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changed call to featurize-nitrosamines #363

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Aug 27, 2024
Merged

changed call to featurize-nitrosamines #363

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469d3f5
changed call to featurize-nitrosamines
ChemMitch Aug 27, 2024
566fff1
updating version of Featureize-Nitrosamines JAR
ChemMitch Aug 27, 2024
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Binary file renamed ...eatureize-Nitrosamines-0.0.2-SNAPSHOT.jar → ...eatureize-Nitrosamines-0.0.3-SNAPSHOT.jar
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49 changes: 32 additions & 17 deletions gsrs-module-substance-example/src/test/java/example/chem/FeatureGenerationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,17 +26,18 @@ void testOneMol() throws Exception{
structure.molfile = molfileText;
List<Map<String, String>> properties = FeatureUtils.calculateFeatures( structure.toChemical());
//properties.get(0).entrySet().forEach(e-> System.out.printf("key: %s = value: %s\n", e.getKey(), e.getValue()));
Assertions.assertEquals("5", properties.get(0).get("categoryScore"));
//Assertions.assertEquals("5", properties.get(0).get("categoryScore"));
Assertions.assertTrue(properties.isEmpty());
}

@Test
void testIVACAFTORType() throws Exception {
Chemical c1= Chemical.parse("c1ccc2c(c1)c(=O)cc[nH]2");

List<Map<String, String>> properties = FeatureUtils.calculateFeatures( c1);
assertEquals(1, properties.size());
List<Map<String, String>> properties = FeatureUtils.calculateFeatures( c1);
Assertions.assertTrue(properties.isEmpty());
/*assertEquals(1, properties.size());
assertEquals("A. Secondary Amine" ,properties.get(0).get("type"));
assertEquals("0,1", properties.get(0).get("Alpha-Hydrogens"));
assertEquals("0,1", properties.get(0).get("Alpha-Hydrogens"));*/
}

@Test
Expand All @@ -45,9 +46,9 @@ void testFostamatibib() throws Exception {

List<Map<String, String>> properties = FeatureUtils.calculateFeatures( c1);

assertEquals(2,properties.size());
assertEquals("A. Multiple Secondary Amine", properties.get(0).get("type"));
assertEquals("0,0", properties.get(0).get("Alpha-Hydrogens"));
assertEquals(0, properties.size());
/*assertEquals("A. Multiple Secondary Amine", properties.get(0).get("type"));
assertEquals("0,0", properties.get(0).get("Alpha-Hydrogens"));*/
}

@Test
Expand All @@ -57,27 +58,41 @@ public void testIsPiperazine() throws Exception {
Chemical c1= Chemical.parse("N1CCNCC1");
List<Map<String, String>> properties = FeatureUtils.calculateFeatures( c1);

assertEquals(2,properties.size());
assertEquals("A. Multiple Secondary Amine", properties.get(0).get("type"));
assertEquals(0, properties.size());
/*assertEquals("A. Multiple Secondary Amine", properties.get(0).get("type"));
assertEquals("2,2", properties.get(0).get("Alpha-Hydrogens"));
assertEquals("YES", properties.get(0).get( FeaturizeNitrosamine.FeaturePairRegistry.PIPERAZINE.getFeatureName()));
assertEquals("YES", properties.get(0).get( FeaturizeNitrosamine.FeaturePairRegistry.PIPERAZINE.getFeatureName()));*/
}

@Test
public void testCarboxylicAcidOnSaltDoesNotCount() throws Exception {
Chemical c1= Chemical.parse("O[C@H]([C@@H](O)C(O)=O)C(O)=O.COC1=CC=C(C[C@@H](C)[NH:20]C[C@H](O)C2=CC=C(O)C(NC=O)=C2)C=C1");
List<Map<String, String>> properties = FeatureUtils.calculateFeatures( c1);
assertEquals(1, properties.size());
assertEquals("A. Secondary Amine", properties.get(0).get("type"));
assertEquals("NO" ,properties.get(0).get(FeaturizeNitrosamine.FeaturePairRegistry.COOH.getFeatureName()));
assertEquals(0, properties.size());
/*assertEquals("A. Secondary Amine", properties.get(0).get("type"));
assertEquals("NO" ,properties.get(0).get(FeaturizeNitrosamine.FeaturePairRegistry.COOH.getFeatureName()));*/
}

@Test
public void testBenzylLikeFeatureShouldNotFindPsuedoAromaticity() throws Exception {
Chemical c1= Chemical.parse("C[C@H]([NH:3]C1=C2N=CNC2=NC=N1)C3=CC4=C(C(Cl)=CC=C4)C(=O)N3C5=CC=CC=C5");
List<Map<String, String>> properties = FeatureUtils.calculateFeatures( c1);
assertEquals(1, properties.size());
assertEquals("A. Secondary Amine", properties.get(0).get("type"));
assertEquals("NO", properties.get(0).get(FeaturizeNitrosamine.FeaturePairRegistry.ARYL_ALPHA.getFeatureName()));
assertEquals(0, properties.size());
/*assertEquals("A. Secondary Amine", properties.get(0).get("type"));
assertEquals("NO", properties.get(0).get(FeaturizeNitrosamine.FeaturePairRegistry.ARYL_ALPHA.getFeatureName()));*/
}

@Test
void testOneRealNitrosamine() throws Exception{
String molfileText = IOUtils.toString(
this.getClass().getResourceAsStream("/molfiles/M8LE2AF05P.mol"),
"UTF-8"
);
GinasChemicalStructure structure = new GinasChemicalStructure();
structure.molfile = molfileText;
List<Map<String, String>> properties = FeatureUtils.calculateFeatures( structure.toChemical());
//properties.get(0).entrySet().forEach(e-> System.out.printf("key: %s = value: %s\n", e.getKey(), e.getValue()));
Assertions.assertEquals("5", properties.get(0).get("categoryScore"));
}

}
2 changes: 1 addition & 1 deletion gsrs-module-substances-core/pom.xml
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Expand Up @@ -332,7 +332,7 @@
<dependency>
<groupId>gov.fda.gsrs</groupId>
<artifactId>Featureize-Nitrosamines</artifactId>
<version>0.0.2-SNAPSHOT</version>
<version>0.0.3-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
40 changes: 16 additions & 24 deletions gsrs-module-substances-core/src/main/java/gsrs/module/substance/utils/FeatureUtils.java
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Expand Up @@ -2,10 +2,8 @@

import gov.nih.ncats.molwitch.Chemical;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.*;

import gov.fda.gsrs.ndsri.FeaturizeNitrosamine;
import gov.fda.gsrs.ndsri.FeaturizeNitrosamine.FeatureJob;
import gov.fda.gsrs.ndsri.FeaturizeNitrosamine.FeatureResponse;
Expand All @@ -14,28 +12,22 @@
@Slf4j
public class FeatureUtils {
public static List<Map<String, String>> calculateFeatures(Chemical chemical) throws Exception{
FeatureJob fj;
try{
fj = FeatureJob.forOneNitrosamine(chemical);
} catch (Exception ex) {
//log.info("forOneNitrosamine failed; using regular constructor");
//fj = new FeatureJob(chemical);

//For now, don't generate properties unless it's a legitimate NNO
try {
Optional<FeatureResponse> response = FeaturizeNitrosamine.forMostPotentNitrosamine(chemical);
List<Map<String,String>> maps = new ArrayList<>();
if( response.isPresent()){
FeatureResponse r = response.get();
Map<String, String> ret = new HashMap<>();
r.getFeatureSet().entrySet().forEach(e-> ret.put(e.getKey(), e.getValue()));
ret.put("categoryScore", Integer.toString( r.getCategoryScore()));
ret.put("sumOfScores", Integer.toString(r.getSumOfScores()));
ret.put("type", r.getType());
maps.add(ret);
}
return maps;
} catch (IllegalArgumentException ex) {
return new ArrayList<>();
}

List<FeatureResponse> resp = FeaturizeNitrosamine.fingerprintNitrosamine(fj);

List<Map<String,String>> maps = new ArrayList<>();
resp.forEach(r->{
Map<String, String> ret = new HashMap<>();
r.getFeatureSet().entrySet().forEach(e-> ret.put(e.getKey(), e.getValue()));
ret.put("categoryScore", Integer.toString( r.getCategoryScore()));
ret.put("sumOfScores", Integer.toString(r.getSumOfScores()));
ret.put("type", r.getType());
maps.add(ret);
});
return maps;
}
}
2 changes: 1 addition & 1 deletion installExtraJars.cmd
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@@ -1,4 +1,4 @@
mvnw.cmd install:install-file -Dfile=extraJars/applications-api-3.1-SNAPSHOT.jar
mvnw.cmd install:install-file -Dfile=extraJars/products-api-3.1.1-SNAPSHOT.jar
mvnw.cmd install:install-file -Dfile=extraJars/clinical-trials-api-3.1.1-SNAPSHOT.jar
mvnw.cmd install:install-file -Dfile=extraJars/Featureize-Nitrosamines-0.0.2-SNAPSHOT.jar
mvnw.cmd install:install-file -Dfile=extraJars/Featureize-Nitrosamines-0.0.3-SNAPSHOT.jar
2 changes: 1 addition & 1 deletion installExtraJars.sh
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@@ -1,4 +1,4 @@
./mvnw install:install-file -Dfile=extraJars/applications-api-3.1-SNAPSHOT.jar
./mvnw install:install-file -Dfile=extraJars/products-api-3.1.1-SNAPSHOT.jar
./mvnw install:install-file -Dfile=extraJars/clinical-trials-api-3.1.1-SNAPSHOT.jar
./mvnw install:install-file -Dfile=extraJars/Featureize-Nitrosamines-0.0.2-SNAPSHOT.jar
./mvnw install:install-file -Dfile=extraJars/Featureize-Nitrosamines-0.0.3-SNAPSHOT.jar