Ola Spjuth olas
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| 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
/ OpenTox server issue
Created
November 11, 2010 11:27
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| 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 |
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| seq1="PQITLWQRPLVTIKIGGQLKEALLDTGADNTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF"; | |
| seq2="PQITLWQRPVVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKTIGTVLVGPTPVNIIGRSLLTQIGCTLNF"; | |
| hivdrc.predictPI(seq1); | |
| hivdrc.predictPI(seq2); |
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| $RFMT $RIREG 1 | |
| A | |
| B | |
| C | |
| $RFMT $RIREG 2 | |
| A | |
| B | |
| weee | |
| hoow | |
| C |
olas
/ PopulateStructureDB.js
Created
December 28, 2009 12:58
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| //============================================================== | |
| // 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
/ matrix_with_lables.csv
Created
November 5, 2009 13:46
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| 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
/ vscreen.js
Created
October 3, 2009 10:34
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| //============================================================== | |
| //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
/ metaprint2d.js
Created
September 28, 2009 12:36
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| //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
/ scripting-MetaPrint2D.js
Created
August 19, 2009 15:36
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| //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
/ dl-align-seqs.js
Created
August 6, 2009 17:00
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| // 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)); |
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