From dad8244909bf1556e8e7bd068bf98083fe1252e1 Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sun, 23 Jul 2023 16:30:26 +0200
Subject: [PATCH] Like *Label, *ChemicalStructure is a new special, expects a
 SMILES and will use CDK Depict (Toolforge) to visualize the chemical
 structure in 2D

---
 scholia/app/static/scholia.js                 | 9 +++++++++
 scholia/app/templates/taxon_metabolome.sparql | 7 +++++--
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/scholia/app/static/scholia.js b/scholia/app/static/scholia.js
index 7e9b34fd0..0602252f0 100644
--- a/scholia/app/static/scholia.js
+++ b/scholia/app/static/scholia.js
@@ -85,6 +85,8 @@ function convertDataTableData(data, columns) {
         var column = columns[i];
         if (column.slice(-11) == 'Description') {
             convertedColumns.push(column.slice(0, column.length - 11) + ' description');
+        } else if (column.slice(-17) == 'ChemicalStructure') {
+            convertedColumns.push(column.slice(0, column.length - 17) + ' structure');
         } else if (column.slice(-5) == 'Label') {
             // pass
         } else if (column.slice(-3) == 'Url') {
@@ -107,6 +109,13 @@ function convertDataTableData(data, columns) {
 		    data[i][key + 'Url'] +
 		    '">' + data[i][key + 'Label'] + '</a>';
 
+	    } else if (key.slice(-17) == 'ChemicalStructure') {
+            convertedRow[key.slice(0, key.length - 17) + ' structure'] = '<img loading="lazy" src="' +
+            'https://cdkdepict.toolforge.org/depict/bow/svg?smi=' +
+		    encodeURIComponent(data[i][key]) +
+            '&abbr=on&hdisp=bridgehead&showtitle=false&zoom=2&annotate=cip' +
+		    '" />';
+
 	    } else if (
 			key + 'Label' in data[i] &&
 			/^http/.test(data[i][key]) &&
diff --git a/scholia/app/templates/taxon_metabolome.sparql b/scholia/app/templates/taxon_metabolome.sparql
index 165c37554..c5516e0c9 100644
--- a/scholia/app/templates/taxon_metabolome.sparql
+++ b/scholia/app/templates/taxon_metabolome.sparql
@@ -1,20 +1,23 @@
 PREFIX target: <http://www.wikidata.org/entity/{{ q }}>
 
 SELECT DISTINCT
-  ?metabolite ?metaboliteLabel ?metaboliteDescription
+  ?metabolite ?metaboliteLabel ?metaboliteChemicalStructure ?metaboliteDescription
 WITH {
   SELECT DISTINCT ?children WHERE {
       ?children (wdt:P171*) target:.
   }
 } AS %taxa 
 WITH {
-  SELECT DISTINCT ?metabolite WHERE {
+  SELECT DISTINCT ?metabolite ?metaboliteChemicalStructure WHERE {
     INCLUDE %taxa
             { ?metabolite wdt:P703 ?children }
     UNION
     { ?metabolite wdt:P1582 ?children }
     VALUES ?chemical { wd:Q11173 wd:Q59199015 wd:Q56256086 wd:Q15711994 }.
     ?metabolite wdt:P31|wdt:P279/wdt:P31 ?chemical .
+    OPTIONAL { ?metabolite wdt:P233 ?canSmiles }
+    OPTIONAL { ?metabolite wdt:P2017 ?isoSmiles }
+    BIND(COALESCE(?isoSmiles, ?canSmiles) AS ?metaboliteChemicalStructure)
   }
 } AS %results {
   INCLUDE %results