Standardize

These examples show how to use different standardize option.

Stereo

indigo.setOption("standardize-stereo", True);

mol1 = indigo.loadMolecule('CCN1C(SC(C)N1)')
mol2 = mol1.clone()

mol2.standardize()

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')
../../_images/indigorenderer_527964ef842912c52f81607c9069f8eb49b9ea7f.svg

Charges

indigo.setOption("standardize-charges", True);

mol1 = indigo.loadMolecule("CN(=O)=O")

mol2 = mol1.clone()

mol2.standardize()

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')
../../_images/indigorenderer_96eefc74e6e2e78efad408324ecb19bfc51d5383.svg

Geometry

indigo.setOption("standardize-keep-largest", "true")
mol1 = indigo.loadMolecule("NN.C.CC.CCC")

mol2 = mol1.clone()

mol2.standardize()

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')
../../_images/indigorenderer_90c91c6042de1bbac803e34b369f29aa357f89c6.svg

Query

indigo.setOption("standardize-charges", "false");
indigo.setOption("standardize-make-non-h-to-c-atoms", "true")
mol1 = indigo.loadQueryMolecule("CN1C=NC(=C1)C(=O)O")

mol2 = mol1.clone()

mol2.standardize()

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')
../../_images/indigorenderer_1f817ae3dd242c35c4553f7682bb37f59933f9c7.svg

Misc

indigo.setOption("standardize-charges", "false");
indigo.setOption("standardize-make-non-h-to-c-atoms", "false")

indigo.setOption("standardize-neutralize-zwitterions", "true")
mol1 = indigo.loadMolecule("[CH++][CH--]")

mol2 = mol1.clone()

mol2.standardize()

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')
../../_images/indigorenderer_a30f078489b272882883e0cf984328fb49110083.svg