Stereocenters options

ignore-stereochemistry-errors

type

boolean

default

false

description

When reading a Molfile/Rxnfile with incorrectly marked stereobonds, ignore them rather than raise an error.

Sometimes molecules contain stereobond marks that do not define stereocenters properly. It can be either mistake made by a user, or stereoconfiguration notation is not known to Indigo. Let’s condside the following molecule:

Input: data/stereoerrors.mol

Stereobond near Oxygen atom is probably set in a wrong direction bny mistake, and when loaded with Indigo one gets an exception about invalid stereobonds configuration:

# Load structure and get exception about stereocenters
try:
    m = indigo.loadMoleculeFromFile('data/stereoerrors.mol')
except IndigoException, ex:
    print("Exception: " + str(ex))

Input: data/stereoerrors.mol

Output:

Exception: molfile loader: direction of bond #1 makes no sense

To load this structure we can ignore such errors:

indigo.setOption("ignore-stereochemistry-errors", True)
m = indigo.loadMoleculeFromFile('data/stereoerrors.mol')

All other valid stereocenters are loaded. All stereobond marks are also loaded even if they correspond to an invalid stereocenter. In the example below we see that layout methods marked only valid stereocenter.

print("Smiles:\n" + m.smiles())

indigo.setOption("render-comment", "Original")
indigoRenderer.renderToFile(m, 'result_1.png')

indigo.setOption("render-comment", "With bond indices")
indigo.setOption("render-bond-ids-visible", True)
indigoRenderer.renderToFile(m, 'result_2.png')
indigo.setOption("render-bond-ids-visible", False)

m.layout()
indigo.setOption("render-comment", "After cleanup")
indigoRenderer.renderToFile(m, 'result_3.png')

Output:

Smiles:
O(C(C(N)=O)C)C([C@H](C)O)=O |&1:7,r|

stereochemistry-bidirectional-mode

type

boolean

default

false

description

Treat stereobond direction bond not only for a pointed stereocenter, but for the neighbour as well.

print("stereochemistry-bidirectional-mode")
# Load structure
m = indigo.loadMoleculeFromFile('data/bidirect.mol')
print("False: " + m.smiles())
indigo.setOption("render-comment", "False")
indigoRenderer.renderToFile(m, 'result_1.png')

#Set option
indigo.setOption("stereochemistry-bidirectional-mode", True)
m2 = indigo.loadMoleculeFromFile('data/bidirect.mol')
print("True: " + m2.smiles())

indigo.setOption("render-comment", "True")
indigoRenderer.renderToFile(m2, 'result_2.png')

Input: data/bidirect.mol

Output:

stereochemistry-bidirectional-mode
False: OCC(C)[C@@H](C)C[C@@H](C)C(C)CN |w:2,9,&1:4,7,r|
True: OCC(C)C(C)CC(C)C(C)CN |w:2,4,7,9,r|

stereochemistry-detect-haworth-projection

type

boolean

default

false

description

Detect Haworth projection

# Load structure
q = indigo.loadQueryMoleculeFromFile('data/projection_ordinary.mol')
t = indigo.loadMoleculeFromFile('data/projection_haworth.mol')

# Render structures
indigo.setOption("render-comment", "projection_ordinary")
indigoRenderer.renderToFile(q, 'result_1.png')
indigo.setOption("render-comment", "projection_haworth")
indigoRenderer.renderToFile(t, 'result_2.png')

# Match with haworth-projection option disabled
matcher = indigo.substructureMatcher(t)
print("match with haworth-projection turned OFF: " + str(matcher.match(q) != None))

# Load and match with haworth-projection option enabled
indigo.setOption("stereochemistry-detect-haworth-projection", "True")
t2 = indigo.loadMoleculeFromFile('data/projection_haworth.mol')
matcher = indigo.substructureMatcher(t2)
print("match with haworth-projection turned ON: " + str(matcher.match(q) != None))

Input: data/projection_ordinary.mol, data/projection_haworth.mol

Output:

match with haworth-projection turned OFF: False
match with haworth-projection turned ON: True