Update on molecule controller to get binding data.

raphamontana · Apr 22, 2020 · 3360b55 · 3360b55
1 parent 4a0fc01
commit 3360b55
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Showing 8 changed files with 1,314 additions and 32 deletions.
diff --git a/docs/chembl_model_schema.xml b/docs/chembl_model_schema.xml
diff --git a/src/web/controllers/moleculeController.js b/src/web/controllers/moleculeController.js
@@ -14,13 +14,16 @@ class MoleculeController {
                 let chembl = ChemblController.fetch(smiles);
                 let pdb = await PDBController.searchLigandBySmiles(smiles);
                 let bindings = [];
-                await Promise.all(
-                    pdb.structuresList.map(async structure => {
-                        let binding = await BMOADController.fetch(structure);
-                        if (binding.length > 0) {
-                            bindings.push(binding);
-                        }
-                    }));
+                if (pdb) {
+                    await Promise.all(
+                        pdb.structuresList.map(async structure => {
+                            let binding = await BMOADController.fetch(structure);
+                            if (binding.length > 0) {
+                                bindings.push(binding);
+                            }
+                        }));
+
+                }
                 molecules.push({
                     smiles: smiles,
                     pubchem: await pubchem,

diff --git a/src/web/controllers/pdbController.js b/src/web/controllers/pdbController.js
@@ -27,7 +27,9 @@ class PDBFactory {
   static LIGANDS_URL =
     "https://www.rcsb.org/pdb/rest/ligandInfo?structureId=<STRUCTUREID>";
 
-  static get RESOLUTION_THRESHOLD() { return 2; }
+  static get RESOLUTION_THRESHOLD() {
+    return 2;
+  }
 
   /**
    * Cast a XML file to a PDBStructure object.
@@ -47,7 +49,11 @@ class PDBFactory {
     let description = json.PDBdescription.PDB[0].$.title;
     let resolution = json.PDBdescription.PDB[0].$.resolution;
     // Create the object.
-    let structure = {structureId, description, resolution};
+    let structure = {
+      structureId,
+      description,
+      resolution
+    };
     return structure;
   }
 
@@ -65,7 +71,7 @@ class PDBFactory {
       ligandList.push(ligand.$.chemicalID);
     });
     // Return the object.
-    return(ligandList);
+    return (ligandList);
   }
 
 
@@ -89,7 +95,7 @@ class PDBFactory {
       let ligandXML = await ligandRes.text();
       let ligands = this.parseLigandInfo(ligandXML);
       let pdbStructure = new PDB.PDBStructure(structure.structureId, structure.description, structure.resolution, ligands);
-      return(pdbStructure);
+      return (pdbStructure);
     } catch (err) {
       console.log(err);
     }
@@ -111,20 +117,24 @@ class PDBFactory {
     });
     // Get ligand data.
     let ligand = json.smilesQueryResult.ligandInfo[0].ligand;
-    let chemicalID = ligand[0].$.chemicalID;
-    let molecularWeight = ligand[0].$.molecularWeight;
-    let chemicalName = ligand[0].chemicalName;
-    let formula = ligand[0].formula;
-    let smiles = ligand[0].smiles;
-    // Get structures list.
-    let structures = [];
-    await Promise.all(
-      ligand.map(async (element) => {
-        let structure = await this.fetchStructure(element.$.structureId);
-        structures.push(structure);
-    }));
+    let pdbLigand;
+    if (ligand) {
+      let chemicalID = ligand[0].$.chemicalID;
+      let molecularWeight = ligand[0].$.molecularWeight;
+      let chemicalName = ligand[0].chemicalName;
+      let formula = ligand[0].formula;
+      let smiles = ligand[0].smiles;
+      // Get structures list.
+      let structures = [];
+      await Promise.all(
+        ligand.map(async (element) => {
+          let structure = await this.fetchStructure(element.$.structureId);
+          structures.push(structure);
+        }));
+      pdbLigand = new PDB.PDBLigand(chemicalID, chemicalName, formula, smiles, molecularWeight, structures);
+    }
     // Create the object.
-    return(new PDB.PDBLigand(chemicalID, chemicalName, formula, smiles, molecularWeight, structures));
+    return (pdbLigand);
   }
 
 
@@ -142,11 +152,11 @@ class PDBFactory {
       const res = await fetch(url);
       if (!res.ok) return;
       let xml = await res.text();
-      return(await this.parsePDB(xml));
+      return (await this.parsePDB(xml));
     } catch (err) {
       console.log(err);
     }
   }
 }
 
-module.exports = PDBFactory;
+module.exports = PDBFactory;
diff --git a/src/web/controllers/pubchemController.js b/src/web/controllers/pubchemController.js
@@ -58,6 +58,10 @@ class PubchemFactory {
             console.log(err);
         }
     }
+
+    static async getSimilarities(cid) {
+
+    }
 }
 
 module.exports = PubchemFactory;