olas

//Create same mol in 2 representations
sam1=cdk.fromSMILES("CN(C)CCC1=CNC2=C1C=C(C=C2)CC1NC(=O)OC1");
sam2=cdk.fromSMILES("CN(C)CCC1=CNc2c1cc(cc2)CC1NC(=O)OC1");

js.print("\n==========\n==========\n")
//Print out sybyl atom types (works fine)
js.print("\n\nPerceive sybyl atom types on molecules directly:\n");
syb1=cdx.perceiveSybylAtomTypes(sam1)
js.print(syb1);

olas

//***************************************************************
// Script that iterates over an SDFile and adds precalculated values 
// from an external file as a property and saves as a new SDFile.
//
// The file with values have one value per row in same order as 
// the molecukes in the SDFile.
//
// Author: Ola Spjuth 
//****************************************************************

olas

//***************************************************************
// Script that iterates over a file, calculates properties
// and stores all in a new SDFile. Requires Sample Data installed.
//
// Author: Ola Spjuth
//****************************************************************

it = cdk.createMoleculeIterator("/Sample Data/SDF/Fragments2.sdf");
list=cdk.createMoleculeList();

olas

/*******************************************************************************
 * Script to predict the susceptibility of an HIV protease sequence for seven
 * drugs based on the proteochemometric model described in:
 * Lapins M, Eklund M, Spjuth O, Prusis P, Wikberg JE.
 * Proteochemometric modeling of HIV protease susceptibility,
 * BMC Bioinformatics. 2008 Apr 10;9:181. .
 *
 * Script accepts a 99 aa sequence as input and delivers susceptbiliy values
 * for the drugs Amprenavir, Atazanavir, Indinavir, Lopinavir, Nelfinavir,
 * Ritonavir, and Saquinavir.

olas

/*******************************************************************************
 * Bioclipse-script to iteratively build a molecule in JChemPaint
 * Author: Ola Spjuth
 * Author: Egon Willighagen
 ******************************************************************************/

//Start with a carbon and open in JCP
mol=cdk.fromSMILES("C")
mol2=cdk.generate2dCoordinates(mol)
ui.open(mol2)

olas

/*******************************************************************************
 * Bioclipse-script to iteratively build a molecule in JChemPaint
 * Author: Ola Spjuth
 ******************************************************************************/

//Start with a carbon and open in JCP
mol=cdk.fromSMILES("C")
mol2=cdk.generate2dCoordinates(mol)
ui.open(mol2)

olas

//Demonstrates basic manipulation of multiple molecules in Bioclipse
//Requires sample data installed in default location
mols=cdk.loadMolecules("/Sample Data/SDF/Fragments2.sdf")
mols.size()
mol=mols.get(3)
cdk.calculateSMILES(mols.get(4))
ui.open(mols)

olas

//Download PDB via Web service at EBI and open in Jmol
res=ws.queryPDB("1d66")
ui.openFiles(res)

//Execute some jmol script commands
jmol.run("select all; spacefill 0; wireframe off; cartoon on;select none")
jmol.run("select !dna; isosurface solvent; select none; color isosurface blue")
jmol.spinOn()

olas

/*******************************************************************************
 * Bioclipse-script to generate different coordinates on a list of molecules.
 * Author: Ola Spjuth
 ******************************************************************************/

//Create list of molecules
mols=cdk.createMoleculeList();
mols.add(cdk.fromSMILES("CCC"));
mols.add(cdk.fromSMILES("CCCNCC"));
mols.add(cdk.fromSMILES("CCNCCOC(C)CC"));

olas

/*******************************************************************************
 * Bioclipse script to calculate 2 descriptors for a molecule.
 * Requires the Chemoinformatics and QSAR features to be installed. 
 *
 * Author: Ola Spjuth
 *
 ******************************************************************************/
mol=cdk.fromSMILES("C1CNCCC1CC(COC)CCNC");
descid="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#bpol";
descid2="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#hBondDonors";