Ola Spjuth olas
olas
/ hivpred.js
Created
January 15, 2009 14:44
Predict drug susceptibility for HIV mutant using XMPP service
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| /******************************************************************************* | |
| * 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. |
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| //Download PDB | |
| res=ws.downloadPDBAsFile("1d66") | |
| ui.open(res) | |
| //Do some jmol visualization | |
| jmol.run("move 0 0 90 00 0 0 0 0 1;set selectionhalos off; select all; spacefill 0; cartoon on;") | |
| jmol.run("select nucleic; isosurface dna1 solvent; delay 1; color isosurface red;"); | |
| jmol.run("delay 1; color isosurface blue; delay 1; color isosurface translucent; move 0 360 90 90 0 0 0 0 4;"); |
olas
/ Calculate descriptors for list of mols.js
Created
April 14, 2009 13:57
Calculate a list of descriptors (no params) for a list of molecules
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| /******************************************************************************* | |
| * Bioclipse-script to calculate a list of descriptors for a list of molecules. | |
| * This script does not support parameters to descriptors and requires the | |
| * Chemoinformatics and QSAR features to be installed. | |
| * | |
| * Author: Ola Spjuth | |
| * | |
| ******************************************************************************/ | |
| //Set up list of descriptors |
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| /******************************************************************************* | |
| * 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"; |
olas
/ gencoords.js
Created
April 15, 2009 13:06
Generate different coordinates on a list of molecules
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| /******************************************************************************* | |
| * 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")); |
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| //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
/ Multiple-mol-manipulation.js
Created
April 15, 2009 14:09
Basic manipulation of multiple mols
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| //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) |
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| /******************************************************************************* | |
| * 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
/ Build a molecule using Bioclipse script for JChemPaint.js
Created
April 17, 2009 20:55
— forked from egonw/buildMolecule.js
Iteratively build mol using JCP
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| /******************************************************************************* | |
| * 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) |
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| /******************************************************************************* | |
| * 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. |
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