added new method to FeatureJob: forOneNitrosamine

.gitignore

@@ -0,0 +1,2 @@
+/Featureize-Nitrosamines.iml
+/target/

pom.xml

@@ -24,7 +24,7 @@
 
     <groupId>gov.fda.gsrs</groupId>
     <artifactId>Featureize-Nitrosamines</artifactId>
-    <version>0.0.1-SNAPSHOT</version>
+    <version>0.0.4-SNAPSHOT</version>
 
     <name>Featurize-Nitrosamines</name>
 

src/main/java/gov/fda/gsrs/ndsri/FeaturizeNitrosamine.java

@@ -327,6 +327,24 @@ public FeatureJob(String name, Chemical c,int forceC, boolean useMap, boolean ad
 			}
 		}
 
+		public static FeatureJob forOneNitrosamine(Chemical c){
+			c.atoms().forEach(a->a.setAtomToAtomMap(0));
+			List<Integer> sites = markAllNitrosamines(c);
+
+			List<Chemical> chems = new ArrayList<>();
+			for(int m:sites){
+				chems.add(removeNitrosamine(c.copy(), m));
+			}
+			if(chems.size()!=1){
+				System.out.println(chems.size());
+				throw new IllegalArgumentException("Wrong number of nitrosamines for this method. Expected 1.");
+			}
+			FeatureJob fj = new FeatureJob(chems.get(0));
+			fj.addNitrosamine=true;
+			fj.useMap=true;
+
+			return fj;
+		}
 	}
 
 
@@ -521,8 +539,7 @@ public static List<FeatureResponse> fingerprintNitrosamine(FeatureJob fj) throws
 				}
 			}
 		}
-
-
+		System.out.printf("computed type: %s\n", type);
 
 		if(atList.size()>0 || !got){
 			int i=1;
@@ -1750,4 +1767,54 @@ public static void run(Stream<String> inputStream, ParsedOptions parsedOptions)
 
 		}
 	}
+
+	public static Optional<FeatureResponse> forMostPotentNitrosamine(Chemical c){
+		c.atoms().forEach(a->a.setAtomToAtomMap(0));
+		List<Integer> sites = markAllNitrosamines(c);
+		if(sites.isEmpty()){
+			throw new IllegalArgumentException("Wrong number of nitrosamines for this method. Expected 1 or more.");
+		}
+
+		List<Chemical> chems = new ArrayList<>();
+		for(int m:sites){
+			chems.add(removeNitrosamine(c.copy(), m));
+		}
+
+		return chems.stream()
+				.map(cc->new FeatureJob(cc))
+				.peek(fj->fj.addNitrosamine=false)
+				.peek(fj->fj.useMap=true)
+				.map(fj->{
+
+					try{
+						return FeaturizeNitrosamine.fingerprintNitrosamine(fj);
+					}catch(Exception e){
+						return new ArrayList<FeatureResponse>();
+					}
+				})
+				.flatMap(r->r.stream())
+				.filter(r->!(r.getType().startsWith("B") || r.getType().startsWith("C"))) //eliminate amides and amide-like items
+				.sorted(Comparator.comparing(fr->fr.getCategoryScore()))
+				.findFirst()
+				.map(fr->{
+					if(fr.getCategoryScore()==1){
+						fr.addFeature("AI Limit (US)", "26.5 ng/day");
+					}else if(fr.getCategoryScore()==2){
+						fr.addFeature("AI Limit (US)", "100 ng/day");
+					}else if(fr.getCategoryScore()==3){
+						fr.addFeature("AI Limit (US)", "400 ng/day");
+					}else if(fr.getCategoryScore()==4){
+						fr.addFeature("AI Limit (US)", "1500 ng/day");
+					}else if(fr.getCategoryScore()==5){
+						fr.addFeature("AI Limit (US)", "1500 ng/day");
+					}
+					if(chems.size()==1){
+						fr.setType("Single N-nitroso group");
+					}else{
+						fr.setType("Most potent of multiple N-nitroso groups");
+					}
+					return fr;
+				});
+	}
+
 }

src/test/java/gov/nih/ncats/molwitch/renderer/FeatureParsingTests.java

@@ -1,13 +1,15 @@
 package gov.nih.ncats.molwitch.renderer;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
 import java.io.IOException;
+import java.io.InputStream;
+import java.util.Arrays;
 import java.util.List;
+import java.util.Optional;
 import java.util.Set;
+import java.util.logging.Logger;
 import java.util.stream.Collectors;
 
+import org.apache.commons.io.IOUtils;
 import org.junit.Ignore;
 import org.junit.Test;
 
@@ -18,8 +20,48 @@
 import gov.fda.gsrs.ndsri.FeaturizeNitrosamine.FeatureResponse;
 import gov.nih.ncats.molwitch.Chemical;
 
+import static org.junit.Assert.*;
+
 public class FeatureParsingTests {
 
+
+	private static class TestMol {
+		private String molFileName;
+		private boolean expectData;
+		private String description;
+
+		public TestMol(String molFileName, boolean expectData, String description) {
+			this.molFileName = molFileName;
+			this.expectData = expectData;
+			this.description = description;
+		}
+
+		public String getMolFileName() {
+			return molFileName;
+		}
+
+		public void setMolFileName(String molFileName) {
+			this.molFileName = molFileName;
+		}
+
+		public boolean isExpectData() {
+			return expectData;
+		}
+
+		public void setExpectData(boolean expectData) {
+			this.expectData = expectData;
+		}
+
+		public String getDescription() {
+			return description;
+		}
+
+		public void setDescription(String description) {
+			this.description = description;
+		}
+
+	}
+
     @Test
     @Ignore
     public void testExportAtomMaps() throws IOException {
@@ -55,8 +97,7 @@ public void testIVACAFTORType() throws Exception {
 
     	FeatureResponse resp1= resp.get(0);
     	resp1.getChemical();
-//    	for()
-
+
     	assertEquals(1,resp.size());
     	assertEquals("A. Secondary Amine" ,resp1.getType());
     	assertEquals("0,1" ,resp1.getFeature(FeaturizeNitrosamine.FeaturePairRegistry.ALPHA_HYDROGENS.getFeatureName()).orElse(null));
@@ -75,8 +116,9 @@ public void testFostamatibib() throws Exception {
     	assertEquals("A. Multiple Secondary Amine" ,resp1.getType());
     	assertEquals("0,0" ,resp1.getFeature(FeaturizeNitrosamine.FeaturePairRegistry.ALPHA_HYDROGENS.getFeatureName()).orElse(null));
     }
-
-    @Test
+
+
+	@Test
     public void testSP3CarbonOnSmallRing() throws Exception {
     	Chemical c1= Chemical.parse("C1CCCCC1");
 
@@ -93,7 +135,7 @@ public void testSP3CarbonOnSmallHeteroRing() throws Exception {
     }
 
     @Test
-    public void testisPiperazine() throws Exception {
+    public void testIsPiperazine() throws Exception {
     	FeaturizeNitrosamine.GLOBAL_SETTINGS.DO_EXTENDED_FEATURES_TOO=true;
 
     	Chemical c1= Chemical.parse("N1CCNCC1");
@@ -116,8 +158,6 @@ public void testisPiperazine() throws Exception {
     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");
 
-    	//TODO: This should really work even without this part
-//    	c1.generateCoordinates();
     	FeatureJob fj = new FeatureJob(c1);
 
     	List<FeatureResponse> resp = FeaturizeNitrosamine.fingerprintNitrosamine(fj);
@@ -316,4 +356,71 @@ public void testAbacavirSulfateSecondaryAmine() throws Exception {
     	assertEquals("0,1" ,resp1.getFeature(FeaturizeNitrosamine.FeaturePairRegistry.ALPHA_HYDROGENS.getFeatureName()).orElse(null));
     }
 	//NC1=NC2=C(N=CN2[C@@H]3C[C@H](CO)C=C3)C(NC4CC4)=N1
+
+	@Test
+	public void testTartaricAcid() throws Exception {
+		//we expect this molecule not to have any nitrosamine potential whatsoever
+		Chemical c1= Chemical.parse("[C@@H]([C@H](C(=O)O)O)(C(=O)O)O");
+
+		FeatureJob fj = new FeatureJob(c1);
+
+		List<FeatureResponse> resp = FeaturizeNitrosamine.fingerprintNitrosamine(fj);
+
+		assertNotNull(resp);
+		System.out.println("got output");
+		assertTrue( resp.isEmpty());
+	}
+
+	@Test
+	public void testAmide() throws Exception {
+		//we expect this molecule not to have any nitrosamine potential whatsoever
+		Chemical c1= Chemical.parse("C(C)CCN(C(N)=N)N=O");
+
+		FeatureJob fj = new FeatureJob(c1);
+
+		List<FeatureResponse> resp = FeaturizeNitrosamine.fingerprintNitrosamine(fj);
+
+		assertNotNull(resp);
+		System.out.println("got output");
+		assertTrue( resp.isEmpty());
+	}
+
+	@Test
+	public void testNitrosamine() throws Exception {
+		Chemical testChemical = Chemical.parse("CCN(CC)N=O");
+		FeatureJob job = new FeatureJob(testChemical);
+		List<FeatureResponse> responses = FeaturizeNitrosamine.fingerprintNitrosamine(job);
+		assertNotNull(responses);
+		for(FeatureResponse resp: responses) {
+			System.out.printf("type: %s\n", resp.getType());
+		}
+	}
+
+	@Test
+	public void testNitrosamideSetFromMolfile() throws Exception {
+		List<TestMol> testData = Arrays.asList(new TestMol("nitrosamiide-like", false,
+				"nitrosamide-like with S expects no output"),
+				new TestMol("nitrosamiide-like2", false,
+						"nitrosamide-like with N expects no output"),
+				new TestMol("nitrosamine_amide", false, "amides are currently not supported by model"),
+				new TestMol("nitrosamine1", true, "nitrosamine produces output"));
+		testData.forEach(m->{
+			try {
+				InputStream stream = getClass().getResourceAsStream("/molfiles/" + m.molFileName + ".mol");
+				String molfileText = IOUtils.toString(stream, "UTF-8");
+				Chemical testChemical = Chemical.parse(molfileText);
+				Optional<FeatureResponse> response = FeaturizeNitrosamine.forMostPotentNitrosamine(testChemical);
+				assertEquals(m.expectData, response.isPresent());
+			} catch (Exception ex){
+				Logger.getLogger(this.getClass().getName()).warning(String.format("failure for %s", m.description));
+				fail();
+			}
+		});
+		/*InputStream stream =getClass().getResourceAsStream("/molfiles/nitrosamiide-like.mol");
+		String molfileText = IOUtils.toString(stream, "UTF-8");
+		Chemical testChemical = Chemical.parse(molfileText);
+		Optional<FeatureResponse> response = FeaturizeNitrosamine.forMostPotentNitrosamine(testChemical);
+		assertFalse(response.isPresent());*/
+	}
+
 }

src/test/resources/molfiles/nitrosamiide.mol

@@ -0,0 +1,24 @@
+
+  ACCLDraw10032421372D
+
+ 10  9  0  0  0  0  0  0  0  0999 V2000
+   11.1697  -12.9221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.3721  -13.3822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.9677  -13.3824    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.7657  -12.9221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.5637  -13.3824    0.0000 N   0  0  3  0  0  0  0  0  0  0  0  0
+   13.5637  -14.3037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.7690  -14.7655    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.3618  -12.9221    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   15.1592  -13.3822    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   14.3634  -14.7643    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+  3  4  1  0  0  0  0
+  4  5  1  0  0  0  0
+  5  6  1  0  0  0  0
+  6  7  1  0  0  0  0
+  5  8  1  0  0  0  0
+  8  9  2  0  0  0  0
+  6 10  2  0  0  0  0
+M  END

src/test/resources/molfiles/nitrosamine1.mol

@@ -0,0 +1,24 @@
+
+  ACCLDraw10032414512D
+
+ 10  9  0  0  0  0  0  0  0  0999 V2000
+   10.4139  -10.4343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.6163  -10.8944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.2119  -10.8946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.0099  -10.4343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.8079  -10.8946    0.0000 N   0  0  3  0  0  0  0  0  0  0  0  0
+   12.8098  -11.8159    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
+   12.0132  -12.2777    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   13.6060  -10.4343    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   14.4034  -10.8944    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   13.6076  -12.2765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+  3  4  1  0  0  0  0
+  4  5  1  0  0  0  0
+  5  6  1  0  0  0  0
+  6  7  1  0  0  0  0
+  5  8  1  0  0  0  0
+  8  9  2  0  0  0  0
+  6 10  1  0  0  0  0
+M  END

src/test/resources/molfiles/nitrosamine_amide.mol

@@ -0,0 +1,24 @@
+
+  ACCLDraw10032421262D
+
+ 10  9  0  0  0  0  0  0  0  0999 V2000
+   11.1697  -12.9221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.3721  -13.3822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.9677  -13.3824    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.7657  -12.9221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.5637  -13.3824    0.0000 N   0  0  3  0  0  0  0  0  0  0  0  0
+   13.5637  -14.3037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.7690  -14.7655    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   14.3618  -12.9221    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   15.1592  -13.3822    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   14.3634  -14.7643    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+  3  4  1  0  0  0  0
+  4  5  1  0  0  0  0
+  5  6  1  0  0  0  0
+  6  7  1  0  0  0  0
+  5  8  1  0  0  0  0
+  8  9  2  0  0  0  0
+  6 10  2  0  0  0  0
+M  END