From 1c420171fb6bc66e01df37e4e04c7944446535e0 Mon Sep 17 00:00:00 2001 From: Mitch Miller Date: Mon, 23 Sep 2024 13:11:58 -0400 Subject: [PATCH 1/3] added defining properties to def hash for mixtures. Also, refactored property-adding def hash code to one place for all substance types --- .../java/example/chem/DefHashCalcTest.java | 26 +++++++++++++++++ .../MixtureDefinitionalElementImpl.java | 1 + .../PolymerDefinitionalElementImpl.java | 1 + .../SSG1DefinitionalElementImpl.java | 1 + ...turallyDiverseDefinitionalElementImpl.java | 25 ++-------------- .../DefinitionalElementImplementation.java | 29 +++++++++++++++++++ 6 files changed, 60 insertions(+), 23 deletions(-) diff --git a/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java b/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java index 848b67c35..c7931ee2c 100644 --- a/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java +++ b/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java @@ -3,18 +3,28 @@ import com.fasterxml.jackson.databind.ObjectMapper; import gsrs.module.substance.definitional.ChemicalSubstanceDefinitionalElementImpl; import gsrs.module.substance.definitional.DefinitionalElement; +import gsrs.module.substance.definitional.MixtureDefinitionalElementImpl; +import gsrs.springUtils.AutowireHelper; import gsrs.substances.tests.AbstractSubstanceJpaEntityTest; import ix.core.chem.StructureProcessor; import ix.core.models.Structure; import ix.ginas.modelBuilders.ChemicalSubstanceBuilder; +import ix.ginas.modelBuilders.MixtureSubstanceBuilder; +import ix.ginas.modelBuilders.SubstanceBuilder; import ix.ginas.models.v1.ChemicalSubstance; import ix.ginas.models.v1.GinasChemicalStructure; +import ix.ginas.models.v1.MixtureSubstance; +import lombok.extern.slf4j.Slf4j; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Test; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.core.io.ClassPathResource; + +import java.io.File; import java.util.ArrayList; import java.util.List; +@Slf4j public class DefHashCalcTest extends AbstractSubstanceJpaEntityTest { @Autowired @@ -85,4 +95,20 @@ public void testOpticalInDefinitionalHashCalcPos() throws Exception { 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 testPropertiesInDefinitionalHashMixtures() throws Exception { + String propertyElementName = "properties.HYDROPHILLIC-LIPOPHILLIC BALANCE (HLB).value"; + File mixtureFile = new ClassPathResource("testJSON/SURFHOPe C-1811_mixture.json").getFile(); + MixtureSubstanceBuilder builder = SubstanceBuilder.from(mixtureFile); + MixtureSubstance mixtureSubstance = builder.build(); + MixtureDefinitionalElementImpl definitionalElement = new MixtureDefinitionalElementImpl(); + AutowireHelper.getInstance().autowireAndProxy(definitionalElement); + + List definitionalElements = new ArrayList<>(); + definitionalElement.computeDefinitionalElements(mixtureSubstance, definitionalElements::add); + definitionalElements.forEach(de-> log.trace("key: {} = {}", de.getKey(), de.getValue())); + Assertions.assertTrue(definitionalElements.stream().anyMatch(de->de.getKey().equals(propertyElementName))); + } + } diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/MixtureDefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/MixtureDefinitionalElementImpl.java index 3151dd876..c29e04c05 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/MixtureDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/MixtureDefinitionalElementImpl.java @@ -72,5 +72,6 @@ private void additionalElementsFor( MixtureSubstance mixtureSubstance, Consumer< definitionalElementFactory.addDefinitionalElementsFor(mixtureSubstance.modifications, consumer); } + addPropertiesToDefHash(mixtureSubstance, consumer, log::trace ); } } diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/PolymerDefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/PolymerDefinitionalElementImpl.java index 0fe417773..e1657d89f 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/PolymerDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/PolymerDefinitionalElementImpl.java @@ -105,6 +105,7 @@ public void computeDefinitionalElements(Object s, Consumer } + addPropertiesToDefHash(polymerSubstance, consumer, log::debug); if (polymerSubstance.properties != null) { for (Property property : polymerSubstance.properties) { if (property.isDefining() && property.getValue() != null) { diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java index 45bae0ed9..4e08f6557 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java @@ -64,6 +64,7 @@ public void computeDefinitionalElements(Object s, Consumer } + addPropertiesToDefHash(ssg1, consumer, log::debug); if( ssg1.properties != null ) { for(Property property : ssg1.properties) { if(property.isDefining() && property.getValue() != null) { diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/StructurallyDiverseDefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/StructurallyDiverseDefinitionalElementImpl.java index 8775b0988..9bf4067d3 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/StructurallyDiverseDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/StructurallyDiverseDefinitionalElementImpl.java @@ -6,6 +6,7 @@ import ix.ginas.models.v1.Parameter; import ix.ginas.models.v1.Property; import ix.ginas.models.v1.StructurallyDiverseSubstance; +import ix.ginas.models.v1.Substance; import lombok.extern.slf4j.Slf4j; import org.springframework.beans.factory.annotation.Autowired; @@ -163,28 +164,6 @@ public void computeDefinitionalElements(Object s, Consumer consumer.accept(infraspecificNameElement); } - if( substance.properties != null ) { - for(Property property : substance.properties) { - if(property.isDefining() && property.getValue() != null) { - String defElementName = String.format("properties.%s.value", - property.getName()); - DefinitionalElement propertyValueDefElement = - DefinitionalElement.of(defElementName, property.getValue().toString(), 2); - consumer.accept(propertyValueDefElement); - log.trace("added def element for property " + defElementName); - for(Parameter parameter : property.getParameters()) { - defElementName = String.format("properties.%s.parameters.%s.value", - property.getName(), parameter.getName()); - if( parameter.getValue() != null) { - DefinitionalElement propertyParamValueDefElement = - DefinitionalElement.of(defElementName, - parameter.getValue().toString(), 2); - consumer.accept(propertyParamValueDefElement); - log.trace("added def element for property parameter " + defElementName); - } - } - } - } - } + addPropertiesToDefHash(substance, consumer, log::trace ); } } diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/services/DefinitionalElementImplementation.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/services/DefinitionalElementImplementation.java index 2887fc80c..1faaa7a07 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/services/DefinitionalElementImplementation.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/services/DefinitionalElementImplementation.java @@ -1,6 +1,9 @@ package gsrs.module.substance.services; import gsrs.module.substance.definitional.DefinitionalElement; +import ix.ginas.models.v1.Parameter; +import ix.ginas.models.v1.Property; +import ix.ginas.models.v1.Substance; import java.util.function.Consumer; @@ -9,4 +12,30 @@ public interface DefinitionalElementImplementation { boolean supports(Object s); void computeDefinitionalElements(Object s, Consumer consumer); + + default void addPropertiesToDefHash(Substance substance, Consumer consumer, Consumer logger) { + if( substance.properties != null ) { + for(Property property : substance.properties) { + if(property.isDefining() && property.getValue() != null) { + String defElementName = String.format("properties.%s.value", + property.getName()); + DefinitionalElement propertyValueDefElement = + DefinitionalElement.of(defElementName, property.getValue().toString(), 2); + consumer.accept(propertyValueDefElement); + logger.accept("added def element for property " + defElementName); + for(Parameter parameter : property.getParameters()) { + defElementName = String.format("properties.%s.parameters.%s.value", + property.getName(), parameter.getName()); + if( parameter.getValue() != null) { + DefinitionalElement propertyParamValueDefElement = + DefinitionalElement.of(defElementName, + parameter.getValue().toString(), 2); + consumer.accept(propertyParamValueDefElement); + logger.accept("added def element for property parameter " + defElementName); + } + } + } + } + } + } } From 23e8900d8b13c8717f82bf056676148da392d6ce Mon Sep 17 00:00:00 2001 From: Mitch Miller Date: Mon, 23 Sep 2024 14:22:32 -0400 Subject: [PATCH 2/3] cleaned up polymers and SSG1 and additional unit test --- .../java/example/chem/DefHashCalcTest.java | 20 ++ ...b6a-6b0d-4733-a1a4-b2b38a569daa_props.json | 1 + .../testJSON/SURFHOPe C-1811_mixture.json | 195 ++++++++++++++++++ .../PolymerDefinitionalElementImpl.java | 24 --- .../SSG1DefinitionalElementImpl.java | 23 --- 5 files changed, 216 insertions(+), 47 deletions(-) create mode 100644 gsrs-module-substance-example/src/test/resources/testJSON/28927b6a-6b0d-4733-a1a4-b2b38a569daa_props.json create mode 100644 gsrs-module-substance-example/src/test/resources/testJSON/SURFHOPe C-1811_mixture.json diff --git a/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java b/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java index c7931ee2c..29a942561 100644 --- a/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java +++ b/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java @@ -4,16 +4,19 @@ import gsrs.module.substance.definitional.ChemicalSubstanceDefinitionalElementImpl; import gsrs.module.substance.definitional.DefinitionalElement; import gsrs.module.substance.definitional.MixtureDefinitionalElementImpl; +import gsrs.module.substance.definitional.StructurallyDiverseDefinitionalElementImpl; import gsrs.springUtils.AutowireHelper; import gsrs.substances.tests.AbstractSubstanceJpaEntityTest; import ix.core.chem.StructureProcessor; import ix.core.models.Structure; import ix.ginas.modelBuilders.ChemicalSubstanceBuilder; import ix.ginas.modelBuilders.MixtureSubstanceBuilder; +import ix.ginas.modelBuilders.StructurallyDiverseSubstanceBuilder; import ix.ginas.modelBuilders.SubstanceBuilder; import ix.ginas.models.v1.ChemicalSubstance; import ix.ginas.models.v1.GinasChemicalStructure; import ix.ginas.models.v1.MixtureSubstance; +import ix.ginas.models.v1.StructurallyDiverseSubstance; import lombok.extern.slf4j.Slf4j; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Test; @@ -111,4 +114,21 @@ public void testPropertiesInDefinitionalHashMixtures() throws Exception { Assertions.assertTrue(definitionalElements.stream().anyMatch(de->de.getKey().equals(propertyElementName))); } + @Test + public void testPropertiesInDefinitionalHashStrDiv() throws Exception { + String propertyElementNameDefining = "properties.DEGREE OF REACTION.value"; + String propertyElementNameNotDefining = "properties.ABSORBING POWER.value"; + File strDivSubFile = new ClassPathResource("testJSON/28927b6a-6b0d-4733-a1a4-b2b38a569daa_props.json").getFile(); + StructurallyDiverseSubstanceBuilder builder = SubstanceBuilder.from(strDivSubFile); + StructurallyDiverseSubstance structurallyDiverseSubstance = builder.build(); + StructurallyDiverseDefinitionalElementImpl definitionalElement = new StructurallyDiverseDefinitionalElementImpl(); + AutowireHelper.getInstance().autowireAndProxy(definitionalElement); + + List definitionalElements = new ArrayList<>(); + definitionalElement.computeDefinitionalElements(structurallyDiverseSubstance, definitionalElements::add); + definitionalElements.forEach(de-> log.trace("key: {} = {}", de.getKey(), de.getValue())); + Assertions.assertEquals(1, definitionalElements.stream().filter(de->de.getKey().equals(propertyElementNameDefining)).count()); + Assertions.assertEquals(0, definitionalElements.stream().filter(de->de.getKey().equals(propertyElementNameNotDefining)).count()); + } + } diff --git a/gsrs-module-substance-example/src/test/resources/testJSON/28927b6a-6b0d-4733-a1a4-b2b38a569daa_props.json b/gsrs-module-substance-example/src/test/resources/testJSON/28927b6a-6b0d-4733-a1a4-b2b38a569daa_props.json new file mode 100644 index 000000000..4c7fa6f30 --- /dev/null +++ b/gsrs-module-substance-example/src/test/resources/testJSON/28927b6a-6b0d-4733-a1a4-b2b38a569daa_props.json @@ -0,0 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+ ], + "access": [], + "languages": [ + "en" + ], + "type": "cn", + "name": "Sucrose sequipalmitostearate (HLB 11)" + }, + { + "references": [ + "6bc5629f-4183-6271-4c9f-7dc9b38165f9" + ], + "access": [], + "languages": [ + "en" + ], + "type": "cn", + "name": "Surfhope SE Cosme C-1811", + "displayName": false + } + ], + "codes": [ + { + "references": [ + "755dd19f-ee8b-8153-6554-6846415a133a" + ], + "access": [], + "code": "25168-73-4", + "type": "GENERIC (FAMILY)", + "codeSystem": "CAS" + } + ], + "notes": [], + "properties": [ + { + "value": { + "average": "11", + "type": "EXACT" + }, + "references": [ + "6bc5629f-4183-6271-4c9f-7dc9b38165f9" + ], + "access": [], + "name": "HYDROPHILLIC-LIPOPHILLIC BALANCE (HLB)", + "propertyType": "PHYSICAL", + "defining": true + } + ], + "relationships": [], + "references": [ + { + "tags": [], + "access": [], + "docType": "STN (SCIFINDER)", + "citation": "STN", + "publicDomain": true, + "uuid": "755dd19f-ee8b-8153-6554-6846415a133a" + }, + { + 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a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/PolymerDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/PolymerDefinitionalElementImpl.java @@ -106,30 +106,6 @@ public void computeDefinitionalElements(Object s, Consumer } addPropertiesToDefHash(polymerSubstance, consumer, log::debug); - if (polymerSubstance.properties != null) { - for (Property property : polymerSubstance.properties) { - if (property.isDefining() && property.getValue() != null) { - String defElementName = String.format("properties.%s.value", - property.getName()); - DefinitionalElement propertyValueDefElement = - DefinitionalElement.of(defElementName, property.getValue().toString(), 2); - consumer.accept(propertyValueDefElement); - log.debug("added def element for property " + defElementName); - for (Parameter parameter : property.getParameters()) { - defElementName = String.format("properties.%s.parameters.%s.value", - property.getName(), parameter.getName()); - if (parameter.getValue() != null) { - DefinitionalElement propertyParamValueDefElement = - DefinitionalElement.of(defElementName, - parameter.getValue().toString(), 2); - consumer.accept(propertyParamValueDefElement); - log.debug("added def element for property parameter " + defElementName); - } - } - } - } - } - } } } diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java index 4e08f6557..0c9edf456 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java @@ -65,28 +65,5 @@ public void computeDefinitionalElements(Object s, Consumer } addPropertiesToDefHash(ssg1, consumer, log::debug); - if( ssg1.properties != null ) { - for(Property property : ssg1.properties) { - if(property.isDefining() && property.getValue() != null) { - String defElementName = String.format("properties.%s.value", - property.getName()); - DefinitionalElement propertyValueDefElement = - DefinitionalElement.of(defElementName, property.getValue().toString(), 2); - consumer.accept(propertyValueDefElement); - log.debug("added def element for property " + defElementName); - for(Parameter parameter : property.getParameters()) { - defElementName = String.format("properties.%s.parameters.%s.value", - property.getName(), parameter.getName()); - if( parameter.getValue() != null) { - DefinitionalElement propertyParamValueDefElement = - DefinitionalElement.of(defElementName, - parameter.getValue().toString(), 2); - consumer.accept(propertyParamValueDefElement); - log.debug("added def element for property parameter " + defElementName); - } - } - } - } - } } } From 0dff42fe9c1fd81be12b1d14280b615a7e5fad37 Mon Sep 17 00:00:00 2001 From: Mitch Miller Date: Thu, 10 Oct 2024 22:07:43 -0400 Subject: [PATCH 3/3] added consideration of properties (marked defining) within definitional hash to _all_ types of substances --- .../java/example/chem/DefHashCalcTest.java | 92 ++++++++++++++++++- ...micalSubstanceDefinitionalElementImpl.java | 1 + .../MixtureDefinitionalElementImpl.java | 4 +- ...nceptDefintionalElementImplementation.java | 1 + .../NucleicAcidDefinitionalElementImpl.java | 3 +- .../PolymerDefinitionalElementImpl.java | 2 +- ...oteinSubstanceDefinitionalElementImpl.java | 2 +- .../SSG1DefinitionalElementImpl.java | 3 +- ...turallyDiverseDefinitionalElementImpl.java | 3 +- .../DefinitionalElementImplementation.java | 14 ++- 10 files changed, 107 insertions(+), 18 deletions(-) diff --git a/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java b/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java index 29a942561..20e7a209d 100644 --- a/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java +++ b/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java @@ -13,10 +13,7 @@ import ix.ginas.modelBuilders.MixtureSubstanceBuilder; import ix.ginas.modelBuilders.StructurallyDiverseSubstanceBuilder; import ix.ginas.modelBuilders.SubstanceBuilder; -import ix.ginas.models.v1.ChemicalSubstance; -import ix.ginas.models.v1.GinasChemicalStructure; -import ix.ginas.models.v1.MixtureSubstance; -import ix.ginas.models.v1.StructurallyDiverseSubstance; +import ix.ginas.models.v1.*; import lombok.extern.slf4j.Slf4j; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Test; @@ -25,6 +22,7 @@ import java.io.File; import java.util.ArrayList; +import java.util.Arrays; import java.util.List; @Slf4j @@ -131,4 +129,90 @@ public void testPropertiesInDefinitionalHashStrDiv() throws Exception { Assertions.assertEquals(0, definitionalElements.stream().filter(de->de.getKey().equals(propertyElementNameNotDefining)).count()); } + @Test + public void testTwoChemicalsNoDefPropertiesEqual() 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\": \"RACEMIC\"\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); + + ChemicalSubstanceBuilder builder = new ChemicalSubstanceBuilder(); + ChemicalSubstance chem =builder + .setStructure(ginasChemicalStructure) + .addName("2-chlorobutane") + .build(); + ChemicalSubstanceDefinitionalElementImpl defHashCalculator = new ChemicalSubstanceDefinitionalElementImpl(); + List definitionalElements = new ArrayList<>(); + defHashCalculator.computeDefinitionalElements(chem, definitionalElements::add); + + ChemicalSubstance chem2 = builder + .setStructure(ginasChemicalStructure) + .addName("2-chlorobutane") + .build(); + List definitionalElements2 = new ArrayList<>(); + defHashCalculator.computeDefinitionalElements(chem2, definitionalElements2::add); + Assertions.assertArrayEquals(definitionalElements.toArray(), definitionalElements2.toArray()); + } + + @Test + public void testTwoChemicalsDefPropertiesNotEqual() 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\": \"RACEMIC\"\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); + + ChemicalSubstanceBuilder builder = new ChemicalSubstanceBuilder(); + ChemicalSubstance chem =builder + .setStructure(ginasChemicalStructure) + .addName("2-chlorobutane") + .build(); + ChemicalSubstanceDefinitionalElementImpl defHashCalculator = new ChemicalSubstanceDefinitionalElementImpl(); + List definitionalElements = new ArrayList<>(); + defHashCalculator.computeDefinitionalElements(chem, definitionalElements::add); + + ChemicalSubstance chem2 = builder + .setStructure(ginasChemicalStructure) + .addName("2-chlorobutane") + .build(); + Property definingBoilingPoint = new Property(); + definingBoilingPoint.setName("Boiling Point"); + definingBoilingPoint.setType("Physical"); + Amount bpAmout = new Amount(); + bpAmout.average = 70d; + bpAmout.units = "degrees C"; + + definingBoilingPoint.setValue(bpAmout); + definingBoilingPoint.setDefining(true); + chem2.properties.add(definingBoilingPoint); + + List definitionalElements2 = new ArrayList<>(); + defHashCalculator.computeDefinitionalElements(chem2, definitionalElements::add); + Assertions.assertFalse(Arrays.equals(definitionalElements.toArray(), definitionalElements2.toArray())); + } } diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ChemicalSubstanceDefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ChemicalSubstanceDefinitionalElementImpl.java index e3f9afed6..db3aae180 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ChemicalSubstanceDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ChemicalSubstanceDefinitionalElementImpl.java @@ -27,6 +27,7 @@ public boolean supports(Object s) { @Override public void computeDefinitionalElements(Object s, Consumer consumer) { + DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer); ChemicalSubstance chemicalSubstance = (ChemicalSubstance) s; Structure structure = chemicalSubstance.getStructure(); if(structure==null){ diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/MixtureDefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/MixtureDefinitionalElementImpl.java index c29e04c05..24cc1aa6e 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/MixtureDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/MixtureDefinitionalElementImpl.java @@ -30,7 +30,8 @@ public boolean supports(Object s) { @Override public void computeDefinitionalElements(Object s, Consumer consumer) { - log.trace("performAddition of mixture substance"); + log.trace("computeDefinitionalElements of mixture substance"); + DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer); MixtureSubstance mixtureSubstance = (MixtureSubstance)s; Mixture mix = mixtureSubstance.mixture; if (mix != null && !mix.components.isEmpty()) { @@ -72,6 +73,5 @@ private void additionalElementsFor( MixtureSubstance mixtureSubstance, Consumer< definitionalElementFactory.addDefinitionalElementsFor(mixtureSubstance.modifications, consumer); } - addPropertiesToDefHash(mixtureSubstance, consumer, log::trace ); } } diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NonSubstanceConceptDefintionalElementImplementation.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NonSubstanceConceptDefintionalElementImplementation.java index aa7b52650..8f1a9e9d4 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NonSubstanceConceptDefintionalElementImplementation.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NonSubstanceConceptDefintionalElementImplementation.java @@ -15,6 +15,7 @@ public boolean supports(Object s) { @Override public void computeDefinitionalElements(Object s, Consumer consumer) { + DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer); String primaryName = ""; for(Name name : ((Substance)s).getAllNames()) { if( name.displayName ){ diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NucleicAcidDefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NucleicAcidDefinitionalElementImpl.java index ca46ca3aa..550eebbd2 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NucleicAcidDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NucleicAcidDefinitionalElementImpl.java @@ -29,6 +29,7 @@ public boolean supports(Object s) { @Override public void computeDefinitionalElements(Object substance, Consumer consumer) { + DefinitionalElementImplementation.super.computeDefinitionalElements(substance, consumer); NucleicAcidSubstance nucleicAcidSubstance = (NucleicAcidSubstance) substance; if(nucleicAcidSubstance.nucleicAcid ==null || nucleicAcidSubstance.nucleicAcid.subunits ==null){ return; @@ -75,10 +76,8 @@ public void computeDefinitionalElements(Object substance, Consumer consumer) { + DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer); PolymerSubstance polymerSubstance = (PolymerSubstance)s; Polymer polymer = polymerSubstance.polymer; @@ -105,7 +106,6 @@ public void computeDefinitionalElements(Object s, Consumer } - addPropertiesToDefHash(polymerSubstance, consumer, log::debug); } } } diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ProteinSubstanceDefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ProteinSubstanceDefinitionalElementImpl.java index e6b328eca..902424b54 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ProteinSubstanceDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ProteinSubstanceDefinitionalElementImpl.java @@ -54,7 +54,7 @@ private List canonicalizeSites(List oldSites, Map @Override public void computeDefinitionalElements(Object substance, Consumer consumer) { - + DefinitionalElementImplementation.super.computeDefinitionalElements(substance, consumer); ProteinSubstance proteinSubstance = (ProteinSubstance)substance; //this implementation is different than the version in GSRS 2.x in that //the old version made a copy of the ProteinSubstance to reorder the subunits and all corresponding Sites diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java index 0c9edf456..aa6a00b4c 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java @@ -27,6 +27,7 @@ public boolean supports(Object s) { @Override public void computeDefinitionalElements(Object s, Consumer consumer) { + DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer); SpecifiedSubstanceGroup1Substance ssg1 = (SpecifiedSubstanceGroup1Substance) s; if(ssg1.specifiedSubstance.constituents != null) { @@ -63,7 +64,5 @@ public void computeDefinitionalElements(Object s, Consumer definitionalElementFactory.addDefinitionalElementsFor(ssg1.modifications, consumer); } - - addPropertiesToDefHash(ssg1, consumer, log::debug); } } diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/StructurallyDiverseDefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/StructurallyDiverseDefinitionalElementImpl.java index 9bf4067d3..24850347d 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/StructurallyDiverseDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/StructurallyDiverseDefinitionalElementImpl.java @@ -32,6 +32,7 @@ public boolean supports(Object s) { @Override public void computeDefinitionalElements(Object s, Consumer consumer) { + DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer); StructurallyDiverseSubstance substance = (StructurallyDiverseSubstance) s; /* @@ -163,7 +164,5 @@ public void computeDefinitionalElements(Object s, Consumer log.trace("adding infraspecificName"); consumer.accept(infraspecificNameElement); } - - addPropertiesToDefHash(substance, consumer, log::trace ); } } diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/services/DefinitionalElementImplementation.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/services/DefinitionalElementImplementation.java index 1faaa7a07..f9a5f913a 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/services/DefinitionalElementImplementation.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/services/DefinitionalElementImplementation.java @@ -6,14 +6,20 @@ import ix.ginas.models.v1.Substance; import java.util.function.Consumer; +import java.util.logging.Logger; public interface DefinitionalElementImplementation { boolean supports(Object s); - void computeDefinitionalElements(Object s, Consumer consumer); + default void computeDefinitionalElements(Object s, Consumer consumer) { + if (s instanceof Substance) { + Logger log= Logger.getLogger(this.getClass().getName()); + addPropertiesToDefHash((Substance) s, consumer, Logger.getLogger(getClass().getName())); + } + } - default void addPropertiesToDefHash(Substance substance, Consumer consumer, Consumer logger) { + default void addPropertiesToDefHash(Substance substance, Consumer consumer, Logger logger) { if( substance.properties != null ) { for(Property property : substance.properties) { if(property.isDefining() && property.getValue() != null) { @@ -22,7 +28,7 @@ default void addPropertiesToDefHash(Substance substance, Consumer