def super_impose_only_on_planar_rings(ringlist, mol, count):
#for now, I'll only extend planar ring systems
pred = OEPartPredAtom(ringlist)
refmol = OECreateOEMol()
old_list = ringlist
ring_count = 0
match_list = []
for j in old_list:
match_list.append(j)
for i in xrange(1, count + 1):
pred.SelectPart(i)
OESubsetMol(refmol, mol, pred)
if chemistry.check_planar(refmol):
#print "keep this ring"
#print ringlist
ring_count = ring_count + 1
else:
#print "reject this ring"
#delete this ring from ring_list
for atom_number in range(0, len(match_list)):
#print match_list[atom_number]
if match_list[atom_number] == i:
match_list[atom_number] = 0
#print 'test'
#adjust ring_numbers
elif match_list[atom_number] > i:
match_list[atom_number] = match_list[atom_number] - 1
#print match_list
return match_list, ring_count
def find_atoms_in_plane(mol, debug):
#only check if ring is planar
#should not be necessary to extend rings as we say exactly which atom matches which one
ri = mol.GetRingInfo()
#print(ri.AtomRings())
atom_list = []
for ring in range(0, len(ri.AtomRings())
): #convert tulple to list so that it can be modified
atom_list.append(
[[]]) #list should also hold information about planarity
for atmidx in ri.AtomRings()[ring]:
atom_list[ring][0].append(atmidx)
#print (atom_list)
for i in range(0, len(atom_list)):
#need to create indepent copy of list
atom_idx_list = atom_list[i][0][:]
#print (atom_idx_list, 'atom_idx_list')
if chemistry.check_planar(mol, atom_idx_list, debug):
atom_list[i].append(True)
else:
atom_list[i].append(False) #ring is not planar
#check if two planar rings are fused together
remove_from_list = []
#print (atom_list)
for i in range(0, len(atom_list)):
#print (i, 'i here')
if atom_list[i][1]: #planar ring
for j in range(1, len(atom_list)):
#print (j, 'j **********')
if atom_list[j][
1] and i != j and j not in remove_from_list: #planar ring, don't compare identical rings
#check if they have atoms in common => fused
for atom_idx in atom_list[j][0]:
#print (atom_idx, 'atom_idx')
if atom_idx in atom_list[i][0]: #fused
for atom_idex_2 in atom_list[i][0]:
if atom_idex_2 not in atom_list[j][0]:
atom_list[j][0].append(atom_idex_2)
#print (atom_list[j][0], "joined list")
remove_from_list.append(i)
#print ('remove form list', remove_from_list)
break #no need to ceck remaining atoms of this list, is already fused and joined
for i in range(0, len(remove_from_list)):
del atom_list[remove_from_list[i] - i] #index will change
#print (atom_list)
count = len(atom_list)
return atom_list, count #---------------------
def find_atoms_in_plane_extend_ring(mol, debug):
#get all (non H) substituents of planr ring atoms that are not part of a ring, if not planar, do not search, as their position might change depending on ring conformation
#should not be necessary as we say exactly which atom matches which one
ri = mol.GetRingInfo()
#print(ri.AtomRings())
atom_list = []
for ring in range(0, len(ri.AtomRings())
): #convert tulple to list so that it can be modified
atom_list.append(
[[]]) #list should also hold information about planarity
for atmidx in ri.AtomRings()[ring]:
atom_list[ring][0].append(atmidx)
#print (atom_list)
for i in range(0, len(atom_list)):
#need to create indepent copy of list
atom_idx_list = atom_list[i][0][:]
#print (atom_idx_list, 'atom_idx_list')
if chemistry.check_planar(mol, atom_idx_list, debug):
atom_list[i].append(True)
for atom in mol.GetAtoms():
#print (atom.GetIdx())
#print (atom_idx_list, 'atom_idx_list 2')
if atom.GetIdx(
) in atom_idx_list: #atom is part of this ring system, check for neighbours
#print (atom.GetIdx(), 'checked')
for neighbour in atom.GetNeighbors():
#print (neighbour.GetIdx(), atom_idx_list)
if neighbour.GetIdx(
) not in atom_idx_list and neighbour.GetAtomicNum(
) != 1: #do not add H
#atom_list[i][0].append(neighbour.GetIdx())
continue
#print ('added',neighbour.GetSmarts(),neighbour.GetAtomicNum())
else:
atom_list[i].append(False) #ring is not planar
#print (atom_list)
count = len(atom_list)
return atom_list, count