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#1300 Stereobond is not preserved after pasting a SMILES structure #1314

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merged 5 commits into from
Oct 10, 2023
Merged

#1300 Stereobond is not preserved after pasting a SMILES structure #1314

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65c299c
suffoxides
even1024 Oct 10, 2023
0a56e18
suffoxides
even1024 Oct 10, 2023
e700dd7
suffoxides
even1024 Oct 10, 2023
d909f49
py format
even1024 Oct 10, 2023
231c475
tests fixed
even1024 Oct 10, 2023
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5 changes: 5 additions & 0 deletions api/tests/integration/ref/formats/smiles.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -81,3 +81,8 @@ C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |wU:3.12,wD:3.3,(-2.40,1.39,;-0.80,1.39,;-0.0
atropisomer:
C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |w:3.3,3.12|
C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |w:3.3,3.12,(-2.40,1.39,;-0.80,1.39,;-0.00,2.77,;0.00,0.00,;1.60,0.00,;2.40,1.39,;4.00,1.39,;4.80,0.00,;6.40,0.00,;4.00,-1.39,;2.40,-1.39,;1.60,-2.77,;-0.80,-1.39,;0.00,-2.77,;-2.40,-1.39,;-3.20,-0.00,)|
*** Suffoxides ***
suffoxide:
C1[S@](=O)CC(=O)C=1C
C1[S@](=O)CC(=O)C=1C
bond:5 stereo:6
13 changes: 13 additions & 0 deletions api/tests/integration/tests/formats/smiles.py
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Expand Up @@ -128,3 +128,16 @@
print(mol.smiles())
mol.layout()
print(mol.smiles())

print("*** Suffoxides ***")
mols_smiles = ["C1=C(C)C(=O)C[S@]1=O"]
for sm in mols_smiles:
print("suffoxide:")
mol = indigo.loadMolecule(sm)
print(mol.smiles())
mol.layout()
print(mol.smiles())
for i in range(mol.countBonds()):
bs = mol.getBond(i).bondStereo()
if bs > 0:
print("bond:%d stereo:%d" % (i, bs))
6 changes: 4 additions & 2 deletions core/indigo-core/molecule/src/molecule_stereocenters.cpp
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Expand Up @@ -1771,7 +1771,8 @@ void MoleculeStereocenters::markBond(BaseMolecule& baseMolecule, int atom_idx)
for (j = 0; j < size; j++)
{
edge_idx = baseMolecule.findEdgeIndex(atom_idx, pyramid[size - 1]);
if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getVertex(pyramid[size - 1]).degree() == 1)
if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getBondOrder(edge_idx) == BOND_SINGLE &&
baseMolecule.getVertex(pyramid[size - 1]).degree() == 1)
break;
rotatePyramid(pyramid);
if (size == 4)
Expand All @@ -1783,7 +1784,8 @@ void MoleculeStereocenters::markBond(BaseMolecule& baseMolecule, int atom_idx)
for (j = 0; j < size; j++)
{
edge_idx = baseMolecule.findEdgeIndex(atom_idx, pyramid[size - 1]);
if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getBondTopology(edge_idx) == TOPOLOGY_CHAIN && getType(pyramid[size - 1]) == 0)
if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getBondOrder(edge_idx) == BOND_SINGLE &&
baseMolecule.getBondTopology(edge_idx) == TOPOLOGY_CHAIN && getType(pyramid[size - 1]) == 0)
break;
rotatePyramid(pyramid);
if (size == 4)
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