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')
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')
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')
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')
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')