From 85ab5b996882db92cfa47a5a77ac01c18bb72d15 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= <mveril@irsamc.ups-tlse.fr>
Date: Mon, 28 Sep 2020 15:39:46 +0200
Subject: [PATCH] Change geometries handling

---
 static/js/GeometriesLoader.js               | 16 ++++++++++
 static/js/Geometry.js                       | 35 +++++++++++++++++++++
 static/js/GeometryParseMetadataExtension.js | 20 ++++++++++++
 3 files changed, 71 insertions(+)
 create mode 100644 static/js/GeometriesLoader.js
 create mode 100644 static/js/Geometry.js
 create mode 100644 static/js/GeometryParseMetadataExtension.js

diff --git a/static/js/GeometriesLoader.js b/static/js/GeometriesLoader.js
new file mode 100644
index 00000000..2df41181
--- /dev/null
+++ b/static/js/GeometriesLoader.js
@@ -0,0 +1,16 @@
+class GeometriesLoader{
+  static async loadForAsync(array){
+    var xyzs=[]
+    for (const item of array) {
+      const mymol=mhchemCE.extract(item.molecule).toLowerCase().replace(" ","_")
+      const myset=item.set.split("#").join("")
+      try {
+        const mol=await Geometry.loadXYZAsync(`/${myset}/${mymol}.xyz`)
+        xyzs.push(mol)  
+      } catch (error) {
+        console.error("Geometry not found",item)
+      } 
+    }
+    return xyzs.flat()
+  }
+}
\ No newline at end of file
diff --git a/static/js/Geometry.js b/static/js/Geometry.js
new file mode 100644
index 00000000..a872de5d
--- /dev/null
+++ b/static/js/Geometry.js
@@ -0,0 +1,35 @@
+class Geometry {
+  constructor(molecule, comment) {
+    this.molecule = molecule
+    this.comment = comment
+  }
+  static async loadXYZAsync(file) {
+    switch (trueTypeOf(file)) {
+      case String.name:
+        file = getFullDataPath("/structures/"+file)
+        var str = await getTextFromFileUrlAsync(file)
+        break;
+      case File.name:
+        var str = await getTextFromUploadedFileAsync(file)
+        break
+    }
+    var xyz = this.loadXYZString(str);
+    xyz.sourceFile = new websiteFile(file)
+    return xyz
+  }
+  static loadXYZString(text) {
+    var lines = text.split("\n")
+    var indexes = lines.findAllIndexes((line) => {
+      return line.match(/^\d+$/)
+    })
+    indexes.push(lines.length)
+    var geoms = []
+    for (let i = 0; i < indexes.length - 1; i++) {
+      const mollines = lines.slice(indexes[i], indexes[i + 1])
+      const comment = mollines[1]
+      const molecule = ChemDoodle.readXYZ(mollines.join("\n"))
+      geoms.push(new Geometry(molecule, comment))
+    }
+    return geoms
+  }
+}
\ No newline at end of file
diff --git a/static/js/GeometryParseMetadataExtension.js b/static/js/GeometryParseMetadataExtension.js
new file mode 100644
index 00000000..6856f196
--- /dev/null
+++ b/static/js/GeometryParseMetadataExtension.js
@@ -0,0 +1,20 @@
+if (!Geometry.prototype.parseMetadata) {
+  Geometry.prototype.parseMetadata = function () {
+    const Ametadata = this.comment.split(",")
+    const molecule = Ametadata[0]
+    const stateRegExp = /^\^(\d+)(.+)$/
+    const m = Ametadata[1].match(stateRegExp)
+    const mul = m[1]
+    const sym = m[2]
+    var meth = null
+    if (Ametadata.length>2) {
+      meth = new method(Ametadata[2],Ametadata[3])
+    }
+    return {
+      molecule:molecule,
+      multiplicity:mul,
+      symmetry:sym,
+      method:meth
+    }
+  }
+}
\ No newline at end of file