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adding stereochemistryComments/'additional stereochemistry' to the def #367

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merged 4 commits into from
Oct 29, 2024
Merged

adding stereochemistryComments/'additional stereochemistry' to the def #367

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fafb49e
adding stereochemistryComments/'additional stereochemistry' to the def
ChemMitch Aug 30, 2024
e4c180b
added 'RACEMIC' to the types of stereochemistry that make
ChemMitch Sep 18, 2024
251f201
Merge branch 'master' into def_hash_chem1
ChemMitch Oct 29, 2024
808d623
adjusted calculation of def hash based on stereochemistry: include
ChemMitch Oct 29, 2024
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89 changes: 87 additions & 2 deletions gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,11 @@
import ix.core.chem.StructureProcessor;
import ix.core.models.Structure;
import ix.ginas.modelBuilders.ChemicalSubstanceBuilder;
import ix.ginas.modelBuilders.SubstanceBuilder;
import ix.ginas.models.v1.ChemicalSubstance;
import ix.ginas.models.v1.GinasChemicalStructure;
import ix.ginas.modelBuilders.MixtureSubstanceBuilder;
import ix.ginas.modelBuilders.StructurallyDiverseSubstanceBuilder;
import ix.ginas.modelBuilders.SubstanceBuilder;
import ix.ginas.models.v1.*;
import lombok.extern.slf4j.Slf4j;
import org.junit.jupiter.api.Assertions;
Expand Down Expand Up @@ -63,6 +65,40 @@ public void testOpticalInDefinitionalHashCalcNeg() throws Exception {
Assertions.assertTrue(definitionalElements.stream().noneMatch(de->de.getKey().equals(opticalActivityKey)));
}

@Test
public void testOpticalInDefinitionalHashCalcNeg2() throws Exception {
String opticalActivityKey="structure.properties.opticalActivity";
String structureJson = "{\n" +
" \"opticalActivity\": \"UNSPECIFIED\",\n" +
" \"molfile\": \"\\n ACCLDraw07282209012D\\n\\n 5 4 0 0 0 0 0 0 0 0999 V2000\\n 10.5000 -8.5938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 11.5229 -8.0032 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0\\n 11.5229 -6.8217 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.5460 -8.5939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 13.5692 -8.0032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0 0 0 0\\n 2 3 1 0 0 0 0\\n 2 4 1 0 0 0 0\\n 4 5 1 0 0 0 0\\nM END\",\n" +
" \"stereoCenters\": 1,\n" +
" \"definedStereo\": 0,\n" +
" \"ezCenters\": 0,\n" +
" \"charge\": 0,\n" +
" \"mwt\": 92.56726,\n" +
" \"count\": 1,\n" +
" \"stereochemistry\": \"UNKNOWN\"\n" +
"}\n" +
"";
ObjectMapper om = new ObjectMapper();
Structure rawStructure = om.readValue(structureJson, Structure.class);
Structure instrumentedStructure =structureProcessor.instrument(rawStructure.toChemical(), true);
GinasChemicalStructure ginasChemicalStructure = new GinasChemicalStructure(instrumentedStructure);
ginasChemicalStructure.setStereoChemistry(Structure.Stereo.UNKNOWN);

ChemicalSubstanceBuilder builder = new ChemicalSubstanceBuilder();
ChemicalSubstance chem =builder
.setStructure(ginasChemicalStructure)
.addName("2-chlorobutane")
.build();
ChemicalSubstanceDefinitionalElementImpl defHashCalculator = new ChemicalSubstanceDefinitionalElementImpl();
List<DefinitionalElement> definitionalElements = new ArrayList<>();
defHashCalculator.computeDefinitionalElements(chem, definitionalElements::add);
definitionalElements.forEach(de-> System.out.printf("key: %s = %s\n", de.getKey(), de.getValue()));
Assertions.assertTrue(definitionalElements.stream().anyMatch(de->de.getKey().equals(opticalActivityKey)));
}


@Test
public void testOpticalInDefinitionalHashCalcPos() throws Exception {
String opticalActivityKey="structure.properties.opticalActivity";
Expand Down Expand Up @@ -94,7 +130,56 @@ public void testOpticalInDefinitionalHashCalcPos() throws Exception {
List<DefinitionalElement> definitionalElements = new ArrayList<>();
defHashCalculator.computeDefinitionalElements(chem, definitionalElements::add);
definitionalElements.forEach(de-> System.out.printf("key: %s = %s\n", de.getKey(), de.getValue()));
Assertions.assertTrue(definitionalElements.stream().anyMatch(de->de.getKey().equals(opticalActivityKey)));
Assertions.assertTrue(definitionalElements.stream().noneMatch(de->de.getKey().equals(opticalActivityKey)));
}

@Test
public void testStereoCommentsInDefinitionalHashCalcPos() throws Exception {
String additionalStereochemistryKey="structure.properties.stereoComments";
String dataFileName ="R0NL28355M.json";
File proteinFile = new ClassPathResource("testJSON/" + dataFileName).getFile();
ChemicalSubstanceBuilder builder = SubstanceBuilder.from(proteinFile);

ChemicalSubstance chem =builder.build();
System.out.printf("atropisomerism: %s\n", chem.getStructure().atropisomerism);
ChemicalSubstanceDefinitionalElementImpl defHashCalculator = new ChemicalSubstanceDefinitionalElementImpl();
List<DefinitionalElement> definitionalElements = new ArrayList<>();
defHashCalculator.computeDefinitionalElements(chem, definitionalElements::add);
definitionalElements.forEach(de-> System.out.printf("key: %s = %s\n", de.getKey(), de.getValue()));
Assertions.assertTrue(definitionalElements.stream().anyMatch(de->de.getKey().equals(additionalStereochemistryKey)));
}

@Test
public void testStereoCommentsInDefinitionalHashCalcNeg() throws Exception {
String additionalStereochemistryKey="structure.properties.stereoComments";
String dataFileName ="R0NL28355M.json";
File proteinFile = new ClassPathResource("testJSON/" + dataFileName).getFile();
ChemicalSubstanceBuilder builder = SubstanceBuilder.from(proteinFile);

ChemicalSubstance chem =builder.build();
chem.getStructure().atropisomerism= Structure.NYU.No;
System.out.printf("atropisomerism: %s\n", chem.getStructure().atropisomerism);
ChemicalSubstanceDefinitionalElementImpl defHashCalculator = new ChemicalSubstanceDefinitionalElementImpl();
List<DefinitionalElement> definitionalElements = new ArrayList<>();
defHashCalculator.computeDefinitionalElements(chem, definitionalElements::add);
definitionalElements.forEach(de-> System.out.printf("key: %s = %s\n", de.getKey(), de.getValue()));
Assertions.assertFalse(definitionalElements.stream().anyMatch(de->de.getKey().equals(additionalStereochemistryKey)));
}

@Test
public void testStereoCommentsInDefinitionalHashCalcNeg2() throws Exception {
String additionalStereochemistryKey="structure.properties.stereoComments";
String dataFileName ="R0NL28355M.json";
File proteinFile = new ClassPathResource("testJSON/" + dataFileName).getFile();
ChemicalSubstanceBuilder builder = SubstanceBuilder.from(proteinFile);

ChemicalSubstance chem =builder.build();
chem.getStructure().stereoComments = null;
ChemicalSubstanceDefinitionalElementImpl defHashCalculator = new ChemicalSubstanceDefinitionalElementImpl();
List<DefinitionalElement> definitionalElements = new ArrayList<>();
defHashCalculator.computeDefinitionalElements(chem, definitionalElements::add);
definitionalElements.forEach(de-> System.out.printf("key: %s = %s\n", de.getKey(), de.getValue()));
Assertions.assertFalse(definitionalElements.stream().anyMatch(de->de.getKey().equals(additionalStereochemistryKey)));
}

@Test
Expand Down
23 changes: 23 additions & 0 deletions gsrs-module-substance-example/src/test/resources/molfiles/M8LE2AF05P.mol
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Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@

Marvin 01132111322D

9 9 0 0 0 0 999 V2000
7.3523 -4.5535 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
7.6081 -3.7619 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
6.9404 -3.2827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2700 -3.7619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5257 -4.5535 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
6.0411 -5.2212 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3916 -3.5035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.8370 -5.2212 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
7.5031 -5.9750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
1 5 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 6 0 0 0
2 7 1 1 0 0 0
1 8 1 0 0 0 0
8 9 2 0 0 0 0
M END
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