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olas / MoleculeImageCreator.java
Created November 29, 2010 13:23
MoleculeImageCreator
package cdk.imagecreator;
import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.Image;
import java.awt.Rectangle;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import java.util.ArrayList;
import java.util.List;
@olas
olas / OpenTox server issue
Created November 11, 2010 11:27
12:22:03.442 DEBUG [n.b.o.qsar.OpenToxDescriptorCalculator] Trying service: http://apps.ideaconsult.net:8080/ambit2/ OTdescriptor: http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
12:22:03.443 DEBUG [n.b.opentox.business.OpentoxManager] Creating data set
12:22:03.747 DEBUG [net.bioclipse.opentox.api.Dataset] Response: http://apps.ideaconsult.net:8080/ambit2/task/485dbe4c-4e96-4d6a-9fa6-663edb07257e
12:22:03.748 DEBUG [net.bioclipse.opentox.api.Dataset] Task: http://apps.ideaconsult.net:8080/ambit2/task/485dbe4c-4e96-4d6a-9fa6-663edb07257e
12:22:04.976 DEBUG [net.bioclipse.opentox.api.Task] Task status: 200
12:22:04.999 DEBUG [net.bioclipse.opentox.api.Task] Task: http://apps.ideaconsult.net:8080/ambit2/task/485dbe4c-4e96-4d6a-9fa6-663edb07257e
12:22:05.000 DEBUG [net.bioclipse.opentox.api.Task] -> 200
@olas
olas / hivdrc.js
Created May 17, 2010 15:50
Invoke HIVDRC services in Bioclipse
seq1="PQITLWQRPLVTIKIGGQLKEALLDTGADNTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF";
seq2="PQITLWQRPVVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKTIGTVLVGPTPVNIIGRSLLTQIGCTLNF";
hivdrc.predictPI(seq1);
hivdrc.predictPI(seq2);
@olas
olas / testfil
Created March 1, 2010 11:10
$RFMT $RIREG 1
A
B
C
$RFMT $RIREG 2
A
B
weee
hoow
C
@olas
olas / PopulateStructureDB.js
Created December 28, 2009 12:58
//==============================================================
// 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");
@olas
olas / matrix_with_lables.csv
Created November 5, 2009 13:46
RESPONSE XLogP LipinskiFailures ALogP ALogp2 AMR
C8H10ClNO3S 9.080000000000000e-001 1.01 0.00 -0.19 0.04 54.00
C13H13NO3S 2.142000000000000e+000 1.84 0.00 0.47 0.22 73.56
C14H15NO3S 2.477000000000000e+000 2.23 0.00 0.92 0.84 77.84
C13H12ClNO3S 2.732000000000000e+000 1.99 0.00 0.84 0.71 78.27
C15H17NO3S 2.773000000000000e+000 2.62 0.00 1.37 1.86 82.12
C18H28N2OSi NaN 3.60 0.00 2.20 4.83 87.25
@olas
olas / vscreen.js
Created October 3, 2009 10:34
//==============================================================
//Filter a StructureDB instance using the VScreen feature
//Author: Ola Spjuth
//==============================================================
var DB = "Drugbank"; //Refer to an existing StructureDB database
//Add some filters
filters=java.util.ArrayList();
//Xlogp should be between -2 and 4
@olas
olas / metaprint2d.js
Created September 28, 2009 12:36
//Script to predict MetaPrint2D for two SMILES using Bioclipse.
//Author: Ola Spjuth
mollist=cdk.createMoleculeList();
mol1=cdk.fromSMILES("CN(C)CCC1=CNC2=C1C=C(C=C2)CC1NC(=O)OC1");
mol2=cdk.fromSMILES("CN(C)CCC1=CNc2c1cc(cc2)CC1NC(=O)OC1");
mollist.add(mol1);
mollist.add(mol2);
res=metaprint2d.calculate(mollist);
js.print("\nMetaprint2D results\n=============\n" + res);
@olas
olas / scripting-MetaPrint2D.js
Created August 19, 2009 15:36
//This is an example how to use MetaPrint2D in a Bioclipse Script
//Author: Ola Spjuth
mollist=cdk.createMoleculeList();
mol1=cdk.fromSMILES("CN(C)CCC1=CNC2=C1C=C(C=C2)CC1NC(=O)OC1");
mol2=cdk.fromSMILES("CN(C)CCC1=CNc2c1cc(cc2)CC1NC(=O)OC1");
mollist.add(mol1);
mollist.add(mol2);
res=metaprint2d.calculate(mollist);
js.print("\nMetaprint2D results\n=============\n" + res);
@olas
olas / dl-align-seqs.js
Created August 6, 2009 17:00
// Download, translate, and align sequences
dl = biows.queryEMBL("Z54287,Z54289");
prots = biojava.DNAtoProtein(dl);
aln = kalignws.alignProteins(prots);
js.print(aln.get(0));
js.print(aln.get(1));