molecules

client/.gitignore

@@ -2,3 +2,4 @@ package-lock.json
 node_modules/
 dist/
 .cache/
+assets/molecules

ops/.gitignore

@@ -1,2 +1,3 @@
 node_modules/
-package-lock.json
+package-lock.json
+molecules/

ops/fetch.molecules.js

@@ -0,0 +1,45 @@
+const request = require('request');
+const fs = require('fs');
+const renderer = require('sdftosvg');
+
+const SVG_OPTS = {
+    backgroundColor: 'none',
+}
+
+function fetch(i) {
+    return new Promise((resolve, reject) => {
+        const url = `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/${i}/record/SDF/?record_type=2d&response_type=save&response_basename=Structure2D_CID_2519`;
+        const output = `./../client/assets/molecules/${i}.svg`;
+
+        request(url, function cb(err, res, body) {
+            if (err) reject(err);
+
+            // write file
+            fs.writeFile(`./molecules/Structure2D_CID_${i}.sdf`, body, function written(err) {
+                if (err) reject(err);
+            });
+
+            // write svg
+            renderer.renderSdfToSvg(body, SVG_OPTS, function(err, svg) {
+                if (err) reject(err);
+                fs.writeFile(output, svg, function written(err) {
+                    if (err) reject(err);
+                    resolve();
+                });
+            });
+        });
+    });
+}
+
+async function loop() {
+    for (var i = 10000; i >= 0; i--) {
+        try {
+            await fetch(i);
+            console.log('finished record', i);
+        } catch (e) {
+            console.error(e);
+        }
+    }
+}
+
+loop();

ops/molecules.js

@@ -0,0 +1,18 @@
+const renderer = require('sdftosvg');
+const uuidv4 = require('uuid/v4');
+const fs = require('fs');
+
+function convert(f) {
+    const uuid = uuidv4();
+    const input = `./molecules/${f}`;
+    const output = `./../client/assets/molecules/${uuid}.svg`;
+    fs.readFile(input, 'utf8', (err, sdf) => {
+        renderer.renderSdfToSvg(sdf, {}, function(err, svg) {
+            if (err) console.error(input, err);
+            fs.writeFile(output, svg, 'utf8', err => {
+                if (err) console.error(err);
+            });
+        });
+    });
+}
+

ops/package.json

@@ -12,6 +12,9 @@
   "license": "UNLICENSED",
   "dependencies": {
     "knex": "^0.15.2",
-    "pg": "^7.4.3"
+    "pg": "^7.4.3",
+    "request": "^2.88.0",
+    "sdftosvg": "0.0.4",
+    "uuid": "^3.3.2"
   }
 }