#45 improvements following discussion with Ruben

tdudgeon · tdudgeon · commit 19e40d841e12 · 2021-08-27T16:36:02.000+01:00
diff --git a/fragnet-search/README.md b/fragnet-search/README.md
@@ -629,41 +629,73 @@ Parameters:
 |------------|-------|----------|-------------|
 | smiles     | URL   | Yes      | The smiles string for the query molecule. |
 | synthon    | Query | Yes      | The smiles string for the synthon molecule. |
+| hops       | Query | Yes      | The number of graph edges to traverse from the query molecule. Typically use 3 or 4. |
 | hacMin     | Query | No       | The minimum heavy atom count of the resulting molecules. |
 | hacMax     | Query | No       | The maximum heavy atom count of the resulting molecules. |
 | racMin     | Query | No       | The minimum ring atom count of the resulting molecules. |
 | racMax     | Query | No       | The maximum ring atom count of the resulting molecules. |
-| hops       | Query | Yes      | The number of graph edges to traverse from the query molecule. Typically use 3 or 4. |
+| limit      | Query | No       | The maximum number of results to fetch. Default is 1000, values over 500 not allowed. |
 
-Note that these searches can be quite slow. Start with a small number of hops, and increase if you have no results.
+Be careful with the query parameters as using a large number of hops may result in queries that take a long time 
+to execute and return a large number of results. Start with a small number of hops, and increase if you get no results.
+To provide some control over this there is a limit to the number of results that will be returned.
+By default this is set to 1000, but it can be adjusted using the `limit` query parameter, but this value cannot be set
+to a value greater than 5000. 
 
-Typcial execution:
+Typical execution:
 ```
 curl "$FRAGNET_SERVER/fragnet-search/rest/v2/search/synthon-expand/OC(Cn1ccnn1)C1CC1?synthon=%5BXe%5Dn1ccnn1&hops=3&hacMin=14&hacMax=18"
 ```
 
-Typcial results:
+The results are in JSON format and comprise an array of molecule info objects (the same data object as is returned by the
+molecule search endpoint). e.g.:
 ```
 [
-  "NC(CCCNCCn1ccnn1)=NO",
-  "NN=C(NCCn1ccnn1)NC1CC1",
-  "CCC(NCCn1ccnn1)C(C)(C)C",
-  "CC(CC(N)=O)NCCCn1ccnn1",
-  "O=C(O)C(=O)C(=O)NCCn1ccnn1",
-  "NN=C(NCCCn1ccnn1)NC1CC1",
-  "CCOC(C)(C)CNCCn1ccnn1",
-  "CCNC(C)CNC(=O)Cn1ccnn1",
-  "CCC(CN)NC(=O)CCn1ccnn1",
-  "CN(C(=O)Cn1ccnn1)C(C)(C)C#N",
-  "O=C(O)C=CC(=O)NCCn1ccnn1",
-  "COCCNC(=NN)NCCn1ccnn1",
-  "CC(NC(=O)CCn1ccnn1)C(N)=O",
-  "CC(C)N(CC#N)C(=O)Cn1ccnn1",
-  "CCC(NCCCn1ccnn1)C(N)=NO",
-  "CN(CCC(=O)O)C(=O)CCn1ccnn1",
-  "NCC=CCNC(=O)CCn1ccnn1",
-  "COC(=O)C=CNCCCn1ccnn1",
-  "NC(CCCCNCCn1ccnn1)=NO"
+   {
+    "id": 3573384,
+    "smiles": "NC(CCCNCCn1ccnn1)=NO",
+    "molType": "NET_FRAG",
+    "labels": [
+      "CanSmi",
+      "Mol",
+      "F2",
+      "V_CS_BB"
+    ],
+    "props": {
+      "inchik": "LMBOOOPIIROSSY-JSGPKCTENA-N",
+      "osmiles": "NC(CCCNCCC1CCCC1)NO",
+      "chac": 5,
+      "neighbours": 2,
+      "hac": 15,
+      "inchis": "InChI=1/C8H16N6O/c9-8(12-15)2-1-3-10-4-6-14-7-5-11-13-14/h5,7,10,15H,1-4,6H2,(H2,9,12)/f/h9H2MA",
+      "cmpd_ids": [
+        "CHEMSPACE-BB:CSC033999226"
+      ]
+    }
+  },
+  {
+    "id": 3287068,
+    "smiles": "OCCc1ccc(-n2ccnn2)cc1",
+    "molType": "NET_FRAG",
+    "labels": [
+      "CanSmi",
+      "Mol",
+      "F2",
+      "V_CS_BB"
+    ],
+    "props": {
+      "inchik": "PTDSMQOYRRMILK-UHFFFAOYNA-N",
+      "osmiles": "OCCC1CCC(C2CCCC2)CC1",
+      "chac": 11,
+      "neighbours": 4,
+      "hac": 14,
+      "inchis": "InChI=1/C10H11N3O/c14-8-5-9-1-3-10(4-2-9)13-7-6-11-12-13/h1-4,6-7,14H,5,8H2MA",
+      "cmpd_ids": [
+        "CHEMSPACE-BB:CSC021068907"
+      ]
+    }
+  },
+  ...
 ]
 ```
 
diff --git a/fragnet-search/src/main/java/org/squonk/fragnet/search/queries/v2/SynthonExpandQuery.java b/fragnet-search/src/main/java/org/squonk/fragnet/search/queries/v2/SynthonExpandQuery.java
@@ -23,10 +23,13 @@
 import org.neo4j.driver.v1.types.Relationship;
 import org.squonk.fragnet.Constants;
 import org.squonk.fragnet.chem.MolStandardize;
+import org.squonk.fragnet.search.model.v2.FragmentGraph;
+import org.squonk.fragnet.search.model.v2.MoleculeNode;
 import org.squonk.fragnet.search.queries.AbstractQuery;
 
 import javax.validation.constraints.NotNull;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.logging.Logger;
@@ -45,7 +48,7 @@ public SynthonExpandQuery(Session session) {
             "-[:FRAG*0..%s]-(:F2)" +
             "<-[e:FRAG]-(c:Mol) WHERE %s" +
             " (split(e.label, '|')[1] = $synthon OR split(e.label, '|')[4] = $synthon)" +
-            " RETURN DISTINCT c";
+            " RETURN DISTINCT c LIMIT $limit";
 
     @Override
     protected String getQueryTemplate() {
@@ -79,28 +82,39 @@ private String expandTemplate(@NotNull Integer hops, Integer hacMin, Integer hac
     }
 
     public List<String> execute(@NotNull String mol, @NotNull String synthon, @NotNull Integer hops,
-                                Integer hacMin, Integer hacMax, Integer racMin, Integer racMax) {
+                                Integer hacMin, Integer hacMax, Integer racMin, Integer racMax, Integer limit) {
 
-        // standardize the mol. It must be in smiles format
-        String stdSmiles = MolStandardize.prepareNonisoMol(mol, Constants.MIME_TYPE_SMILES);
-        String stdSynthon = MolStandardize.prepareNonisoMol(synthon, Constants.MIME_TYPE_SMILES);
+        if (limit == null) {
+            limit = 1000;
+        }
+        if (limit > 5000) {
+            throw new IllegalArgumentException("Limits over 5000 are not supported");
+        }
 
+        // standardize the mol. It must be in smiles format
+        final String stdSmiles = MolStandardize.prepareNonisoMol(mol, Constants.MIME_TYPE_SMILES);
+        final String stdSynthon = MolStandardize.prepareNonisoMol(synthon, Constants.MIME_TYPE_SMILES);
+        final int limitf = limit;
         final String query = expandTemplate(hops, hacMin, hacMax, racMin, racMax);
 
-        HashSet<String> values = getSession().writeTransaction((tx) -> {
+        HashMap<String, MoleculeNode> values = getSession().writeTransaction((tx) -> {
             LOG.info("Executing Synthon Query: " + query);
-            StatementResult result = tx.run(query, parameters(new Object[]{"smiles", stdSmiles, "synthon", stdSynthon}));
-            HashSet<String> smiles = new HashSet<>();
+            StatementResult result = tx.run(query, parameters(new Object[]{
+                    "smiles", stdSmiles, "synthon", stdSynthon, "limit", limitf}));
+            HashMap<String, MoleculeNode> molNodes = new HashMap<>();
             while (result.hasNext()) {
                 Record rec = result.next();
                 Value val = rec.get(0);
                 Node node = val.asNode();
                 String smi = node.get("smiles").asString();
-                smiles.add(smi);
+                if (!molNodes.containsKey(smi)) {
+                    molNodes.put(smi, FragmentGraph.generateMoleculeNode(node));
+                }
+
             }
-            return smiles;
+            return molNodes;
         });
 
-        return new ArrayList(values);
+        return new ArrayList(values.values());
     }
 }
diff --git a/fragnet-search/src/main/java/org/squonk/fragnet/service/v2/FragnetSearchRouteBuilder.java b/fragnet-search/src/main/java/org/squonk/fragnet/service/v2/FragnetSearchRouteBuilder.java
@@ -263,11 +263,12 @@ public void configure() throws Exception {
                 .get("synthon-expand/{smiles}").description("Find expansions of a molecule using a particular synthon")
                 .param().name("smiles").type(RestParamType.path).description("SMILES query").endParam()
                 .param().name("synthon").type(RestParamType.query).description("SMILES synthon").endParam()
+                .param().name("hops").type(RestParamType.query).description("Number of edge traversals").endParam()
                 .param().name("hacMin").type(RestParamType.query).description("Heavy atom count reduction ").endParam()
                 .param().name("hacMax").type(RestParamType.query).description("Heavy atom count increase ").endParam()
                 .param().name("racMin").type(RestParamType.query).description("Ring atom count reduction").endParam()
                 .param().name("racMax").type(RestParamType.query).description("Ring atom count increase").endParam()
-                .param().name("hops").type(RestParamType.query).description("Number of edge traversals").endParam()
+                .param().name("limit").type(RestParamType.query).description("Max number of results to be returned").endParam()
                 .produces("application/json")
                 .route()
                 .process((Exchange exch) -> {
@@ -787,14 +788,15 @@ void executeSynthonExpand(Exchange exch) {
         Integer hacMax = message.getHeader("hacMax", Integer.class);
         Integer racMin = message.getHeader("racMin", Integer.class);
         Integer racMax = message.getHeader("racMax", Integer.class);
+        Integer limit = message.getHeader("limit", Integer.class);
 
         List<String> smiles;
         try (Session session = graphdb.getSession()) {
             // execute the query
             SynthonExpandQuery query = new SynthonExpandQuery(session);
 
             long n0 = System.nanoTime();
-            smiles = query.execute(queryMol, synthon, hops, hacMin, hacMax, racMin, racMax);
+            smiles = query.execute(queryMol, synthon, hops, hacMin, hacMax, racMin, racMax, limit);
             long n1 = System.nanoTime();
             synthonExpandNeo4jSearchDuration.inc((double) (n1 - n0));
             if (smiles == null || smiles.isEmpty()) {
