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refactoder CS and CHEMBL to separate classes
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <projectDescription> | ||
| <name>net.bioclipse.ds.models_site</name> | ||
| <comment></comment> | ||
| <projects> | ||
| </projects> | ||
| <buildSpec> | ||
| <buildCommand> | ||
| <name>org.eclipse.pde.FeatureBuilder</name> | ||
| <arguments> | ||
| </arguments> | ||
| </buildCommand> | ||
| </buildSpec> | ||
| <natures> | ||
| <nature>org.eclipse.pde.FeatureNature</nature> | ||
| </natures> | ||
| </projectDescription> |
155 changes: 155 additions & 0 deletions
155
...ipse.ds.chemspider/src/net/bioclipse/ds/chemspider/CopyOfSimilaritySearchChEMBLModel.java
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| @@ -0,0 +1,155 @@ | ||
| package net.bioclipse.ds.chemspider; | ||
|
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| import java.text.DecimalFormat; | ||
| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
|
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| import org.apache.log4j.Logger; | ||
| import org.eclipse.core.runtime.IProgressMonitor; | ||
|
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| import net.bioclipse.cdk.business.ICDKManager; | ||
| import net.bioclipse.cdk.domain.ICDKMolecule; | ||
| import net.bioclipse.chemspider.Activator; | ||
| import net.bioclipse.chemspider.business.IChemspiderManager; | ||
| import net.bioclipse.core.business.BioclipseException; | ||
| import net.bioclipse.ds.model.AbstractDSTest; | ||
| import net.bioclipse.ds.model.DSException; | ||
| import net.bioclipse.ds.model.ITestResult; | ||
| import net.bioclipse.ds.model.result.ExternalMoleculeMatch; | ||
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| /** | ||
| * Model for DS based on ChemSpider SimilaritySearch. | ||
| * | ||
| * @author Ola Spjuth | ||
| * | ||
| */ | ||
| public class CopyOfSimilaritySearchChEMBLModel extends AbstractDSTest{ | ||
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| private static final String TANIMOTO_DISTANCE = "distance.tanimoto"; | ||
| private static final int MAX_NEIGHBORS = 15; | ||
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| private static final Logger logger = Logger.getLogger(CopyOfSimilaritySearchChEMBLModel.class); | ||
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| private float tanimoto; | ||
| DecimalFormat formatter = new DecimalFormat( "0.00" ); | ||
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| @Override | ||
| public List<String> getRequiredParameters() { | ||
| List<String> ret=new ArrayList<String>(); | ||
| ret.add( TANIMOTO_DISTANCE ); | ||
| return ret; | ||
| } | ||
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| @Override | ||
| public void initialize(IProgressMonitor monitor) throws DSException { | ||
| super.initialize(monitor); | ||
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| tanimoto=Float.parseFloat(getParameters().get(TANIMOTO_DISTANCE)); | ||
| logger.debug("Chemspider similaritysearch is using tanimoto: " + tanimoto); | ||
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| } | ||
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| @Override | ||
| protected List<? extends ITestResult> doRunTest(ICDKMolecule molecule, | ||
| IProgressMonitor monitor) { | ||
|
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| //Managers we need | ||
| IChemspiderManager chemspider = Activator.getDefault().getJavaChemspiderManager(); | ||
| ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager(); | ||
|
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| //Hold results here | ||
| ArrayList<ExternalMoleculeMatch> results = new ArrayList<ExternalMoleculeMatch>(); | ||
|
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| //Do chemspider search | ||
| List<ICDKMolecule> resultMols=null; | ||
| try { | ||
| resultMols = chemspider.similaritySearch(molecule, tanimoto, monitor); | ||
| } catch (BioclipseException e1) { | ||
| return returnError("Service failed to complete. Incorrect security token?", e1.getMessage()); | ||
| } | ||
| if (resultMols==null) | ||
| return returnError("Null results",""); | ||
| logger.debug("Model " + getName() + " had " + resultMols.size() + " hits"); | ||
|
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| // List<ICDKMolecule> resultMols = new ArrayList<ICDKMolecule>(); | ||
| // try { | ||
| // resultMols.add(cdk.fromSMILES("CCC")); | ||
| // } catch (BioclipseException e1) { | ||
| // e1.printStackTrace(); | ||
| // } | ||
|
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| //Set up results, reduce to max 15 results | ||
| logger.debug("Setting up results..."); | ||
| for (ICDKMolecule cdkmol : resultMols.subList(0, Math.min(resultMols.size(), MAX_NEIGHBORS))){ | ||
|
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| //We calculate tanimoto locally for now | ||
| String distance = "N/A"; | ||
| try { | ||
| distance = "" + formatter.format(cdk.calculateTanimoto(molecule, cdkmol)); | ||
| } catch (BioclipseException e) { | ||
| logger.error("Could not calculate tanimoto: " + e.getMessage()); | ||
| } | ||
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| //Get name and other params from stored props on mol, set in chemspider manager | ||
| String molname=(String) cdkmol.getProperty("chemspider.commonname", null); | ||
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| logger.debug("Hit: " + molname + " ; distance: " + distance); | ||
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| ExternalMoleculeMatch match = new ExternalMoleculeMatch(molname + " (tanimoto=" + distance + ")" , cdkmol, | ||
| ITestResult.INFORMATIVE); | ||
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| Map<String, Map<String, String>> categories = new HashMap<String, Map<String,String>>(); | ||
| Map<String,String> props = new HashMap<String, String>(); | ||
| Integer csid = (Integer) cdkmol.getProperty("chemspider.id", null); | ||
| props.put("Chemspider ID" , "" + csid); | ||
| props.put("InChI" , "" + cdkmol.getProperty("chemspider.inchi", null)); | ||
| props.put("InChIkey" , "" + cdkmol.getProperty("chemspider.inchikey", null)); | ||
| props.put("AlogP" , "" + cdkmol.getProperty("chemspider.alogp", null)); | ||
| props.put("XlogP" , "" + cdkmol.getProperty("chemspider.xlogp", null)); | ||
| props.put("Average mass" , "" + cdkmol.getProperty("chemspider.averagemass", null)); | ||
| props.put("Molecular formula" , "" + cdkmol.getProperty("chemspider.mf", null)); | ||
| props.put("Molecular wheight" , "" + cdkmol.getProperty("chemspider.mw", null)); | ||
| props.put("Monoisotopic mass" , "" + cdkmol.getProperty("chemspider.monoisotopicmass", null)); | ||
| props.put("Nominal mass" , "" + cdkmol.getProperty("chemspider.nominalmass", null)); | ||
| categories.put("Chemspider", props); | ||
|
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| //Look up interactions in ChEMBL | ||
| try { | ||
| List<ChemblInteraction> chemblInteractions = ChemblLookup.lookupCSID(csid); | ||
| // List<ChemblInteraction> chemblInteractions = ChemblLookup.lookupCSID(10368587); | ||
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| if (chemblInteractions!=null){ | ||
| for (ChemblInteraction ci : chemblInteractions){ | ||
| Map<String,String> ciprops = new HashMap<String, String>(); | ||
| if (ci.getRelation()!=null) | ||
| ciprops.put("Value" , ci.getRelation() + ci.getValue()); | ||
| else | ||
| ciprops.put("Value" , ci.getValue()); | ||
| ciprops.put("Unit" , ci.getUnit()); | ||
| ciprops.put("Target type" , ci.getTargetType()); | ||
| ciprops.put("Interaction type" , ci.getInteractionType()); | ||
| ciprops.put("Description" , ci.getDescription()); | ||
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| categories.put("Target: " + ci.getTitle(), ciprops); | ||
| } | ||
| } | ||
| else{ | ||
| logger.debug("No ChEMBL interactions for CID=" + csid); | ||
| } | ||
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| } catch (BioclipseException e) { | ||
| logger.error("Error querying chembl: " + e.getMessage()); | ||
| } | ||
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| match.setProperties(categories); | ||
| results.add(match); | ||
| } | ||
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| return results; | ||
| } | ||
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| } |
80 changes: 80 additions & 0 deletions
80
....bioclipse.ds.chemspider/src/net/bioclipse/ds/chemspider/SimilaritySearchChEMBLModel.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| package net.bioclipse.ds.chemspider; | ||
|
|
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| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
|
|
||
| import org.apache.log4j.Logger; | ||
| import org.eclipse.core.runtime.IProgressMonitor; | ||
|
|
||
| import net.bioclipse.cdk.domain.ICDKMolecule; | ||
| import net.bioclipse.core.business.BioclipseException; | ||
| import net.bioclipse.ds.model.ITestResult; | ||
| import net.bioclipse.ds.model.result.ExternalMoleculeMatch; | ||
|
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| /** | ||
| * Model for DS based on ChemSpider SimilaritySearch, | ||
| * annotates with ChEMBL interaction data. | ||
| * | ||
| * @author Ola Spjuth | ||
| * | ||
| */ | ||
| public class SimilaritySearchChEMBLModel extends SimilaritySearchModel{ | ||
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| private static final Logger logger = Logger.getLogger(SimilaritySearchChEMBLModel.class); | ||
|
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| @Override | ||
| protected List<? extends ITestResult> doRunTest(ICDKMolecule molecule, | ||
| IProgressMonitor monitor) { | ||
|
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| List<? extends ITestResult> matches = super.doRunTest(molecule, monitor); | ||
| List<ExternalMoleculeMatch> toRemove = new ArrayList<ExternalMoleculeMatch>(); | ||
|
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| for (ITestResult tr : matches){ | ||
| if (!(tr instanceof ExternalMoleculeMatch)) { | ||
| continue; | ||
| } | ||
| ExternalMoleculeMatch match = (ExternalMoleculeMatch)tr; | ||
|
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| Map<String, Map<String, String>> categories = match.getProperties(); | ||
| Map<String, String> csprops = categories.get("Chemspider"); | ||
| int csid=Integer.parseInt(csprops.get("Chemspider ID")); | ||
|
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| //Look up interactions in ChEMBL | ||
| try { | ||
| List<ChemblInteraction> chemblInteractions = ChemblLookup.lookupCSID(csid); | ||
| // List<ChemblInteraction> chemblInteractions = ChemblLookup.lookupCSID(10368587); | ||
|
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| if (chemblInteractions!=null){ | ||
| for (ChemblInteraction ci : chemblInteractions){ | ||
| Map<String,String> ciprops = new HashMap<String, String>(); | ||
| if (ci.getRelation()!=null) | ||
| ciprops.put("Value" , ci.getRelation() + ci.getValue()); | ||
| else | ||
| ciprops.put("Value" , ci.getValue()); | ||
| ciprops.put("Unit" , ci.getUnit()); | ||
| ciprops.put("Target type" , ci.getTargetType()); | ||
| ciprops.put("Interaction type" , ci.getInteractionType()); | ||
| ciprops.put("Description" , ci.getDescription()); | ||
|
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| categories.put("Target: " + ci.getTitle(), ciprops); | ||
| } | ||
| } | ||
| else{ | ||
| logger.debug("No ChEMBL interactions for CID=" + csid); | ||
| toRemove.add(match); | ||
| } | ||
|
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| } catch (BioclipseException e) { | ||
| logger.error("Error querying chembl: " + e.getMessage()); | ||
| } | ||
|
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| } | ||
|
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| //Remove the ones with no ChEMBL data | ||
| matches.removeAll(toRemove); | ||
| return matches; | ||
| } | ||
|
|
||
| } |
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