Calculating Properties¶

This examples shows how to calculate different molecule and reaction properties

Canonical Smiles¶

The following code prints canonical smiles string for a given structure:

# indigo = Indigo()
#
# Load structure
mol = indigo.loadMolecule('CC1=C(Cl)C=CC2=C1NS(=O)S2')

#print canonical smiles for the molecule
print(mol.canonicalSmiles())

Output:

CC1=C(Cl)C=CC2SS(=O)NC=21

The example below prints canonical smiles string for a given reaction:

# indigo = Indigo()
#
# Load structure
rxn = indigo.loadReaction('[CH2:1]=[CH:2][CH:3]=[CH:4][CH2:5][H:6]>>[H:6][CH2:1][CH:2]=[CH:3][CH:4]=[CH2:5]')

#print canonical smiles for the reaction
print(rxn.canonicalSmiles())

Output:

[CH3:1][CH:3]=[CH:5][CH:4]=[CH2:2]>>[CH3:2][CH:4]=[CH:5][CH:3]=[CH2:1]

Enumeration of Tautomers¶

The following code prints the list of tautomers for a given molecule:

# indigo = Indigo()
# indigoRenderer = IndigoRenderer(indigo)
#
# Load structure
molecule = indigo.loadMolecule('OC1C2C=NNC=2N=CN=1')

#print the list of tautomers for the molecule
iter = indigo.iterateTautomers(molecule, 'INCHI')
lst = list()
array = indigo.createArray()
index = 1
for imol in iter:
    mol = imol.clone()
    lst.append(mol.canonicalSmiles())
    mol.setProperty("grid-comment", str(index))
    array.arrayAdd(mol)
    index += 1

lst.sort()
print "\n".join(map(lambda x, y: str(x) + ") " + y, range(1, len(lst) + 1), lst))

indigo.setOption("render-grid-margins", "20, 10")
indigo.setOption("render-grid-title-offset", "5")
indigo.setOption("render-grid-title-property", "grid-comment")
indigoRenderer.renderGridToFile(array, None, 4, 'result.png')

../../_images/indigorenderer_fc243baf7f8fdbed66cf377264e9c87e13195acd.svg

Output:

1) O=C1N=CN=C2NNC=C21
2) O=C1N=CNC2=NNC=C21
3) O=C1N=CNC2NN=CC=21
4) O=C1NC=NC2=NNC=C21
5) O=C1NC=NC2NN=CC=21
6) OC1=NC=NC2=NNC=C21
7) OC1=NC=NC2NN=CC=21
8) OC1N=CN=C2NN=CC2=1
9) OC1N=CNC2=NN=CC2=1
10) OC1NC=NC2=NN=CC2=1

If the molecule is aromatized before enumeration, the list of tautomers will be aromatized (if possible):

# indigo = Indigo()
# indigoRenderer = IndigoRenderer(indigo)
#
# Load structure
molecule = indigo.loadMolecule('OC1C2C=NNC=2N=CN=1')
molecule.aromatize()

#print the list of tautomers for the molecule
iter = indigo.iterateTautomers(molecule, 'INCHI')
lst = list()
array = indigo.createArray()
index = 1
for imol in iter:
    mol = imol.clone()
    lst.append(mol.canonicalSmiles())
    mol.setProperty("grid-comment", str(index))
    array.arrayAdd(mol)
    index += 1

lst.sort()
print "\n".join(map(lambda x, y: str(x) + ") " + y, range(1, len(lst) + 1), lst))

indigo.setOption("render-grid-margins", "20, 10")
indigo.setOption("render-grid-title-offset", "5")
indigo.setOption("render-grid-title-property", "grid-comment")
indigoRenderer.renderGridToFile(array, None, 4, 'result.png')

../../_images/indigorenderer_2c90f4df5002473895e899ae4c03ffa810da31f2.svg

Output:

1) O=C1N=CN=C2NNC=C21
2) O=C1N=CNc2[nH][n]cc21
3) O=C1N=CNc2[n][nH]cc21
4) O=C1NC=Nc2[nH][n]cc21
5) O=C1NC=Nc2[n][nH]cc21
6) Oc1[nH]c[n]c2[n][n]cc21
7) Oc1[n]c[nH]c2[n][n]cc21
8) Oc1[n]c[n]c2[nH][n]cc21
9) Oc1[n]c[n]c2[n][nH]cc21

Please notice that the number of tautomers could be different in aromatized and dearomatized forms. This happens because some aromatized forms could have different dearomatized representations.

The following code uses reaction SMARTS algorithm (may give different set of tautomers):

# indigo = Indigo()
# indigoRenderer = IndigoRenderer(indigo)
#
# Load structure
molecule = indigo.loadMolecule('OC1C2C=NNC=2N=CN=1')
molecule.aromatize()

#print the list of tautomers for the molecule
iter = indigo.iterateTautomers(molecule, 'RSMARTS')
lst = list()
array = indigo.createArray()
index = 1
for imol in iter:
    mol = imol.clone()
    lst.append(mol.canonicalSmiles())
    mol.setProperty("grid-comment", str(index))
    array.arrayAdd(mol)
    index += 1

lst.sort()
print "\n".join(map(lambda x, y: str(x) + ") " + y, range(1, len(lst) + 1), lst))

indigo.setOption("render-grid-margins", "20, 10")
indigo.setOption("render-grid-title-offset", "5")
indigo.setOption("render-grid-title-property", "grid-comment")
indigoRenderer.renderGridToFile(array, None, 4, 'result.png')

../../_images/indigorenderer_30af5691078187d43876f72d8d301b0e7f483e0c.svg

Output:

1) O=C1N=CN=C2NN=CC21
2) O=C1N=CN=C2NNC=C21
3) O=C1N=CNC2=NN=CC21
4) O=C1N=CNc2[nH][n]cc21
5) O=C1N=CNc2[n][nH]cc21
6) O=C1NC=NC2=NN=CC21
7) O=C1NC=Nc2[nH][n]cc21
8) O=C1NC=Nc2[n][nH]cc21
9) OC1N=CNc2[nH][n]cc21
10) OC1N=CNc2[n][nH]cc21
11) OC1NC=Nc2[nH][n]cc21
12) OC1NC=Nc2[n][nH]cc21
13) Oc1[nH]c[n]c2[n][n]cc21
14) Oc1[n]c[nH]c2[n][n]cc21
15) Oc1[n]c[n]c2[nH][n]cc21
16) Oc1[n]c[n]c2[n][nH]cc21

Sgroups search¶

The following code prints results of SGroups search requests with different criteria:

# indigo = Indigo()
#
# Load structure
indigo.setOption("molfile-saving-mode", "3000")
file1 = "data/all_features_mol.mol"
m = indigo.loadMoleculeFromFile(file1)

sgs = m.findSGroups("SG_TYPE", "SUP")

for sg in sgs:
   print("Superatom with label %s found" % (m.getSuperatom(sg.getSGroupIndex())).getSGroupName());

sgs = m.findSGroups("SG_LABEL", "Z")
print("SGroups with label Z:")
for sg in sgs:
   print("SGroup Index = %d " % sg.getSGroupIndex() + ", SGroup Type = %s" % sg.getSGroupType());

sgs = m.findSGroups("SG_CLASS", "AA")
print("SGroups with class AA:")
for sg in sgs:
   print("SGroup Index = %d " % sg.getSGroupIndex() + ", SGroup Type = %s" % sg.getSGroupType());

sgs = m.findSGroups("SG_DISPLAY_OPTION", "0")
print("SGroups expanded:")
for sg in sgs:
   print("SGroup Index = %d " % sg.getSGroupIndex() + ", SGroup Type = %s" % sg.getSGroupType());

sgs = m.findSGroups("SG_BRACKET_STYLE", "0")
print("SGroups with square brackets:")
for sg in sgs:
   print("SGroup Index = %d " % sg.getSGroupIndex() + ", SGroup Type = %s" % sg.getSGroupType());

sgs = m.findSGroups("SG_DATA", "Selection")
print("SGroups with data contains Selection:")
for sg in sgs:
   print("SGroup Index = %d " % sg.getSGroupIndex() + ", SGroup Type = %s" % sg.getSGroupType());

sgs = m.findSGroups("SG_DATA_NAME", "comment")
print("SGroups with data field name comment:")
for sg in sgs:
   print("SGroup Index = %d " % sg.getSGroupIndex() + ", SGroup Type = %s" % sg.getSGroupType());

sgs = m.findSGroups("SG_DATA_DISPLAY", "detached")
print("SGroups with detached data field:")
for sg in sgs:
   print("SGroup Index = %d " % sg.getSGroupIndex() + ", SGroup Type = %s" % sg.getSGroupType());

sgs = m.findSGroups("SG_DATA_LOCATION", "relative")
print("SGroups with relative data field:")
for sg in sgs:
   print("SGroup Index = %d " % sg.getSGroupIndex() + ", SGroup Type = %s" % sg.getSGroupType());

sgs = m.findSGroups("SG_ATOMS", "103, 104")
print("SGroups with atoms 103 and 104:")
for sg in sgs:
   print("SGroup Index = %d " % sg.getSGroupIndex() + ", SGroup Type = %s" % sg.getSGroupType());

sgs = m.findSGroups("SG_BONDS", "249, 245")
print("SGroups with bonds 245 and 249:")
for sg in sgs:
   print("SGroup Index = %d " % sg.getSGroupIndex() + ", SGroup Type = %s" % sg.getSGroupType());

Input: data/all_features_mol.mol

Output:

Superatom with label PhN found
SGroups with label Z:
SGroup Index = 9 , SGroup Type = 3
SGroup Index = 10 , SGroup Type = 3
SGroups with class AA:
SGroups expanded:
SGroup Index = 0 , SGroup Type = 2
SGroups with square brackets:
SGroup Index = 0 , SGroup Type = 2
SGroup Index = 1 , SGroup Type = 1
SGroup Index = 2 , SGroup Type = 3
SGroup Index = 3 , SGroup Type = 3
SGroup Index = 4 , SGroup Type = 3
SGroup Index = 5 , SGroup Type = 0
SGroup Index = 6 , SGroup Type = 4
SGroup Index = 7 , SGroup Type = 4
SGroup Index = 8 , SGroup Type = 4
SGroup Index = 9 , SGroup Type = 3
SGroup Index = 10 , SGroup Type = 3
SGroups with data contains Selection:
SGroup Index = 1 , SGroup Type = 1
SGroups with data field name comment:
SGroup Index = 1 , SGroup Type = 1
SGroups with detached data field:
SGroup Index = 1 , SGroup Type = 1
SGroups with relative data field:
SGroup Index = 1 , SGroup Type = 1
SGroups with atoms 103 and 104:
SGroup Index = 3 , SGroup Type = 3
SGroups with bonds 245 and 249:
SGroup Index = 9 , SGroup Type = 3

CIP Descriptors¶

This examples show how to calculate CIP stereo descriptors for different molecules. Descriptors calculation is activated by corresponding Indigo option molfile-saving-add-stereo-desc and descriptors are added into generated mol file as data S-groups with special name field INDIGO_CIP_DESC. Setting Indigo option molfile-saving-add-stereo-desc to 0 (or false) (the default value) disables descriptors calculation and removes all such data S-groups during corresponding mol file generation.

# indigo = Indigo()
# indigoRenderer = IndigoRenderer(indigo)
#
# Load structure
file = "data/RS-example.mol"
mol1 = indigo.loadMoleculeFromFile(file)
mol2 = mol1.clone();

indigo.setOption("molfile-saving-add-stereo-desc", "1");
mol2.molfile()

array = indigo.createArray()

mol1.setProperty("grid-comment", "before")
mol2.setProperty("grid-comment", "after")

array.arrayAdd(mol1)
array.arrayAdd(mol2)

indigo.setOption("render-grid-title-property", "grid-comment")
indigo.setOption("render-grid-margins", "20, 10")
indigo.setOption("render-grid-title-offset", "10")

indigoRenderer.renderGridToFile(array, None, 2, 'result.png')

Input: data/RS-example.mol

../../_images/indigorenderer_a11f5612124e3f20e97042077ba45271dec84e04.svg

# indigo = Indigo()
# indigoRenderer = IndigoRenderer(indigo)
#
# Load structure
file = "data/ZE-example.mol"
mol1 = indigo.loadMoleculeFromFile(file)
mol2 = mol1.clone();

indigo.setOption("molfile-saving-add-stereo-desc", "1");
mol2.molfile()

array = indigo.createArray()

mol1.setProperty("grid-comment", "before")
mol2.setProperty("grid-comment", "after")

array.arrayAdd(mol1)
array.arrayAdd(mol2)

indigo.setOption("render-grid-title-property", "grid-comment")
indigo.setOption("render-grid-margins", "20, 10")
indigo.setOption("render-grid-title-offset", "10")

indigoRenderer.renderGridToFile(array, None, 2, 'result.png')

Input: data/ZE-example.mol

../../_images/indigorenderer_b5d4da9a52ff2a8e8e5c6d507e60e5bdf717a529.svg

# indigo = Indigo()
# indigoRenderer = IndigoRenderer(indigo)
#
# Load structure
file = "data/Z-example.mol"
mol1 = indigo.loadMoleculeFromFile(file)
mol2 = mol1.clone();

indigo.setOption("molfile-saving-add-stereo-desc", "1");
mol2.molfile()

array = indigo.createArray()

mol1.setProperty("grid-comment", "before")
mol2.setProperty("grid-comment", "after")

array.arrayAdd(mol1)
array.arrayAdd(mol2)

indigo.setOption("render-grid-title-property", "grid-comment")
indigo.setOption("render-grid-margins", "20, 10")
indigo.setOption("render-grid-title-offset", "10")

indigoRenderer.renderGridToFile(array, None, 2, 'result.png')

Input: data/Z-example.mol

../../_images/indigorenderer_8aed5a13a2f543ef8cf2e508b672a72c19b8231b.svg

There are also several examples for complicated structures when different software provides different CIP stereo descriptors estimations:

The first case is the molecule with isotope inclusion.

# indigo = Indigo()
# indigoRenderer = IndigoRenderer(indigo)
#
# Load structure
file1 = "data/C14_R_iso.mol"
file2 = "data/C14_R_iso_2.mol"
mol1 = indigo.loadMoleculeFromFile(file1)
mol2 = indigo.loadMoleculeFromFile(file2)

indigo.setOption("molfile-saving-add-stereo-desc", "1");
mol1.molfile()
mol2.molfile()

array = indigo.createArray()

mol1.setProperty("grid-comment", "first variant")
mol2.setProperty("grid-comment", "second variant")

array.arrayAdd(mol1)
array.arrayAdd(mol2)

indigo.setOption("render-grid-title-property", "grid-comment")
indigo.setOption("render-grid-margins", "20, 10")
indigo.setOption("render-grid-title-offset", "10")

indigoRenderer.renderGridToFile(array, None, 2, 'result.png')

Input: data/C14_R_iso.mol, data/C14_R_iso_2.mol

../../_images/indigorenderer_24ad54f604eff1be4c07b95fd60e607fae100e55.svg

The second case is the molecule with cyclic ligands and heterocycles.

# indigo = Indigo()
# indigoRenderer = IndigoRenderer(indigo)
#
# Load structure
file1 = "data/P-92_2_1_3_ex1.mol"
file2 = "data/P-92_2_1_3_ex2.mol"
mol1 = indigo.loadMoleculeFromFile(file1)
mol2 = indigo.loadMoleculeFromFile(file2)

indigo.setOption("molfile-saving-add-stereo-desc", "1");
mol1.molfile()
mol2.molfile()

array = indigo.createArray()

mol1.setProperty("grid-comment", "first variant")
mol2.setProperty("grid-comment", "second variant")

array.arrayAdd(mol1)
array.arrayAdd(mol2)

indigo.setOption("render-grid-title-property", "grid-comment")
indigo.setOption("render-grid-margins", "20, 10")
indigo.setOption("render-grid-title-offset", "10")

indigoRenderer.renderGridToFile(array, None, 2, 'result.png')

Input: data/P-92_2_1_3_ex1.mol, data/P-92_2_1_3_ex2.mol

../../_images/indigorenderer_e785f179a232809bccec3d2e9207be0064ddca50.svg