flex plus searching is now like flex searching with the addition of salt stripping of the query structure

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

gsrs-module-substance-example/salt_data_public.tsv

@@ -0,0 +1,84 @@
+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
+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

gsrs-module-substance-example/src/main/resources/salt_data_public.tsv

@@ -0,0 +1,84 @@
+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
+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

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)
+        );
+    }
+}

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());
     }
 

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

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;
+}

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 {