_lowest_numbered_neighbor( atom1, atom2)
neigh2 = get_lowest_numbered_neighbor( atom2, atom1)
st = cis_trans_stereochemistry( references=[neigh1,atom1,atom2,neigh2],
value=self.stereo_remap[sign])
self.structure.add_stereochemistry( st)
def read_double_bond_stereo_layer(self):
def get_lowest_numbered_neighbor(atom, verbotten_atom):
neighs = [
(n.properties_.get('inchi_number', 1000000), n)
for n in atom.neighbors
if n is not verbotten_atom and "inchi_number" in n.properties_
]
if neighs:
neighs.sort(reverse=True)
return neighs[0][1]
else:
# we take the only one that is there (if any)
neighs = [n for n in atom.neighbors if n is not verbotten_atom]
if neighs:
return neighs[0]
else:
raise oasa_inchi_error(
"No neigbors on atom with stereo information!")
layer = self.get_layer("b")
if not layer:
return
for a1, a2, sign in re.findall("(\d+)-(\d+)([-+?u])", layer):
atom1 = self.get_atom_with_inchi_number(int(a1))
atom2 = self.get_atom_with_inchi_number(int(a2))
bond = self.structure.get_edge_between(atom1, atom2)
# we need neighbors with lowest inchi_number
neigh1 = get_lowest_numbered_neighbor(atom1, atom2)
neigh2 = get_lowest_numbered_neighbor(atom2, atom1)
st = cis_trans_stereochemistry(
references=[neigh1, atom1, atom2, neigh2],
value=self.stereo_remap[sign])
self.structure.add_stereochemistry(st)
def detect_stereochemistry_from_coords(self, omit_rings=True):
import stereochemistry, geometry
def add_neighbor_double_bonds(bond, path):
for _e in bond.get_neighbor_edges():
if _e.order == 2 and _e not in path:
path.append(_e)
add_neighbor_double_bonds(_e, path)
# double bonds
# detect clusters of double bonds
double_paths = []
processed = set()
for e in self.edges:
if e.order == 2 and e not in processed:
if omit_rings and not self.is_edge_a_bridge(e):
continue
path = [e]
add_neighbor_double_bonds(e, path)
if len(path) % 2:
double_paths.append(path)
processed |= set(path)
# detect config on these paths
for path in double_paths:
vertices = []
for bond in path:
vertices.extend(bond.vertices)
ends = [v for v in vertices if vertices.count(v) == 1]
if len(
ends
) != 2: # two ends is the only thing we are prepared to handle
continue
end1, end2 = ends
# set stereochemistry for all neighbors of both ends
for e1, n1 in end1.get_neighbor_edge_pairs():
plane1 = geometry.plane_normal_from_3_points(
(n1.x, n1.y, n1.z), (end1.x, end1.y, end1.z),
(end2.x, end2.y, end2.z))
if plane1 == None:
continue # some coords were missing
if not e1 in path:
for e2, n2 in end2.get_neighbor_edge_pairs():
if not e2 in path:
plane2 = geometry.plane_normal_from_3_points(
(end1.x, end1.y, end1.z),
(end2.x, end2.y, end2.z), (n2.x, n2.y, n2.z))
#cos_angle = geometry.same_or_oposite_side( plane1, plane2)
cos_angle = geometry.angle_between_planes(
plane1, plane2)
if cos_angle < 0:
value = stereochemistry.cis_trans_stereochemistry.OPPOSITE_SIDE
else:
value = stereochemistry.cis_trans_stereochemistry.SAME_SIDE
if len(path) == 1:
center = path[0]
else:
center = None
refs = [n1, end1, end2, n2]
st = stereochemistry.cis_trans_stereochemistry(
center=center, value=value, references=refs)
to_remove = None
to_add = None
for st1 in self.stereochemistry:
if set(st1.references) == set(st.references):
if st.value == st1.value:
break
else:
to_remove = st1
break
else:
self.add_stereochemistry(st)
if to_remove:
self.remove_stereochemistry(to_remove)
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']
def detect_stereochemistry_from_coords( self, omit_rings=True):
import stereochemistry,geometry
def add_neighbor_double_bonds( bond, path):
for _e in bond.get_neighbor_edges():
if _e.order == 2 and _e not in path:
path.append( _e)
add_neighbor_double_bonds( _e, path)
# double bonds
# detect clusters of double bonds
double_paths = []
processed = set()
for e in self.edges:
if e.order == 2 and e not in processed:
if omit_rings and not self.is_edge_a_bridge( e):
continue
path = [e]
add_neighbor_double_bonds( e, path)
if len( path) % 2:
double_paths.append( path)
processed |= set( path)
# detect config on these paths
for path in double_paths:
vertices = []
for bond in path:
vertices.extend( bond.vertices)
ends = [v for v in vertices if vertices.count(v) == 1]
if len( ends) != 2: # two ends is the only thing we are prepared to handle
continue
end1, end2 = ends
# set stereochemistry for all neighbors of both ends
for e1,n1 in end1.get_neighbor_edge_pairs():
plane1 = geometry.plane_normal_from_3_points( (n1.x,n1.y,n1.z),(end1.x,end1.y,end1.z),(end2.x,end2.y,end2.z))
if plane1 == None:
continue # some coords were missing
if not e1 in path:
for e2,n2 in end2.get_neighbor_edge_pairs():
if not e2 in path:
plane2 = geometry.plane_normal_from_3_points( (end1.x,end1.y,end1.z),(end2.x,end2.y,end2.z),(n2.x,n2.y,n2.z))
#cos_angle = geometry.same_or_oposite_side( plane1, plane2)
cos_angle = geometry.angle_between_planes( plane1, plane2)
if cos_angle < 0:
value = stereochemistry.cis_trans_stereochemistry.OPPOSITE_SIDE
else:
value = stereochemistry.cis_trans_stereochemistry.SAME_SIDE
if len( path) == 1:
center = path[0]
else:
center = None
refs = [n1,end1,end2,n2]
st = stereochemistry.cis_trans_stereochemistry( center=center, value=value, references=refs)
to_remove = None
to_add = None
for st1 in self.stereochemistry:
if set( st1.references) == set( st.references):
if st.value == st1.value:
break
else:
to_remove = st1
break
else:
self.add_stereochemistry( st)
if to_remove:
self.remove_stereochemistry( to_remove)
