From b4a956ec9cc08f8e0698ab90c597633fb6ddbd57 Mon Sep 17 00:00:00 2001
From: Mitch Miller <mitch.miller@thinkscience.us>
Date: Mon, 5 Aug 2024 20:13:26 -0400
Subject: [PATCH 1/2] added salt stripping to flex plus searching made unit
 tests pass

---
 gsrs-module-substance-example/pom.xml         |   9 +-
 .../salt_data_public.tsv                      |  61 ++++
 .../src/main/resources/salt_data_public.tsv   |  61 ++++
 .../java/example/chem/SaltRemovalTest.java    |  59 ++++
 .../structureSearch/FlexSearchTest.java       |  25 +-
 .../src/test/resources/application-test.conf  |   1 +
 .../StructureHandlingConfiguration.java       |  15 +
 .../substance/SubstanceCoreConfiguration.java |   5 +-
 .../controllers/SubstanceController.java      |  35 +-
 .../module/substance/utils/ChemicalUtils.java | 322 ++++++++++++++++++
 .../module/substance/utils/ChemicalUtils.java |  12 +-
 11 files changed, 576 insertions(+), 29 deletions(-)
 create mode 100644 gsrs-module-substance-example/salt_data_public.tsv
 create mode 100644 gsrs-module-substance-example/src/main/resources/salt_data_public.tsv
 create mode 100644 gsrs-module-substance-example/src/test/java/example/chem/SaltRemovalTest.java
 create mode 100644 gsrs-module-substances-core/src/main/java/gsrs/module/substance/StructureHandlingConfiguration.java
 create mode 100644 gsrs-module-substances-core/src/main/java/gsrs/module/substance/utils/ChemicalUtils.java

diff --git a/gsrs-module-substance-example/pom.xml b/gsrs-module-substance-example/pom.xml
index 59894fd2c..6298ba351 100644
--- a/gsrs-module-substance-example/pom.xml
+++ b/gsrs-module-substance-example/pom.xml
@@ -31,8 +31,8 @@
             <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-compiler-plugin</artifactId>
             <configuration>
-                <source>8</source>
-                <target>8</target>
+                <source>11</source>
+                <target>11</target>
             </configuration>
         </plugin>
         <!-- Uncomment this for maven public release deployment
@@ -370,5 +370,10 @@
             <artifactId>jackson-annotations</artifactId>
             <version>${jackson.version}</version>
         </dependency>
+        <dependency>
+            <groupId>javax.annotation</groupId>
+            <artifactId>javax.annotation-api</artifactId>
+            <version>1.3.2</version>
+        </dependency>
     </dependencies>
 </project>
diff --git a/gsrs-module-substance-example/salt_data_public.tsv b/gsrs-module-substance-example/salt_data_public.tsv
new file mode 100644
index 000000000..cda7922fc
--- /dev/null
+++ b/gsrs-module-substance-example/salt_data_public.tsv
@@ -0,0 +1,61 @@
+InChI Key	SMILES	Occurrences
+VEXZGXHMUGYJMC-UHFFFAOYSA-N	Cl	7206
+FKNQFGJONOIPTF-UHFFFAOYSA-N	[Na+]	3488
+XLYOFNOQVPJJNP-UHFFFAOYSA-N	O	1608
+NPYPAHLBTDXSSS-UHFFFAOYSA-N	[K+]	811
+XLYOFNOQVPJJNP-UHFFFAOYSA-M	[OH-]	791
+CPELXLSAUQHCOX-UHFFFAOYSA-N	Br	645
+BHPQYMZQTOCNFJ-UHFFFAOYSA-N	[Ca+2]	526
+QAOWNCQODCNURD-UHFFFAOYSA-N	OS(=O)(=O)O	510
+AFVFQIVMOAPDHO-UHFFFAOYSA-N	CS(=O)(=O)O	350
+XMBWDFGMSWQBCA-UHFFFAOYSA-N	I	326
+JLVVSXFLKOJNIY-UHFFFAOYSA-N	[Mg+2]	316
+QGZKDVFQNNGYKY-UHFFFAOYSA-N	N	300
+QTBSBXVTEAMEQO-UHFFFAOYSA-N	CC(=O)O	280
+GPRLSGONYQIRFK-UHFFFAOYSA-N	[H+]	277
+REDXJYDRNCIFBQ-UHFFFAOYSA-N	[Al+3]	270
+VZCYOOQTPOCHFL-UPHRSURJSA-N	OC(=O)/C=C\C(O)=O	259
+PTFCDOFLOPIGGS-UHFFFAOYSA-N	[Zn+2]	241
+VEXZGXHMUGYJMC-UHFFFAOYSA-M	[Cl-]	240
+FEWJPZIEWOKRBE-JCYAYHJZSA-N	[C@@H]([C@H](C(=O)O)O)(C(=O)O)O	214
+NBIIXXVUZAFLBC-UHFFFAOYSA-N	OP(=O)(O)O	212
+JPVYNHNXODAKFH-UHFFFAOYSA-N	[Cu+2]	172
+VZCYOOQTPOCHFL-OWOJBTEDSA-N	OC(=O)/C=C/C(O)=O	164
+KRKNYBCHXYNGOX-UHFFFAOYSA-N	C(C(=O)O)C(CC(=O)O)(C(=O)O)O	162
+VTLYFUHAOXGGBS-UHFFFAOYSA-N	[Fe+3]	139
+HBBGRARXTFLTSG-UHFFFAOYSA-N	[Li+]	139
+JZMJDSHXVKJFKW-UHFFFAOYSA-M	COS(=O)(=O)[O-]	126
+CWYNVVGOOAEACU-UHFFFAOYSA-N	[Fe+2]	124
+QAOWNCQODCNURD-UHFFFAOYSA-L	O=S(=O)([O-])[O-]	120
+JOXIMZWYDAKGHI-UHFFFAOYSA-N	Cc1ccc(cc1)S(=O)(=O)O	116
+QTBSBXVTEAMEQO-UHFFFAOYSA-M	CC(=O)[O-]	110
+KDYFGRWQOYBRFD-UHFFFAOYSA-N	C(CC(=O)O)C(=O)O	99
+MUBZPKHOEPUJKR-UHFFFAOYSA-N	C(=O)(C(=O)O)O	98
+NHNBFGGVMKEFGY-UHFFFAOYSA-N	[N+](=O)([O-])[O-]	97
+XDFCIPNJCBUZJN-UHFFFAOYSA-N	[Ba+2]	95
+KRHYYFGTRYWZRS-UHFFFAOYSA-N	F	90
+WAEMQWOKJMHJLA-UHFFFAOYSA-N	[Mn+2]	85
+GSEJCLTVZPLZKY-UHFFFAOYSA-N	C(CO)N(CCO)CCO	80
+GRYLNZFGIOXLOG-UHFFFAOYSA-N	[N+](=O)(O)[O-]	77
+AHKZTVQIVOEVFO-UHFFFAOYSA-N	[O-2]	72
+BVKZGUZCCUSVTD-UHFFFAOYSA-L	C(=O)([O-])[O-]	71
+LELOWRISYMNNSU-UHFFFAOYSA-N	C#N	70
+XMBWDFGMSWQBCA-UHFFFAOYSA-M	[I-]	69
+QGZKDVFQNNGYKY-UHFFFAOYSA-O	[NH4+]	65
+XLJKHNWPARRRJB-UHFFFAOYSA-N	[Co+2]	64
+FOIXSVOLVBLSDH-UHFFFAOYSA-N	[Ag+]	63
+CPELXLSAUQHCOX-UHFFFAOYSA-M	[Br-]	63
+KRKNYBCHXYNGOX-UHFFFAOYSA-K	C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O	62
+JDIBGQFKXXXXPN-UHFFFAOYSA-N	[Bi+3]	61
+KDXKERNSBIXSRK-YFKPBYRVSA-N	C(CCN)C[C@@H](C(=O)O)N	59
+BFGKITSFLPAWGI-UHFFFAOYSA-N	[Cr+3]	59
+RVPVRDXYQKGNMQ-UHFFFAOYSA-N	[Pb+2]	59
+HRGDZIGMBDGFTC-UHFFFAOYSA-N	[Pt+2]	59
+PWYYWQHXAPXYMF-UHFFFAOYSA-N	[Sr+2]	58
+HZAXFHJVJLSVMW-UHFFFAOYSA-N	C(CO)N	57
+JVTAAEKCZFNVCJ-UHFFFAOYSA-N	CC(C(=O)O)O	57
+ZBCBWPMODOFKDW-UHFFFAOYSA-N	C(CO)NCCO	56
+ODKSFYDXXFIFQN-BYPYZUCNSA-N	C(C[C@@H](C(=O)O)N)CNC(=N)N	54
+MBBZMMPHUWSWHV-BDVNFPICSA-N	CNC[C@@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O	52
+GBNDTYKAOXLLID-UHFFFAOYSA-N	[Zr+4]	51
+YGSDEFSMJLZEOE-UHFFFAOYSA-N	c1ccc(c(c1)C(=O)O)O	51
diff --git a/gsrs-module-substance-example/src/main/resources/salt_data_public.tsv b/gsrs-module-substance-example/src/main/resources/salt_data_public.tsv
new file mode 100644
index 000000000..cda7922fc
--- /dev/null
+++ b/gsrs-module-substance-example/src/main/resources/salt_data_public.tsv
@@ -0,0 +1,61 @@
+InChI Key	SMILES	Occurrences
+VEXZGXHMUGYJMC-UHFFFAOYSA-N	Cl	7206
+FKNQFGJONOIPTF-UHFFFAOYSA-N	[Na+]	3488
+XLYOFNOQVPJJNP-UHFFFAOYSA-N	O	1608
+NPYPAHLBTDXSSS-UHFFFAOYSA-N	[K+]	811
+XLYOFNOQVPJJNP-UHFFFAOYSA-M	[OH-]	791
+CPELXLSAUQHCOX-UHFFFAOYSA-N	Br	645
+BHPQYMZQTOCNFJ-UHFFFAOYSA-N	[Ca+2]	526
+QAOWNCQODCNURD-UHFFFAOYSA-N	OS(=O)(=O)O	510
+AFVFQIVMOAPDHO-UHFFFAOYSA-N	CS(=O)(=O)O	350
+XMBWDFGMSWQBCA-UHFFFAOYSA-N	I	326
+JLVVSXFLKOJNIY-UHFFFAOYSA-N	[Mg+2]	316
+QGZKDVFQNNGYKY-UHFFFAOYSA-N	N	300
+QTBSBXVTEAMEQO-UHFFFAOYSA-N	CC(=O)O	280
+GPRLSGONYQIRFK-UHFFFAOYSA-N	[H+]	277
+REDXJYDRNCIFBQ-UHFFFAOYSA-N	[Al+3]	270
+VZCYOOQTPOCHFL-UPHRSURJSA-N	OC(=O)/C=C\C(O)=O	259
+PTFCDOFLOPIGGS-UHFFFAOYSA-N	[Zn+2]	241
+VEXZGXHMUGYJMC-UHFFFAOYSA-M	[Cl-]	240
+FEWJPZIEWOKRBE-JCYAYHJZSA-N	[C@@H]([C@H](C(=O)O)O)(C(=O)O)O	214
+NBIIXXVUZAFLBC-UHFFFAOYSA-N	OP(=O)(O)O	212
+JPVYNHNXODAKFH-UHFFFAOYSA-N	[Cu+2]	172
+VZCYOOQTPOCHFL-OWOJBTEDSA-N	OC(=O)/C=C/C(O)=O	164
+KRKNYBCHXYNGOX-UHFFFAOYSA-N	C(C(=O)O)C(CC(=O)O)(C(=O)O)O	162
+VTLYFUHAOXGGBS-UHFFFAOYSA-N	[Fe+3]	139
+HBBGRARXTFLTSG-UHFFFAOYSA-N	[Li+]	139
+JZMJDSHXVKJFKW-UHFFFAOYSA-M	COS(=O)(=O)[O-]	126
+CWYNVVGOOAEACU-UHFFFAOYSA-N	[Fe+2]	124
+QAOWNCQODCNURD-UHFFFAOYSA-L	O=S(=O)([O-])[O-]	120
+JOXIMZWYDAKGHI-UHFFFAOYSA-N	Cc1ccc(cc1)S(=O)(=O)O	116
+QTBSBXVTEAMEQO-UHFFFAOYSA-M	CC(=O)[O-]	110
+KDYFGRWQOYBRFD-UHFFFAOYSA-N	C(CC(=O)O)C(=O)O	99
+MUBZPKHOEPUJKR-UHFFFAOYSA-N	C(=O)(C(=O)O)O	98
+NHNBFGGVMKEFGY-UHFFFAOYSA-N	[N+](=O)([O-])[O-]	97
+XDFCIPNJCBUZJN-UHFFFAOYSA-N	[Ba+2]	95
+KRHYYFGTRYWZRS-UHFFFAOYSA-N	F	90
+WAEMQWOKJMHJLA-UHFFFAOYSA-N	[Mn+2]	85
+GSEJCLTVZPLZKY-UHFFFAOYSA-N	C(CO)N(CCO)CCO	80
+GRYLNZFGIOXLOG-UHFFFAOYSA-N	[N+](=O)(O)[O-]	77
+AHKZTVQIVOEVFO-UHFFFAOYSA-N	[O-2]	72
+BVKZGUZCCUSVTD-UHFFFAOYSA-L	C(=O)([O-])[O-]	71
+LELOWRISYMNNSU-UHFFFAOYSA-N	C#N	70
+XMBWDFGMSWQBCA-UHFFFAOYSA-M	[I-]	69
+QGZKDVFQNNGYKY-UHFFFAOYSA-O	[NH4+]	65
+XLJKHNWPARRRJB-UHFFFAOYSA-N	[Co+2]	64
+FOIXSVOLVBLSDH-UHFFFAOYSA-N	[Ag+]	63
+CPELXLSAUQHCOX-UHFFFAOYSA-M	[Br-]	63
+KRKNYBCHXYNGOX-UHFFFAOYSA-K	C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O	62
+JDIBGQFKXXXXPN-UHFFFAOYSA-N	[Bi+3]	61
+KDXKERNSBIXSRK-YFKPBYRVSA-N	C(CCN)C[C@@H](C(=O)O)N	59
+BFGKITSFLPAWGI-UHFFFAOYSA-N	[Cr+3]	59
+RVPVRDXYQKGNMQ-UHFFFAOYSA-N	[Pb+2]	59
+HRGDZIGMBDGFTC-UHFFFAOYSA-N	[Pt+2]	59
+PWYYWQHXAPXYMF-UHFFFAOYSA-N	[Sr+2]	58
+HZAXFHJVJLSVMW-UHFFFAOYSA-N	C(CO)N	57
+JVTAAEKCZFNVCJ-UHFFFAOYSA-N	CC(C(=O)O)O	57
+ZBCBWPMODOFKDW-UHFFFAOYSA-N	C(CO)NCCO	56
+ODKSFYDXXFIFQN-BYPYZUCNSA-N	C(C[C@@H](C(=O)O)N)CNC(=N)N	54
+MBBZMMPHUWSWHV-BDVNFPICSA-N	CNC[C@@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O	52
+GBNDTYKAOXLLID-UHFFFAOYSA-N	[Zr+4]	51
+YGSDEFSMJLZEOE-UHFFFAOYSA-N	c1ccc(c(c1)C(=O)O)O	51
diff --git a/gsrs-module-substance-example/src/test/java/example/chem/SaltRemovalTest.java b/gsrs-module-substance-example/src/test/java/example/chem/SaltRemovalTest.java
new file mode 100644
index 000000000..a8ee9d0ce
--- /dev/null
+++ b/gsrs-module-substance-example/src/test/java/example/chem/SaltRemovalTest.java
@@ -0,0 +1,59 @@
+package example.chem;
+
+import example.GsrsModuleSubstanceApplication;
+import gov.nih.ncats.molwitch.Chemical;
+
+import gsrs.module.substance.utils.ChemicalUtils;
+import gsrs.substances.tests.AbstractSubstanceJpaFullStackEntityTest;
+import lombok.extern.slf4j.Slf4j;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.security.test.context.support.WithMockUser;
+
+import java.io.*;
+import java.util.stream.Stream;
+
+@Slf4j
+@SpringBootTest(classes = GsrsModuleSubstanceApplication.class)
+@WithMockUser(username = "admin", roles = "Admin")
+class SaltRemovalTest extends AbstractSubstanceJpaFullStackEntityTest {
+
+    @Autowired
+    private ChemicalUtils chemicalUtils;
+
+    @Test
+    void testRemoveSalts() throws IOException {
+
+        String inputSmiles = "C[C@H]1[C@@]2([H])CC[C@@]3([H])[C@]4([H])CC=C5C[C@H](CC[C@]5(C)[C@@]4([H])CC[C@]23CN1C)N(C)C.Br.Br";
+        Chemical chemical = Chemical.parseMol(inputSmiles);
+        double massBefore = chemical.getMass();
+        Chemical cleaned = chemicalUtils.stripSalts(chemical);
+        double massAfter = cleaned.getMass();
+        log.warn("formula before: {}; after: {}", chemical.getFormula(), cleaned.getFormula());
+        Assertions.assertTrue(massAfter < massBefore, String.format("formula before: %s; after: %s", chemical.getFormula(), cleaned.getFormula()));
+    }
+
+    @ParameterizedTest
+    @MethodSource("inputData")
+    void testSaltRemoval(String smiles, int atomCountChange) throws IOException {
+        Chemical chemical = Chemical.parseMol(smiles);
+        Chemical cleaned = chemicalUtils.stripSalts(chemical);
+        Assertions.assertEquals(atomCountChange, (chemical.getAtomCount() - cleaned.getAtomCount()),
+                String.format("formula before: %s; after: %s", chemical.getFormula(), cleaned.getFormula()));
+    }
+
+    private static Stream<Arguments> inputData() {
+        return Stream.of(
+                Arguments.of("C[C@H]1[C@@]2([H])CC[C@@]3([H])[C@]4([H])CC=C5C[C@H](CC[C@]5(C)[C@@]4([H])CC[C@]23CN1C)N(C)C.Br.Br", 2),
+                Arguments.of("CCC1C(Cc2cncn2C)COC1=O.Cl", 1),
+                Arguments.of("c1cc(ccc1C(=C2C=CC(=O)C=C2)c3ccc(cc3)[O-])[O-].[Na+].[Na+]", 2),
+                Arguments.of("[F-][Ti+4]([F-])([F-])([F-])([F-])[F-].[Li+].[Li+]", 2),
+                Arguments.of("Cc1c(CCN2CCC(=C(c3ccc(cc3)F)c4ccc(cc4)F)CC2)c(=O)n5ccsc5n1.[C@@H]([C@H](C(=O)O)O)(C(=O)O)O", 10)
+        );
+    }
+}
diff --git a/gsrs-module-substance-example/src/test/java/example/structureSearch/FlexSearchTest.java b/gsrs-module-substance-example/src/test/java/example/structureSearch/FlexSearchTest.java
index c9dd893a8..05d791609 100644
--- a/gsrs-module-substance-example/src/test/java/example/structureSearch/FlexSearchTest.java
+++ b/gsrs-module-substance-example/src/test/java/example/structureSearch/FlexSearchTest.java
@@ -1,10 +1,12 @@
 package example.structureSearch;
 
 import example.GsrsModuleSubstanceApplication;
+import gov.nih.ncats.molwitch.Chemical;
 import gsrs.legacy.structureIndexer.StructureIndexerService;
 import gsrs.module.substance.controllers.SubstanceController;
 import gsrs.module.substance.controllers.SubstanceLegacySearchService;
 import gsrs.module.substance.indexers.SubstanceDefinitionalHashIndexer;
+import gsrs.module.substance.utils.ChemicalUtils;
 import gsrs.springUtils.AutowireHelper;
 import gsrs.startertests.TestGsrsValidatorFactory;
 import gsrs.startertests.TestIndexValueMakerFactory;
@@ -59,6 +61,9 @@ public class FlexSearchTest extends AbstractSubstanceJpaFullStackEntityTest {
     @Autowired
     private SubstanceLegacySearchService searchService;
 
+    @Autowired
+    private ChemicalUtils chemicalUtils;
+
     private String fileName = "testdumps/tartrate_set.gsrs";
 
     private boolean loadedData = false;
@@ -107,7 +112,7 @@ public void generateFlexSearchQuery() throws Exception {
         AutowireHelper.getInstance().autowireAndProxy(controller);
         log.trace("created and wired controller");
 
-        String hash=  controller.makeFlexSearchMoietyClauses(structureStd, false) + ")";
+        String hash=  controller.makeFlexSearchMoietyClauses(structureStd) + ")";
         log.trace("search hash: {}", hash);
         assertTrue(hash.contains("root_moieties_properties_STEREO_INSENSITIVE_HASH"));
     }
@@ -134,9 +139,9 @@ public void generateFlexPlusSearchQuery() throws Exception {
         AutowireHelper.getInstance().autowireAndProxy(controller);
         log.trace("created and wired controller");
 
-        String hash=  controller.makeFlexSearchMoietyClauses(structureStd, true) + ")";
+        String hash=  controller.makeFlexSearchMoietyClauses(structureStd) + ")";
         log.trace("search hash: {}", hash);
-        assertTrue(hash.contains("root_moieties_properties_EXACT_HASH"));
+        assertTrue(hash.contains("root_moieties_properties_STEREO_INSENSITIVE_HASH"));
     }
 
     @Test
@@ -155,11 +160,10 @@ public void runFlexSearchQueryTartaric() throws Exception {
                 .build()
                 .instrument()
                 .getStructure();
-        String sins= structureStd.getStereoInsensitiveHash();
         SubstanceController controller = new SubstanceController();
         AutowireHelper.getInstance().autowireAndProxy(controller);
 
-        String hash=  controller.makeFlexSearch(structureStd, false);
+        String hash=  controller.makeFlexSearch(structureStd);
         log.trace("search hash: {}", hash);
         SearchRequest request = new SearchRequest.Builder()
                 .kind(Substance.class)
@@ -177,7 +181,6 @@ public void runFlexSearchQueryTartaric() throws Exception {
     @WithMockUser(value = "admin", roles = "Admin")
     public void runFlexSearchQuerySodiumTartrate() throws Exception {
         String molfileSource = "molfiles/sodium_tartrate.mol";
-
         File molfile = new ClassPathResource(molfileSource).getFile();
         Structure structureStd = structureProcessor.taskFor(Files.readString(molfile.toPath()))
                 .standardize(true)
@@ -187,7 +190,7 @@ public void runFlexSearchQuerySodiumTartrate() throws Exception {
         SubstanceController controller = new SubstanceController();
         AutowireHelper.getInstance().autowireAndProxy(controller);
 
-        String hash = controller.makeFlexSearch(structureStd, false);
+        String hash = controller.makeFlexSearch(structureStd);
         log.trace("search hash: {}", hash);
         SearchRequest request = new SearchRequest.Builder()
                 .kind(Substance.class)
@@ -210,10 +213,14 @@ public void runFlexPlusSearchQuerySodiumTartrate() throws Exception {
                 .build()
                 .instrument()
                 .getStructure();
+        Chemical cleanedChemical = chemicalUtils.stripSalts(structureStd.toChemical());
+        Structure cleanedStructure = new Structure();
+        cleanedStructure.molfile = cleanedChemical.toMol();
+
         SubstanceController controller = new SubstanceController();
         AutowireHelper.getInstance().autowireAndProxy(controller);
 
-        String hash = controller.makeFlexSearch(structureStd,true);
+        String hash = controller.makeFlexSearch(cleanedStructure);
         log.trace("search hash: {}", hash);
         SearchRequest request = new SearchRequest.Builder()
                 .kind(Substance.class)
@@ -223,7 +230,7 @@ public void runFlexPlusSearchQuerySodiumTartrate() throws Exception {
         log.trace("search results: (total: {})", substances.size());
         substances.forEach(s-> log.trace("ID {} - {}", s.uuid, s.getName()));
 
-        int expectedNumber = 1;
+        int expectedNumber = 7;
         assertEquals(expectedNumber, substances.size());
     }
 
diff --git a/gsrs-module-substance-example/src/test/resources/application-test.conf b/gsrs-module-substance-example/src/test/resources/application-test.conf
index 71856845f..fd6b9dfa9 100644
--- a/gsrs-module-substance-example/src/test/resources/application-test.conf
+++ b/gsrs-module-substance-example/src/test/resources/application-test.conf
@@ -586,3 +586,4 @@ gsrs.importAdapterFactories.substances =
 		}
 	]
 
+gsrs.substance.structures.saltFilePath=salt_data_public.tsv
\ No newline at end of file
diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/StructureHandlingConfiguration.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/StructureHandlingConfiguration.java
new file mode 100644
index 000000000..3fd6d4859
--- /dev/null
+++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/StructureHandlingConfiguration.java
@@ -0,0 +1,15 @@
+package gsrs.module.substance;
+
+import lombok.Data;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+@ConfigurationProperties("gsrs.substance.structures")
+@Data
+@Slf4j
+public class StructureHandlingConfiguration {
+
+    private String saltFilePath;
+}
diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/SubstanceCoreConfiguration.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/SubstanceCoreConfiguration.java
index f3c9b96cf..23365cdb7 100644
--- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/SubstanceCoreConfiguration.java
+++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/SubstanceCoreConfiguration.java
@@ -12,6 +12,7 @@
 import gsrs.module.substance.standardizer.NameStandardizerConfiguration;
 import gsrs.module.substance.standardizer.StructureStandardizerConfiguration;
 import gsrs.module.substance.standardizer.SubstanceSynchronizer;
+import gsrs.module.substance.utils.ChemicalUtils;
 import gsrs.module.substance.utils.MolWeightCalculatorProperties;
 import gsrs.module.substance.utils.SubstanceMatchViewGenerator;
 import gsrs.module.substance.utils.SubstanceResultListRecordGenerator;
@@ -61,7 +62,9 @@
         ImportMetadataLegacySearchService.class,
         SubstanceFieldNameDecoratorConfiguration.class,
         SubstanceSynchronizer.class,
-        StructureProcessorConfiguration.class
+        StructureProcessorConfiguration.class,
+        StructureHandlingConfiguration.class,
+        ChemicalUtils.class
 })
 public class SubstanceCoreConfiguration {
 
diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/controllers/SubstanceController.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/controllers/SubstanceController.java
index 3197d3576..fc3b87205 100644
--- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/controllers/SubstanceController.java
+++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/controllers/SubstanceController.java
@@ -28,6 +28,7 @@
 import javax.servlet.http.HttpServletRequest;
 import javax.validation.constraints.NotBlank;
 
+import gsrs.module.substance.utils.ChemicalUtils;
 import org.freehep.graphicsio.svg.SVGGraphics2D;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.DependsOn;
@@ -171,6 +172,9 @@ public ResultListRecordGenerator getResultListRecordGenerator() {
     @Autowired
     private PrincipalServiceImpl principalService;
 
+    @Autowired
+    private ChemicalUtils chemicalUtils;
+
     @Override
     public SearchOptions instrumentSearchOptions(SearchOptions so) {
 
@@ -354,7 +358,6 @@ public static Optional<StructureStandardizerPresets> value(String s){
     @Autowired
     private ApprovalService approvalService;
 
-
     @Override
     protected LegacyGsrsSearchService<Substance> getlegacyGsrsSearchService() {
         return legacySearchService;
@@ -740,8 +743,21 @@ public Object structureSearchGet(
             hash = "root_structure_properties_EXACT_HASH:" + structure.getExactHash();
         }else if(sanitizedRequest.getType() == SubstanceStructureSearchService.StructureSearchType.FLEX
             || sanitizedRequest.getType() == SubstanceStructureSearchService.StructureSearchType.FLEX_PLUS){
+            if( sanitizedRequest.getType() == SubstanceStructureSearchService.StructureSearchType.FLEX_PLUS) {
+                log.trace("running a flex plus search - remove salts");
+
+                Structure copy = new GinasChemicalStructure();
+                copy.molfile = structure.molfile;
+                Chemical clean = chemicalUtils.stripSalts(copy.toChemical());
+                //make another Structure, without salt
+                Structure saltStripped = new Structure();
+                saltStripped.molfile = clean.toMol();
+                hash = makeFlexSearch(saltStripped);
+            } else {
+                hash= makeFlexSearch(structure);
+            }
             //note we purposefully don't have the lucene path so it finds moieties and polymers etc
-            hash= makeFlexSearch(structure, (sanitizedRequest.getType() == SubstanceStructureSearchService.StructureSearchType.FLEX_PLUS));
+
             log.trace("search hash: {} for search of type {}", hash, sanitizedRequest.getType());
                     //"root_moieties_properties_STEREO_INSENSITIVE_HASH:" + sins + " )";
         }
@@ -1871,21 +1887,21 @@ public List<Text> getHardcodedConfigsBackup() throws JsonProcessingException {
         return items;
     }
 
-    public String makeFlexSearch(Structure structure, boolean plus) {
-        String sins= plus ? structure.getExactHash() : structure.getStereoInsensitiveHash();
+    public String makeFlexSearch(Structure structure) {
+        String sins= structure.getStereoInsensitiveHash();
         StringBuilder stringBuilder = new StringBuilder();
         stringBuilder.append("(");
-        stringBuilder.append( plus ? "root_structure_properties_EXACT_HASH" : "root_structure_properties_STEREO_INSENSITIVE_HASH");
+        stringBuilder.append(  "root_structure_properties_STEREO_INSENSITIVE_HASH");
         stringBuilder.append(":\"");
         stringBuilder.append(sins);
         stringBuilder.append("\" OR ");
-        stringBuilder.append(makeFlexSearchMoietyClauses(structure, plus));
+        stringBuilder.append(makeFlexSearchMoietyClauses(structure));
         stringBuilder.append(")");
         return stringBuilder.toString();
         //return "( root_structure_properties_STEREO_INSENSITIVE_HASH:\"" + sins + "\" OR " + makeFlexSearchMoietyClauses(structure, plus) + ")";
     }
 
-    public String makeFlexSearchMoietyClauses(Structure structure, boolean plus) {
+    public String makeFlexSearchMoietyClauses(Structure structure) {
 
         List<Structure> moieties = new ArrayList<>();
         try {
@@ -1899,8 +1915,8 @@ public String makeFlexSearchMoietyClauses(Structure structure, boolean plus) {
             String moietySearchString= moieties.stream()
                     .map(m->{
                         StringBuilder sb = new StringBuilder();
-                        sb.append(plus ? "root_moieties_properties_EXACT_HASH:\"" :  "root_moieties_properties_STEREO_INSENSITIVE_HASH:\"");
-                        sb.append(plus ? m.getExactHash() : m.getStereoInsensitiveHash());
+                        sb.append("root_moieties_properties_STEREO_INSENSITIVE_HASH:\"");
+                        sb.append( m.getStereoInsensitiveHash());
                         sb.append("\"");
                         return sb.toString();
                     })
@@ -1914,4 +1930,5 @@ public String makeFlexSearchMoietyClauses(Structure structure, boolean plus) {
             throw new RuntimeException(e);
         }
     }
+
 }
diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/utils/ChemicalUtils.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/utils/ChemicalUtils.java
new file mode 100644
index 000000000..492a010d6
--- /dev/null
+++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/utils/ChemicalUtils.java
@@ -0,0 +1,322 @@
+package gsrs.module.substance.utils;
+
+import gov.nih.ncats.molwitch.Atom;
+import gov.nih.ncats.molwitch.Bond;
+import gov.nih.ncats.molwitch.Chemical;
+import gsrs.module.substance.StructureHandlingConfiguration;
+import lombok.extern.slf4j.Slf4j;
+import org.junit.Assert;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import javax.annotation.PostConstruct;
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.util.*;
+import java.util.concurrent.ConcurrentHashMap;
+
+@Slf4j
+@Component
+public class ChemicalUtils {
+    private final static String electroneglist=
+            "H	hydrogen	2.2	non-metal\n" +
+                    "He	helium	no data 	non-metal\n" +
+                    "Li	lithium	0.98	metal\n" +
+                    "Be	beryllium	1.57	metal\n" +
+                    "B	boron	2.04	\n" +
+                    "C	carbon	2.55	non-metal\n" +
+                    "N	nitrogen	3.04	non-metal\n" +
+                    "O	oxygen	3.44	non-metal\n" +
+                    "F	fluorine	3.98	non-metal\n" +
+                    "Ne	neon	no data 	non-metal\n" +
+                    "Na	sodium	0.93	metal\n" +
+                    "Mg	magnesium	1.31	metal\n" +
+                    "Al	aluminium	1.61	metal\n" +
+                    "Si	silicon	1.9	\n" +
+                    "P	phosphorus	2.19	non-metal\n" +
+                    "S	sulfur	2.58	non-metal\n" +
+                    "Cl	chlorine	3.16	non-metal\n" +
+                    "Ar	argon	no data 	non-metal\n" +
+                    "K	potassium	0.82	metal\n" +
+                    "Ca	calcium	1	metal\n" +
+                    "Sc	scandium	1.36	metal\n" +
+                    "Ti	titanium	1.54	metal\n" +
+                    "V	vanadium	1.63	metal\n" +
+                    "Cr	chromium	1.66	metal\n" +
+                    "Mn	manganese	1.55	metal\n" +
+                    "Fe	iron	1.83	metal\n" +
+                    "Co	cobalt	1.88	metal\n" +
+                    "Ni	nickel	1.91	metal\n" +
+                    "Cu	copper	1.9	metal\n" +
+                    "Zn	zinc	1.65	metal\n" +
+                    "Ga	gallium	1.81	metal\n" +
+                    "Ge	germanium	2.01	\n" +
+                    "As	arsenic	2.18	\n" +
+                    "Se	selenium	2.55	non-metal\n" +
+                    "Br	bromine	2.96	non-metal\n" +
+                    "Kr	krypton	3	non-metal\n" +
+                    "Rb	rubidium	0.82	metal\n" +
+                    "Sr	strontium	0.95	metal\n" +
+                    "Y	yttrium	1.22	metal\n" +
+                    "Zr	zirconium	1.33	metal\n" +
+                    "Nb	niobium	1.6	metal\n" +
+                    "Mo	molybdenum	2.16	metal\n" +
+                    "Tc	technetium	1.9	metal\n" +
+                    "Ru	ruthenium	2.2	metal\n" +
+                    "Rh	rhodium	2.28	metal\n" +
+                    "Pd	palladium	2.2	metal\n" +
+                    "Ag	silver	1.93	metal\n" +
+                    "Cd	cadmium	1.69	metal\n" +
+                    "In	indium	1.78	metal\n" +
+                    "Sn	tin	1.96	metal\n" +
+                    "Sb	antimony	2.05	\n" +
+                    "Te	tellurium	2.1	\n" +
+                    "I	iodine	2.66	non-metal\n" +
+                    "Xe	xenon	2.6	non-metal\n" +
+                    "Cs	caesium	0.79	metal\n" +
+                    "Ba	barium	0.89	metal\n" +
+                    "La	lanthanum	1.1	metal\n" +
+                    "Ce	cerium	1.12	metal\n" +
+                    "Pr	praseodymium	1.13	metal\n" +
+                    "Nd	neodymium	1.14	metal\n" +
+                    "Pm	promethium	no data 	metal\n" +
+                    "Sm	samarium	1.17	metal\n" +
+                    "Eu	europium	no data 	metal\n" +
+                    "Gd	gadolinium	1.2	metal\n" +
+                    "Tb	terbium	no data 	metal\n" +
+                    "Dy	dysprosium	1.22	metal\n" +
+                    "Ho	holmium	1.23	metal\n" +
+                    "Er	erbium	1.24	metal\n" +
+                    "Tm	thulium	1.25	metal\n" +
+                    "Yb	ytterbium	no data 	metal\n" +
+                    "Lu	lutetium	1.27	metal\n" +
+                    "Hf	hafnium	1.3	metal\n" +
+                    "Ta	tantalum	1.5	metal\n" +
+                    "W	tungsten	2.36	metal\n" +
+                    "Re	rhenium	1.9	metal\n" +
+                    "Os	osmium	2.2	metal\n" +
+                    "Ir	iridium	2.2	metal\n" +
+                    "Pt	platinum	2.28	metal\n" +
+                    "Au	gold	2.54	metal\n" +
+                    "Hg	mercury	2	metal\n" +
+                    "Tl	thallium	1.62	metal\n" +
+                    "Pb	lead	2.33	metal\n" +
+                    "Bi	bismuth	2.02	metal\n" +
+                    "Po	polonium	2	metal\n" +
+                    "At	astatine	2.2	\n" +
+                    "Rn	radon	no data 	non-metal\n" +
+                    "Fr	francium	0.7	metal\n" +
+                    "Ra	radium	0.9	metal\n" +
+                    "Ac	actinium	1.1	metal\n" +
+                    "Th	thorium	1.3	metal\n" +
+                    "Pa	protactinium	1.5	metal\n" +
+                    "U	uranium	1.38	metal\n" +
+                    "Np	neptunium	1.36	metal\n" +
+                    "Pu	plutonium	1.28	metal\n" +
+                    "Am	americium	1.3	metal\n" +
+                    "Cm	curium	1.3	metal\n" +
+                    "Bk	berkelium	1.3	metal\n" +
+                    "Cf	californium	1.3	metal\n" +
+                    "Es	einsteinium	1.3	metal\n" +
+                    "Fm	fermium	1.3	metal\n" +
+                    "Md	mendelevium	1.3	metal\n" +
+                    "No	nobelium	1.3	metal";
+
+    @Autowired
+    private StructureHandlingConfiguration structureHandlingConfiguration;
+
+    private Map<String, String> saltData;
+
+    @PostConstruct
+    private void setUpSalts() {
+        log.warn("in setUpSalts, structureHandlingConfiguration.getSaltFilePath(): {}", structureHandlingConfiguration.getSaltFilePath());
+        saltData = new HashMap<>();
+        try {
+            File file = new File(structureHandlingConfiguration.getSaltFilePath());
+            Assert.assertTrue("input salt data file must exist!", file.exists());
+            List<String> lines = Files.readAllLines(file.toPath());
+            for (String line : lines) {
+                String[] lineParts = line.split("\\t");
+                saltData.put(lineParts[0], lineParts[1]);
+            }
+        }
+        catch (Exception ex){
+            log.error("Error loading salt data {}", ex.getMessage());
+            ex.printStackTrace();
+        }
+        log.warn("completed loading of salt data -- {} records", saltData.keySet().size());
+    }
+
+    public static class MetalicNature{
+        enum ATOM_METAL_TYPE{
+            METAL,
+            NONMETAL,
+            METALLIOD
+        }
+        double en;
+        ATOM_METAL_TYPE atype;
+        public MetalicNature(double en, ATOM_METAL_TYPE atype){
+            this.en=en;
+            this.atype=atype;
+        }
+        public boolean shouldBeIonic(MetalicNature mn2){
+            //if(Math.abs(this.en-mn2.en)>1.6){
+            //}
+            return (this.atype == ATOM_METAL_TYPE.METAL && mn2.atype == ATOM_METAL_TYPE.NONMETAL) ||
+                    (this.atype == ATOM_METAL_TYPE.NONMETAL && mn2.atype == ATOM_METAL_TYPE.METAL);
+        }
+        public boolean isMetal(){
+            return ATOM_METAL_TYPE.METAL==this.atype;
+        }
+        public boolean isNonMetal(){
+            return ATOM_METAL_TYPE.NONMETAL==this.atype;
+        }
+
+    }
+    static Map<String,MetalicNature> EN_MAP = new ConcurrentHashMap<String,MetalicNature>();
+    static{
+        for(String line:electroneglist.split("\n")){
+            String[] parts=line.split("\t");
+            double score = -1;
+            try{
+                score = Double.valueOf(parts[2]);
+            }catch(Exception e){
+
+            }
+
+            String symbol=parts[0];
+            MetalicNature.ATOM_METAL_TYPE atype= MetalicNature.ATOM_METAL_TYPE.METALLIOD;
+            try{
+                atype= MetalicNature.ATOM_METAL_TYPE.valueOf(parts[3].toUpperCase().replace("-", ""));
+            }catch(Exception e){
+
+            }
+
+            EN_MAP.put(symbol,new MetalicNature(score, atype));
+
+        }
+    }
+
+
+    public static boolean breakBondsToMetals(Chemical c){
+        Set<Bond> toRemove = new HashSet<Bond>();
+
+        for (Atom ca : c.getAtoms()) {
+            MetalicNature en1 = EN_MAP.get(ca.getSymbol());
+            if(en1==null)continue;
+            for (Atom ca2 : ca.getNeighbors()) {
+
+                for (Bond cb : ca.getBonds()) {
+                    if (cb.getOtherAtom(ca).equals(ca2)) {
+                        MetalicNature en2=EN_MAP.get(ca2.getSymbol());
+                        if(en2!=null){
+                            if(en1.shouldBeIonic(en2)){
+
+                                if(toRemove.add(cb)){
+                                    int order=cb.getBondType().getOrder();
+                                    if(en1.isMetal()){
+                                        ca.setCharge(ca.getCharge()+order);
+                                        ca2.setCharge(ca2.getCharge()-order);
+                                    }else{
+                                        ca.setCharge(ca.getCharge()-order);
+                                        ca2.setCharge(ca2.getCharge()+order);
+                                    }
+                                }
+                            }
+                        }
+                    }
+                    //}
+                }
+            }
+        }
+        boolean changed=false;
+        for(Bond cb1:toRemove){
+            c.removeBond(cb1);
+            changed=true;
+        }
+        return changed;
+    }
+
+    public static boolean removeMetals(Chemical c){
+        Set<Bond> toRemove = new HashSet<Bond>();
+        Set<Atom> atomsToRemove = new HashSet<>();
+        for (Atom ca : c.getAtoms()) {
+            MetalicNature en1 = EN_MAP.get(ca.getSymbol());
+            if(en1==null)continue;
+            for (Atom ca2 : ca.getNeighbors()) {
+                for (Bond cb : ca.getBonds()) {
+                    if (cb.getOtherAtom(ca).equals(ca2)) {
+                        MetalicNature en2=EN_MAP.get(ca2.getSymbol());
+                        if(en2!=null){
+                            if(en1.shouldBeIonic(en2)){
+
+                                if(toRemove.add(cb)){
+                                    int order=cb.getBondType().getOrder();
+                                    if(en1.isMetal()){
+                                        //ca.setCharge(ca.getCharge()+order);
+                                        ca2.setCharge(ca2.getCharge()-order);
+                                        atomsToRemove.add(ca);
+                                    }else{
+                                        ca.setCharge(ca.getCharge()-order);
+                                        //ca2.setCharge(ca2.getCharge()+order);
+                                        atomsToRemove.add(ca2);
+                                    }
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
+        boolean changed=false;
+        for(Bond cb1:toRemove){
+            c.removeBond(cb1);
+            changed=true;
+        }
+        for(Atom a:atomsToRemove){
+            c.removeAtom(a);
+            changed=true;
+        }
+        return changed;
+    }
+
+    public Chemical stripSalts(Chemical inputChemical) {
+        List<Chemical> chemicals = new ArrayList<>();
+        inputChemical.getConnectedComponents().forEach(c ->
+        {
+            String componentInchiKey = "";
+            try  {
+                componentInchiKey =c.toInchi().getKey();
+            }
+            catch(IOException ex) {
+                log.error("Error computing inchi for fragment ", ex);
+            }
+            if (!saltData.containsKey(componentInchiKey))
+            {
+                chemicals.add(c);
+            }
+        });
+        if (chemicals.size() == 1)
+        {
+            return chemicals.get(0);
+        }
+        if (!chemicals.isEmpty())
+        {
+            int maxAtoms = 0;
+            int indexOfMaxAtoms = -1;
+            for (int i = 0; i < chemicals.size(); i++)
+            {
+                Chemical chemical = chemicals.get(i);
+                if (chemical.getAtomCount() > maxAtoms)
+                {
+                    maxAtoms = chemical.getAtomCount();
+                    indexOfMaxAtoms = i;
+                }
+            }
+            return chemicals.get(indexOfMaxAtoms);
+        }
+        return null;
+    }
+
+}
diff --git a/gsrs-ncats-substance-extension/src/main/java/gsrs/module/substance/utils/ChemicalUtils.java b/gsrs-ncats-substance-extension/src/main/java/gsrs/module/substance/utils/ChemicalUtils.java
index 85d24b9b5..698ba7e7c 100644
--- a/gsrs-ncats-substance-extension/src/main/java/gsrs/module/substance/utils/ChemicalUtils.java
+++ b/gsrs-ncats-substance-extension/src/main/java/gsrs/module/substance/utils/ChemicalUtils.java
@@ -3,7 +3,6 @@
 import gov.nih.ncats.molwitch.Atom;
 import gov.nih.ncats.molwitch.Chemical;
 import gov.nih.ncats.molwitch.Bond;
-import ix.ginas.models.v1.GinasChemicalStructure;
 import lombok.extern.slf4j.Slf4j;
 
 import java.io.IOException;
@@ -11,6 +10,7 @@
 import java.util.concurrent.ConcurrentHashMap;
 
 @Slf4j
+@Deprecated
 public class ChemicalUtils {
     private final static String electroneglist=
             "H	hydrogen	2.2	non-metal\n" +
@@ -248,8 +248,8 @@ public static boolean removeMetals(Chemical c){
         return changed;
     }
 
-    public static Chemical stripSalts3(Chemical inputChemical, Map<String, String> salts) {
-        List<Chemical> chemicals = new ArrayList();
+    public static Chemical stripSalts(Chemical inputChemical, Map<String, String> salts) {
+        List<Chemical> chemicals = new ArrayList<>();
         inputChemical.getConnectedComponents().forEach(c ->
         {
             String componentInchiKey = "";
@@ -268,7 +268,7 @@ public static Chemical stripSalts3(Chemical inputChemical, Map<String, String> s
         {
             return chemicals.get(0);
         }
-        if (chemicals.size() > 0)
+        if (!chemicals.isEmpty())
         {
             int maxAtoms = 0;
             int indexOfMaxAtoms = -1;
@@ -286,8 +286,4 @@ public static Chemical stripSalts3(Chemical inputChemical, Map<String, String> s
         return null;
     }
 
-    private void experiment() {
-        Chemical c = new Chemical();
-        Atom a = c.getAtom(1);
-    }
 }

From 401e5e38c648eeebf3f7c85d2f16be8b54152e68 Mon Sep 17 00:00:00 2001
From: Mitch Miller <mitch.miller@thinkscience.us>
Date: Mon, 5 Aug 2024 21:06:23 -0400
Subject: [PATCH 2/2] single salt data file

---
 gsrs-module-substance-example/pom.xml         |  5 ----
 .../salt_data_public.tsv                      | 23 +++++++++++++++++++
 .../src/main/resources/salt_data_public.tsv   | 23 +++++++++++++++++++
 3 files changed, 46 insertions(+), 5 deletions(-)

diff --git a/gsrs-module-substance-example/pom.xml b/gsrs-module-substance-example/pom.xml
index 6298ba351..2c5a0bba6 100644
--- a/gsrs-module-substance-example/pom.xml
+++ b/gsrs-module-substance-example/pom.xml
@@ -370,10 +370,5 @@
             <artifactId>jackson-annotations</artifactId>
             <version>${jackson.version}</version>
         </dependency>
-        <dependency>
-            <groupId>javax.annotation</groupId>
-            <artifactId>javax.annotation-api</artifactId>
-            <version>1.3.2</version>
-        </dependency>
     </dependencies>
 </project>
diff --git a/gsrs-module-substance-example/salt_data_public.tsv b/gsrs-module-substance-example/salt_data_public.tsv
index cda7922fc..39c6ac13d 100644
--- a/gsrs-module-substance-example/salt_data_public.tsv
+++ b/gsrs-module-substance-example/salt_data_public.tsv
@@ -59,3 +59,26 @@ ODKSFYDXXFIFQN-BYPYZUCNSA-N	C(C[C@@H](C(=O)O)N)CNC(=N)N	54
 MBBZMMPHUWSWHV-BDVNFPICSA-N	CNC[C@@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O	52
 GBNDTYKAOXLLID-UHFFFAOYSA-N	[Zr+4]	51
 YGSDEFSMJLZEOE-UHFFFAOYSA-N	c1ccc(c(c1)C(=O)O)O	51
+SRSXLGNVWSONIS-UHFFFAOYSA-N	c1ccc(cc1)S(=O)(=O)O	49
+QAOWNCQODCNURD-UHFFFAOYSA-M	OS(=O)(=O)[O-]	46
+WLJNZVDCPSBLRP-UHFFFAOYSA-N	c1ccc2c(c1)cc(c(c2Cc3c4ccccc4cc(c3O)C(=O)O)O)C(=O)O	46
+WPYMKLBDIGXBTP-UHFFFAOYSA-N	c1ccc(cc1)C(=O)O	45
+WLZRMCYVCSSEQC-UHFFFAOYSA-N	[Cd+2]	43
+LENZDBCJOHFCAS-UHFFFAOYSA-N	C(C(CO)(CO)N)O	41
+LCKIEQZJEYYRIY-UHFFFAOYSA-N	[Ti+4]	39
+BQPIGGFYSBELGY-UHFFFAOYSA-N	[Hg+2]	39
+NBIIXXVUZAFLBC-UHFFFAOYSA-K	O=P([O-])([O-])[O-]	39
+MUBZPKHOEPUJKR-UHFFFAOYSA-L	C(=O)(C(=O)[O-])[O-]	39
+GLUUGHFHXGJENI-UHFFFAOYSA-N	C1CNCCN1	39
+VEQPNABPJHWNSG-UHFFFAOYSA-N	[Ni+2]	38
+RJOJUSXNYCILHH-UHFFFAOYSA-N	[Gd+3]	38
+RWSOTUBLDIXVET-UHFFFAOYSA-M	[SH-]	37
+DTQVDTLACAAQTR-UHFFFAOYSA-N	C(=O)(C(F)(F)F)O	37
+JOXIMZWYDAKGHI-UHFFFAOYSA-M	Cc1ccc(cc1)S(=O)(=O)[O-]	35
+XQTIWNLDFPPCIU-UHFFFAOYSA-N	[Ce+3]	34
+CRBHXDCYXIISFC-UHFFFAOYSA-N	C[N+](C)(C)CC[O-]	33
+KIWBPDUYBMNFTB-UHFFFAOYSA-M	CCOS(=O)(=O)[O-]	33
+JAWGVVJVYSANRY-UHFFFAOYSA-N	[Co+3]	32
+ZMZDMBWJUHKJPS-UHFFFAOYSA-N	C(#N)S	32
+RGHNJXZEOKUKBD-SQOUGZDYSA-N	C([C@H]([C@H]([C@@H]([C@H](C(=O)O)O)O)O)O)O	31
+CKLJMWTZIZZHCS-REOHCLBHSA-L	C([C@@H](C(=O)[O-])N)C(=O)[O-]	31
diff --git a/gsrs-module-substance-example/src/main/resources/salt_data_public.tsv b/gsrs-module-substance-example/src/main/resources/salt_data_public.tsv
index cda7922fc..39c6ac13d 100644
--- a/gsrs-module-substance-example/src/main/resources/salt_data_public.tsv
+++ b/gsrs-module-substance-example/src/main/resources/salt_data_public.tsv
@@ -59,3 +59,26 @@ ODKSFYDXXFIFQN-BYPYZUCNSA-N	C(C[C@@H](C(=O)O)N)CNC(=N)N	54
 MBBZMMPHUWSWHV-BDVNFPICSA-N	CNC[C@@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O	52
 GBNDTYKAOXLLID-UHFFFAOYSA-N	[Zr+4]	51
 YGSDEFSMJLZEOE-UHFFFAOYSA-N	c1ccc(c(c1)C(=O)O)O	51
+SRSXLGNVWSONIS-UHFFFAOYSA-N	c1ccc(cc1)S(=O)(=O)O	49
+QAOWNCQODCNURD-UHFFFAOYSA-M	OS(=O)(=O)[O-]	46
+WLJNZVDCPSBLRP-UHFFFAOYSA-N	c1ccc2c(c1)cc(c(c2Cc3c4ccccc4cc(c3O)C(=O)O)O)C(=O)O	46
+WPYMKLBDIGXBTP-UHFFFAOYSA-N	c1ccc(cc1)C(=O)O	45
+WLZRMCYVCSSEQC-UHFFFAOYSA-N	[Cd+2]	43
+LENZDBCJOHFCAS-UHFFFAOYSA-N	C(C(CO)(CO)N)O	41
+LCKIEQZJEYYRIY-UHFFFAOYSA-N	[Ti+4]	39
+BQPIGGFYSBELGY-UHFFFAOYSA-N	[Hg+2]	39
+NBIIXXVUZAFLBC-UHFFFAOYSA-K	O=P([O-])([O-])[O-]	39
+MUBZPKHOEPUJKR-UHFFFAOYSA-L	C(=O)(C(=O)[O-])[O-]	39
+GLUUGHFHXGJENI-UHFFFAOYSA-N	C1CNCCN1	39
+VEQPNABPJHWNSG-UHFFFAOYSA-N	[Ni+2]	38
+RJOJUSXNYCILHH-UHFFFAOYSA-N	[Gd+3]	38
+RWSOTUBLDIXVET-UHFFFAOYSA-M	[SH-]	37
+DTQVDTLACAAQTR-UHFFFAOYSA-N	C(=O)(C(F)(F)F)O	37
+JOXIMZWYDAKGHI-UHFFFAOYSA-M	Cc1ccc(cc1)S(=O)(=O)[O-]	35
+XQTIWNLDFPPCIU-UHFFFAOYSA-N	[Ce+3]	34
+CRBHXDCYXIISFC-UHFFFAOYSA-N	C[N+](C)(C)CC[O-]	33
+KIWBPDUYBMNFTB-UHFFFAOYSA-M	CCOS(=O)(=O)[O-]	33
+JAWGVVJVYSANRY-UHFFFAOYSA-N	[Co+3]	32
+ZMZDMBWJUHKJPS-UHFFFAOYSA-N	C(#N)S	32
+RGHNJXZEOKUKBD-SQOUGZDYSA-N	C([C@H]([C@H]([C@@H]([C@H](C(=O)O)O)O)O)O)O	31
+CKLJMWTZIZZHCS-REOHCLBHSA-L	C([C@@H](C(=O)[O-])N)C(=O)[O-]	31