health start, removed chemspipy dep, UX update

README.md

@@ -1,11 +1,9 @@
-# MolCalc - Molecule Calculator
+# The Molecule Calculator (MolCAlc)
 
 Hosted at [dgu.ki.ku.dk/molcalc](http://dgu.ki.ku.dk/molcalc)
 
-
 ![Editor Screenshot](https://raw.github.com/jensengroup/molcalc/master/manual/screenshots/molcalc_editor.png)
 
-
 MolCalc is a web interface that allows anyone to build
 small molecules  and estimate molecular properties such as molecular structure,
 heats of formation and other thermodynamic properties,
@@ -25,34 +23,58 @@ MolCalc uses
 
 and the source is released under the GPL license.
 
-
 ## Installation Instructions
 
 If you want to install it on your own server
 with PHP support, of course.
 
 ### Dependency
 
-* Python 2.x
+* Python 2.7
 
 * [OpenBabel w/ Python Bindings and PNG Support](http://openbabel.org/docs/dev/Installation/install.html)
+  Make sure that the the correct libs are installed before compile open babel. See above link.
 
 * [GAMESS](http://www.msg.ameslab.gov/gamess/)
 
+* mod rewrite. MolCalc uses a .htaccess script for redirecting the web requests. Please make sure mod\_rewrite
+  is enabled. On ubuntu this is done by running the command
+
+  sudo a2enmod rewrite
+
+* A Chemspider API Token. [Sign up for a Chemspider user](http://www.chemspider.com/controls/Login/RegForm.aspx)
+  This is used for searches on common names in the editor.
+
 
 ### Installation
 
-1. Clone
+1. Clone the molcalc repo the correct folder
+
+2. copy and paste settings.default to settings
+
+3. fill in settings;
+   gamess: The path to the rungms executable
+   tmp: The path for the tmp folder (for writing tmp gamess log files)
+   chemspider: The chemspider API token.
+
+5. Run the test.php via a browser to check if everything is setup correctly.
+
+4. Done, Happy calculating
+
+
+### Changelog
+
+Changes in 1.2
 
-2. cp settings.default settings
+1. Removed Chemspider dependicies. Now only using Cactus for naming.
 
-3. fill in settings
+2. Removed OpenBabel charge script. Now using JSMOL FF for partial charges instead.
 
-4. Done
+3. Update UX with small improvements
 
 ### Credits
 
-MolCalc 1.1 is written by Jimmy Charnley Kromann based on an idea by Jan Jensen.
+MolCalc s written by Jimmy Charnley Kromann based on an idea by Jan Jensen.
 The development of MolCalc is supported by the University of Copenhagen through
 the Education at its Best Initiative (Den Gode Uddannelse).
 

application/check.php

@@ -111,16 +111,16 @@
 // Get Common name and Inchi code
 // Sometimes inchi didnt work with this search, sometimes not with smiles
 $smiles   = shell_exec('babel -ixyz coordinates.xyz -osmiles --title " "');
-$inchi    = shell_exec('babel -ixyz coordinates.xyz -oinchi --title " "');
-$inchikey = shell_exec('babel -ixyz coordinates.xyz -oinchikey --title " "');
 $smiles   = str_replace("\n",'', $smiles);
 $smiles   = preg_replace("/\s+/",'', $smiles);
+$inchi    = shell_exec('babel -ixyz coordinates.xyz -oinchi --title " "');
 $inchi    = str_replace("\n",'', $inchi);
+$inchikey = shell_exec('babel -ixyz coordinates.xyz -oinchikey --title " "');
 $inchikey = str_replace("\n",'', $inchikey);
 $inchikey = preg_replace("/\s+/",'', $inchikey);
 $name     = "";
-//$name  = shell_exec('../../tools/molecule_name.py "'.$smiles.'"'); 
 
+// TODO Check if SMILES is empty
 
 if(!strpos($smiles, "."))
 {
@@ -147,6 +147,11 @@ function get_http_response_code($url) {
     return substr($headers[0], 9, 3);
   }
 
+  // TODO Cactus name
+  // Check if the response is HTML code
+  // because catus response is a .html file
+  // when SMILE is empty
+
   if(get_http_response_code($cactus) != "404"){
     $names = file_get_contents($cactus);
     // for 'names'

application/views/editor.php

@@ -65,7 +65,7 @@
 								<!--<li class="action load"><a rel="" class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Load molecule structure</span></span><span class="text">Load</span></a></li>-->
 								<li class="action save"><a rel="" class="button"><span class="hvrHlpCnt "><span class="hvrHlp">Temporarily save state </span></span>	<span class="text">Save</span></a></li>
 								<li class="action restore"><a rel="" class="button"><span class="hvrHlpCnt "><span class="hvrHlp">Restore saved state</span></span>	<span class="text">Restore</span></a></li>
-								<li class="action minimise"><a rel="" class="button"><span class="hvrHlpCnt "><span class="hvrHlp">Minimize geometry using MMFF forcefield</span></span><span class="text">Minimize</span></a></li>
+								<li class="action minimise"><a rel="" class="button"><span class="hvrHlpCnt "><span class="hvrHlp">Minimise geometry using MMFF forcefield</span></span><span class="text">Minimise</span></a></li>
 							</ul>
 							<div class="clean"></div>
 						</div>
@@ -83,15 +83,15 @@
 						</div>
 						<div class="actions atoms">
 							<ul>
-								<li class="action atom"><a rel="H"  class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Hydrogen</span></span><span class="text">H</span></a></li>
+                <li class="action atom"><a rel="H"  class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Hydrogen</span></span><span class="text">H</span></a></li>
 								<li class="action atom"><a rel="Li" class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Lithium</span></span><span class="text">Li</span></a></li>
 								<li class="action atom"><a rel="Be" class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Beryllium</span></span><span class="text">Be</span></a></li>
-								<!--<li class="action atom"><a rel="B"  class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Boron</span></span><span class="text">B</span></a></li> --><!-- not in pm3 -->
+                <!--<li class="action atom"><a rel="B"  class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Boron</span></span><span class="text">B</span></a></li> --><!-- not in pm3 -->
 								<li class="action atom"><a rel="C"  class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Carbon</span></span><span class="text">C</span></a></li>
 								<li class="action atom"><a rel="N"  class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Nitrogen</span></span><span class="text">N</span></a></li>
 								<li class="action atom"><a rel="O"  class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Oxygen</span></span><span class="text">O</span></a></li>
 								<li class="action atom"><a rel="F"  class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Fluorine</span></span><span class="text">F</span></a></li>
-								<li class="action atom"><a rel="Ne" class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Neon</span></span><span class="text">Ne</span></a></li>
+                <li class="action atom"><a rel="Ne" class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Neon</span></span><span class="text">Ne</span></a></li>
 								<li class="action atom"><a rel="Na" class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Sodium</span></span><span class="text">Na</span></a></li>
 								<li class="action atom"><a rel="Mg" class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Magnesium</span></span><span class="text">Mg</span></a></li>
 								<li class="action atom"><a rel="Al" class="button"><span class="hvrHlpCnt"><span class="hvrHlp">Aluminium</span></span><span class="text">Al</span></a></li>

application/views/header.inc.php

@@ -78,7 +78,7 @@
 			<a href="<?php print BASEURL ?>">
 				<h1>
           <span class="sep">MolCalc</span>
-          <span class="ret">Molecule Calculator</span>
+          <span class="ret">The Molecule Calculator</span>
         </h1>
 			</a>
 		</section>

assets/molstruc/check.php

@@ -1,8 +1,8 @@
 <?php
 
-// Check if ChemSpider can find the molecule
-// and return image source,
-// otherwise return 0
+ /* Using Cactus to find chemical structure from
+  * search pattern.
+  */
 
 if(isset($_GET['search']))
 {
@@ -14,14 +14,31 @@
   die();
 }
 
-$search = str_replace("%20", " ", $search);
 
-// Search Chemspider, and get MF results
-$smiles = shell_exec('../../tools/molecule_search_mol.py "'.$search.'"');
-$smiles = str_replace("\n", '', $smiles);
+# Prepare search, if in SMILES format.
+$search = str_replace(" ", "%20", $search);
+$search = str_replace("[", "%5B", $search);
+$search = str_replace("]", "%5D", $search);
+$search = str_replace("@", "%40", $search);
+//$search = str_replace(")", "", $search);
+//$search = str_replace("(", "", $search);
+$search = str_replace("=", "%3D", $search); #double bond
+$search = str_replace("#", "%23", $search); #triple bond
 
-if($smiles == "0")
+$cactus_inchi  = "http://cactus.nci.nih.gov/chemical/structure/".$search."/iupac_name";
+$cactus_smiles = "http://cactus.nci.nih.gov/chemical/structure/".$search."/smiles";
+
+// IF 404
+function get_http_response_code($url) {
+  $headers = get_headers($url);
+  return substr($headers[0], 9, 3);
+}
+
+if(get_http_response_code($cactus_smiles) != "404")
 {
+  $smiles = file_get_contents($cactus_smiles);
+  $smiles = str_replace("\n",'',$smiles);
+}else{
   print "0";
   die();
 }

assets/molstruc/search.php

@@ -1,21 +1,35 @@
 <?php
 
-  // TODO
-  // Check also for POST information, because
-  // some search patterns are too destroted (like inchi)
+ /* Using Cactus to find chemical structure from
+  * search pattern.
+  * The use babel to generate 3D structure based in inchi
+  */
 
-  if(isset($_GET['search']))
-  {
-    $search = $_GET['search'];
-  }
-  else
-  {
-    print "0";
-    die();
-  }
+if(isset($_GET['search']))
+{
+  $search = $_GET['search'];
+}
+else
+{
+  print "0";
+  die();
+}
 
-$search = str_replace("%20", " ", $search);
-// Search for $search in webspider database
-//print shell_exec('../../tools/molecule_search.py '.$search.' | obabel -imol -oxyz -h --gen3d');
-print shell_exec('../../tools/molecule_search.py "'.$search.'" | obabel -iinchi -oxyz -h --gen3d');
+# Prepare search, if in SMILES format.
+$search = str_replace(" ", "%20", $search);
+$search = str_replace("[", "%5B", $search);
+$search = str_replace("]", "%5D", $search);
+$search = str_replace("@", "%40", $search);
+//$search = str_replace(")", "", $search);
+//$search = str_replace("(", "", $search);
+$search = str_replace("=", "%3D", $search); #double bond
+$search = str_replace("#", "%23", $search); #triple bond
+
+$cactus_inchi  = "http://cactus.nci.nih.gov/chemical/structure/".$search."/inchi";
+$cactus_smiles = "http://cactus.nci.nih.gov/chemical/structure/".$search."/smiles";
+
+$inchi = file_get_contents($cactus_inchi);
+$inchi = str_replace("\n", '', $inchi);
+
+print shell_exec("echo \"".$inchi."\" | obabel -iinchi -oxyz -h --gen3d");
 

assets/script/jquery.prompt.js

@@ -27,6 +27,14 @@ $(function()
   // this could be java applets like Jmol
 	var hideElements = $('.canvas');
 
+
+  // Center Div plugin
+  jQuery.fn.center = function () 
+  {
+    var top_margin = Math.max(($(window).height() - $(this).outerHeight() )/ 2);
+    this.css('margin-top',top_margin+'px');
+    return this;
+  }
 
 	/**
 	 * Prompt gives the user a prompt message to respond too.
@@ -35,6 +43,7 @@ $(function()
 	{
     // Define the parent block
     var stamp = new Date().getTime();
+    this.stamp = stamp;
     this.parentblock = $('<div></div>');
     this.parentblock.attr('id', stamp);
     this.parentblock.hide();
@@ -77,6 +86,7 @@ $(function()
       var btn = $('<a class="button">'+msg+'</a>');
       btn.click(action);
       this.responselist.append($('<li></li>').append(btn));
+      return btn;
     }
 
     this.addCancelBtn = function addCancelBtn(msg)
@@ -88,6 +98,11 @@ $(function()
       });
     }
 
+    this.getStamp = function getStamp()
+    {
+      return this.stamp;
+    }
+
     this.show = function show()
     {
       //if(this.responselist.find('li').size() > 0)
@@ -115,14 +130,23 @@ $(function()
       this.parentblock.html(html);
       this.parentblock.show();
 
+      box.center();
+
+      $(window).resize(function() {
+        box.center();
+      });
+
     }
 
     function hide()
     {
-      $('#'+stamp).fadeOut(100, function() 
+      $('#'+stamp).fadeOut(100, function()
       {
         hideElements.show();
       });
+
+      // Unbind window resize
+      $(window).unbind('resize');
     }
 
     this.cancel = function cancel()

assets/script/views/editor.js

@@ -98,16 +98,17 @@ $(function(){
       var askuser = new $.Prompt();
       askuser.setTitle('Load Structure');
 
-      var message = $('<div></div>');
+      var message = $('<div class="form"></div>');
 
       // Search Field
-      var field = $('<input placeholder="Search" type="text" style="width:50%;" />');
+      var field = $('<input placeholder="fx. Ethanol" type="text" />');
       message.append(field);
-      message.append('<p>Large molecules will be ignored.</p>');
+      message.append('<span><br />Large molecules will be ignored.</span>');
 
       askuser.setMessage(message);
 
-      askuser.addResponseBtn('Load', function() {
+      var load_button = askuser.addResponseBtn('Load', function()
+      {
         var state = field.attr('class');
         if (state != 'success') return false;
         var val = field.val().replace(/\s/g,"%20");
@@ -120,11 +121,17 @@ $(function(){
       askuser.show();
       field.focus();
 
+      load_button.addClass('inactive');
 
       /* AJAX Search */
       var min_length = 2; // min length before searching
       var req = null; // init ajax request
-      field.keyup(function() {
+
+      field.keyup(function()
+      {
+          load_button.removeClass('inactive');
+          load_button.addClass('inactive');
+
           var that = $(this);
           value = that.val();
           if(req != null) req.abort();
@@ -146,6 +153,7 @@ $(function(){
                     }
                     else
                     {
+                      load_button.removeClass('inactive')
                       that.addClass('success');
                     }
                 }
@@ -314,6 +322,7 @@ $(function(){
         partial_charge = atominfo[i].partialCharge;
         elem_no = atominfo[i].elemno;
 
+        mole_charges += formal_charge;
         mole_charges += partial_charge;
         core_charges += elem_no;
       }