get files directly from pdb

boscoh · Jun 28, 2015 · 6637579 · 6637579
1 parent 59deee6
commit 6637579
Show file tree

Hide file tree

Showing 4 changed files with 31 additions and 60 deletions.
diff --git a/js/dataserver.js b/js/dataserver.js
@@ -4,15 +4,18 @@ jolecule_server = function(pdb_id) {
   return {
     pdb_id: pdb_id,
     get_protein_data: function(process_protein_data) {
-        $.get(
-            '/pdb/' + pdb_id + '.txt',
-            // 'http://www.rcsb.org/pdb/files/' + pdb_id + '.pdb', 
-            function(data) {
-                process_protein_data({
-                    'pdb_id': pdb_id,
-                    'pdb_text': data,
-                });
+        if (pdb_id.length == 4) {
+            var url = 'http://www.rcsb.org/pdb/files/' + pdb_id + '.pdb'
+        } else {
+            var url = '/pdb/' + pdb_id + '.txt'
+        }
+        var success = function(data) {
+            process_protein_data({
+                'pdb_id': pdb_id,
+                'pdb_text': data,
             });
+        }
+        $.get(url, success);
     },
     get_views: function(process_views) {
         $.getJSON('/pdb/' + pdb_id + '.views.json', process_views);

diff --git a/js/embedjolecule.js b/js/embedjolecule.js
@@ -191,38 +191,6 @@ function EmbedJolecule(params) {
     this.residue_selector.change(change_fn);
   }
 
-  this.show_help_dialog = function() {
-    var help_div = $('<div>');
-
-    var cancel_button = link_button(
-      'cancel', 'clear', 'jolecule-button', 
-      function() { help_div.remove(); });
-
-    help_div
-      .addClass('jolecule-dialog')
-      .css('width', Math.min(350, this.div.width()-40))
-      .append("<br>")
-      .append("<a href='http://jolecule.appspot.com'>JOLECULE</a> ")
-      .append("(c) 2012, <a href='http://boscoh.com'>Bosco Ho</a>")
-      .append("<br>")
-      .append("<br>")
-      .append("<ul>")
-      .append("<li>[shift]-mouse/right-mouse: zoom/rotate</li>")
-      .append("<li>click on atom: center on atom</li>")
-      .append("<li>drag on center atom: add a distance label</li>")
-      .append("<li>double-click on center atom: add atom label</li>")
-      .append("<li>[neigh]: show all neighbouring residues of center atom</li>")
-      .append("</ul>")
-      .append("<br>")
-      .append("<br>")
-      .append(cancel_button)
-      .append("<br>")
-      .append('<br>')
-    ;
-
-    stick_in_center(this.div, help_div, 0, 0);
-  }
-
   this.create_header_div = function() {
     var _this = this;
 

diff --git a/js/protein.js b/js/protein.js
@@ -54,8 +54,8 @@ var Protein = function() {
   aa = ['ALA', 'CYS', 'ASP', 'GLU', 'PHE', 'GLY', 'HIS',
          'ILE', 'LYS', 'LEU', 'MET', 'ASN', 'PRO', 'GLN',
          'ARG', 'SER', 'THR', 'TRP', 'VAL', 'TYR'];
-  dna = ['DA', 'DT', 'DG', 'DC'];
-  rna = ['RA', 'RT', 'RG', 'RU'];
+  dna = ['DA', 'DT', 'DG', 'DC', 'A', 'T', 'G', 'C'];
+  rna = ['RA', 'RU', 'RC', 'RG', 'A', 'T', 'G', 'C', 'U'];
   chonp = ['C', 'H', 'O', 'N', 'P'];
 
   function delete_numbers(text) {
@@ -993,25 +993,25 @@ var Scene = function(protein) {
   }
 
   this.hide_atomic_details_for_move = function() {
-    if (this.saved_show === null) {
-      if (this.is_too_much_atomic_detail()) {
-        this.saved_show = clone_dict(
-            this.current_view.show);
-        this.current_view.show.hydrogen = false; 
-        this.current_view.show.sidechain = false; 
-        this.current_view.show.water = false; 
-        this.changed = true;
-      }
-    }
+    // if (this.saved_show === null) {
+    //   if (this.is_too_much_atomic_detail()) {
+    //     this.saved_show = clone_dict(
+    //         this.current_view.show);
+    //     this.current_view.show.hydrogen = false; 
+    //     this.current_view.show.sidechain = false; 
+    //     this.current_view.show.water = false; 
+    //     this.changed = true;
+    //   }
+    // }
   }
 
   this.restore_atomic_details_after_move = function() {
-    if (this.saved_show === null) {
-      return;
-    }
-    this.current_view.show = clone_dict(this.saved_show);
-    this.saved_show = null;
-    this.changed = true;
+    // if (this.saved_show === null) {
+    //   return;
+    // }
+    // this.current_view.show = clone_dict(this.saved_show);
+    // this.saved_show = null;
+    // this.changed = true;
   }
 
   this.make_default_view = function(default_html) {

diff --git a/static/jolecule.css b/static/jolecule.css
@@ -102,8 +102,8 @@ h1, h2, h3, h4, h5, h6, h7 {
     letter-spacing: 0.3em;
     line-height: 2em;
     color: #555;
-    flex: 0 0;
-    -webkit-flex: 0 0;
+    flex: 50px 0 0;
+    -webkit-flex: 50px 0 0;
 }
 .jolecule-selected-box {
     border: 1px dotted #D66;