PopulateStructureDB.js

//==============================================================
// Create a sample StructureDB instance and populate it with 
// 10 molecules from SMILES.
//
// Author: Ola Spjuth <ola(AT)bioclipse.net>
//==============================================================

//Create a project to hold temporary SDFile
project=ui.newProject("cheatsheet");

//Set up list of molecules
mols = java.util.ArrayList();
mols.add(cdk.fromSMILES("C(=O)N(Cc1ccco1)C(c1cc2ccccc2cc1)C(=O)NCc1ccccc1"));
mols.add(cdk.fromSMILES("C(=O)(CNC(=O)OC(C)(C)C)N(Cc1oc(C(F)(F)F)cc1)C(c1ccccc1)C(=O)NCc1ccccc1"));
mols.add(cdk.fromSMILES("C(=O)(C=CC)N(CCCCCCC)C(c1cc2c(cccc2)c2ccccc12)C(=O)NC(C)(C)C"));
mols.add(cdk.fromSMILES("O=S(=O)(N)CC1=NOC2=CC=CC=C12"));
mols.add(cdk.fromSMILES("O=C1CCC5(O)(C4N(CCC25(C=3C(OC12)=C(O)C=CC=3C4))CC6CC6)"));
mols.add(cdk.fromSMILES("O=NN(C(=O)NCCCl)CCCl"));
mols.add(cdk.fromSMILES("O=P1(OCCCN1(CCCl))(NCCCl)"));
mols.add(cdk.fromSMILES("N=1C=NN(C=1)CC=2C=CC=3NC=C(C=3(C=2))CCN(C)C"));
mols.add(cdk.fromSMILES("O=C(O)C2N(C(=O)C(NC(C(=O)OCC)CCC1=CC=CC=C1)C)C3CCCC3(C2)"));
mols.add(cdk.fromSMILES("O=C(O)C2N(C(=O)C(NC(C(=O)OCC)CCC1=CC=CC=C1)C)C3CCCC3(C2)"));

//Save list of molecules to file
cdk.saveSDFile("cheatsheet/vs.sdf", mols);

//Import file to StructureDB
structuredb.addMoleculesFromSDF("myDB","/cheatsheet/vs.sdf")