Merge branch 'readXYZ'

content/dataset.html

@@ -25,6 +25,11 @@ draft: false
 <script src="/js/indexDB.js"></script>
 <script src="/js/ArrayExtensions.js"></script>
 <script src="/js/mhchemCE.js"></script>
+<link rel="stylesheet" href="/css/ChemDoodleWeb.css" type="text/css">
+<script type="text/javascript" src="/js/ChemDoodleWeb.js"></script>
+<script src="/js/Geometry.js"></script>
+<script src="/js/GeometriesLoader.js"></script>
+<script src="/js/GeometryParseMetadataExtension.js"></script>
 <script>
   function adjustSticky() {
     const height = $("nav").height()
@@ -135,6 +140,15 @@ draft: false
     })
     processingIndicator.isActive = false
     reloadCustomFiles()
+    reloadGeoms()
+  }
+  async function reloadGeoms(){
+    window.geoms = await GeometriesLoader.loadForAsync(uniq(window.defaultDats.map(d=>{
+    return {
+      set:d.set.name,
+      molecule:d.molecule
+    }
+    })))
   }
   async function reloadCustomFiles() {
     window.dats = window.defaultDats;

static/css/ChemDoodleWeb.css

@@ -0,0 +1,30 @@
+/*
+//
+// ChemDoodle Web Components 9.1.0
+//
+// https://web.chemdoodle.com
+//
+// Copyright 2009-2020 iChemLabs, LLC.  All rights reserved.
+//
+// The ChemDoodle Web Components library is licensed under version 3
+// of the GNU GENERAL PUBLIC LICENSE.
+//
+// You may redistribute it and/or modify it under the terms of the
+// GNU General Public License as published by the Free Software Foundation,
+// either version 3 of the License, or (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program.  If not, see <http://www.gnu.org/licenses/>.
+//
+// Please contact iChemLabs <https://www.ichemlabs.com/contact-us> for
+// alternate licensing options.
+//
+*/
+canvas.ChemDoodleWebComponent {
+	border: 1px solid black;
+}

static/js/ArrayExtensions.js

@@ -6,4 +6,13 @@ if (!Array.prototype.findAsync) {
       }
     }
   }
+  if (!Array.prototype.findAllIndexes) {
+    Array.prototype.findAllIndexes = function (Callback) {
+      return this.reduce(function(a, e, i) {
+        if (Callback(e))
+          a.push(i)
+        return a
+    }, [])
+    }
+  }
 }

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()
+  }
+}

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
+  }
+}

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
+    }
+  }
+}

static/js/data.js

@@ -228,6 +228,34 @@ class dataFileBase {
     //metadata RegExp (start with #; maybe somme spaces; : ; maybe somme space; datas)
     return /^#\s*([A-Za-z_]+)\s*:\s*(.*)$/;
   }
+  async getGeometryAsync(state = null) {
+    var text = await getTextFromFileUrlAsync(`/data/structures/${this.set.name.replace("#", "")}/${this.molecule.toLowerCase()}.xyz`)
+    var lines = text.split("\n")
+    var indexes = lines.findAllIndexes((line) => {
+      return line.match(/^\d+$/)
+    })
+    indexes.push(lines.length)
+    var molsstr = []
+    for (let i = 0; i < indexes.length - 1; i++) {
+      molsstr.push(lines.slice(indexes[i], indexes[i + 1]).join('\n'))
+    }
+    molsstr.filter((molstr) => {
+      var params = molstr.split("\n")[1].split(",")
+      return (state === null || params[0] === `^${state.multiplicity}${state.symetry}`) && params[1] == `${this.method.name},${this.method.basis}`
+    })
+    return molsstr.map((molstr) => {
+      var params = molstr.split("\n")[1].split(",")
+      var regex=/^\^(\d+)(.+)$/
+      var m=params[1].match(regex)
+      return {
+        name: this.molecule,
+        multiplicity:m[1],
+        symmetry:m[2],
+        method:this.geometry,
+        geometry:ChemDoodle.readXYZ(molstr)
+      }
+    })
+  }
   CopyExcitationsTypeFrom(data) {
     for (const ex of this.excitations) {
       const ex2 = data.excitations.find((e) => {