fix: updated molecules santise scripts

NFDI4Chem · Dec 28, 2023 · 6625be7 · 6625be7
1 parent 145168f
commit 6625be7
Showing 1 changed file with 80 additions and 10 deletions.
diff --git a/app/Console/Commands/SanitizeMolecules.php b/app/Console/Commands/SanitizeMolecules.php
@@ -27,25 +27,95 @@ class SanitizeMolecules extends Command
      */
     public function handle()
     {
-        $molecules = Molecule::whereNull('canonical_smiles')->get();
+        $molecules = Molecule::all();
 
         foreach ($molecules as $molecule) {
             echo $molecule->id;
             echo "\r\n";
-            $molecule->MOL = '
-            '.$molecule->MOL;
-            $standardisedMOL = $this->standardizeMolecule($molecule->sdf);
-            $molecule->canonical_smiles = $standardisedMOL['canonical_smiles'];
-            $molecule->standard_inchi = $standardisedMOL['inchi'];
-            $molecule->inchi_key = $standardisedMOL['inchikey'];
-            $molecule->save();
+            $inchi = $molecule->standard_inchi;
+            if ($inchi) {
+                $data = $this->fetchPubChemIUPACProperties($inchi);
+                $molecule->synonyms = $data['synonyms'];
+                $molecule->iupac_name = (array_key_exists('IUPACName', $data['properties']) ? $data['properties']['IUPACName'] : $molecule->iupac_name);
+                $molecule->molecular_formula = (array_key_exists('MolecularFormula', $data['properties']) ? $data['properties']['MolecularFormula'] : $molecule->molecular_formula);
+                $molecule->molecular_weight = (array_key_exists('MolecularWeight', $data['properties']) ? $data['properties']['MolecularWeight'] : $molecule->molecular_weight);
+                $molecule->Save();
+            }
+            if (! $molecule->canonical_smiles) {
+                echo $molecule->id;
+                echo "\r\n";
+                $molecule->sdf = '
+                '.$molecule->sdf;
+                $standardisedMOL = $this->standardizeMolecule($molecule->sdf);
+                $molecule->canonical_smiles = array_key_exists('canonical_smiles', $standardisedMOL) ? $standardisedMOL['canonical_smiles'] : null;
+                $molecule->standard_inchi = array_key_exists('inchi', $standardisedMOL) ? $standardisedMOL['inchi'] : null;
+                $molecule->inchi_key = array_key_exists('canonicalinchikey_smiles', $standardisedMOL) ? $standardisedMOL['inchikey'] : null;
+                $molecule->save();
+            }
+            if ($molecule->canonical_smiles) {
+                $cas = $this->fetchCAS($molecule->canonical_smiles);
+                $molecule->cas = $cas;
+                $molecule->save();
+            }
+        }
+    }
+
+    protected function fetchPubChemIUPACProperties($inchi)
+    {
+        $cid_response = Http::get('https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchi/cids/JSON?inchi='.urlencode($inchi));
+        $cid_data = $cid_response->json();
+        $cid = null;
+        if (array_key_exists('IdentifierList', $cid_data)) {
+            $cids = $cid_data['IdentifierList']['CID'];
+            $cid = $cids[0];
+        }
+        $synonyms = '';
+        $properties = [];
+        if ($cid) {
+            $synonyms_response = Http::get('https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/'.$cid.'/Synonyms/JSON');
+            $synonyms_data = $synonyms_response->json();
+            if (! array_key_exists('Fault', $synonyms_data)) {
+                $synonyms = implode(',', $synonyms_data['InformationList']['Information'][0]['Synonym']);
+            }
+
+            $properties_response = Http::get('https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/'.$cid.'/property/IUPACName,MolecularWeight,MolecularFormula/JSON');
+            $properties_data = $properties_response->json();
+            if (! array_key_exists('Fault', $properties_data)) {
+                $properties = $properties_data['PropertyTable']['Properties'][0];
+            }
+        }
+
+        return [
+            'synonyms' => $synonyms,
+            'properties' => $properties,
+        ];
+    }
+
+    protected function fetchCAS($smiles)
+    {
+        try {
+            $response = Http::get('https://commonchemistry.cas.org/api/search?q='.$smiles);
+            if (! $response->failed()) {
+                $data = $response->json();
+                if ($data['count'] > 0) {
+                    $cas = $data['results'][0]['rn'];
+
+                    return $cas;
+                }
+            }
+        } catch (\Illuminate\Http\Client\ConnectionException $e) {
+            echo 'timed out: '.$smiles;
         }
     }
 
     protected function standardizeMolecule($mol)
     {
-        $response = Http::post('https://dev.api.naturalproducts.net/latest/chem/standardize', $mol);
+        try {
+            $response = Http::post('https://api.naturalproducts.net/latest/chem/standardize', $mol);
 
-        return $response->json();
+            return $response->json();
+        } catch (\Illuminate\Http\Client\ConnectionException $e) {
+            echo 'timed out: '.$mol;
+        }
     }
 }