Force cubic geometry by default

pdbfixer/html/addHydrogens.html

@@ -26,10 +26,18 @@ function validateForm() {
 function applyPaddingToWaterBox(padding) {
 function applyPaddingToWaterBox(padding) {
     padding = parseFloat(padding);
     padding = parseFloat(padding);
     if(!padding || padding<0) padding = 0;
     if(!padding || padding<0) padding = 0;
-    for (var i = pbcxyz.length; i--;) {
-        pbcxyz[i].value = Math.ceil((padding+molxyz[i])*1000) / 1000;
+    if (document.getElementById('cubicPaddingCheckBox').checked){
+        var maxAxis = Math.max.apply(Math, molxyz);
+        for (var i = pbcxyz.length; i--;) {
+            pbcxyz[i].value = Math.ceil((padding+maxAxis)*1000) / 1000;
+        }
+    }
+    else {
+        for (var i = pbcxyz.length; i--;) {
+            pbcxyz[i].value = Math.ceil((padding+molxyz[i])*1000) / 1000;
+        }
     }
     }
-}   
+}    
 </script>
 </script>
 <form id="mainform" method="post" action="/">
 <form id="mainform" method="post" action="/">
 <h1>Delete Heterogens</h1>
 <h1>Delete Heterogens</h1>
@@ -51,12 +59,15 @@ Add a water box surrounding the model?
 <div id="waterInputs" style="margin-left:50px">
 <div id="waterInputs" style="margin-left:50px">
     <table style="text-align:right">
     <table style="text-align:right">
         <tr>
         <tr>
-        <td>Box dimensions (in nm):</td>
+        <td>Type box dimensions (in nm):</td>
         <td><input type="text" id="boxxfield" name="boxx" size="8"></td>
         <td><input type="text" id="boxxfield" name="boxx" size="8"></td>
         <td><input type="text" id="boxyfield" name="boxy" size="8"></td>
         <td><input type="text" id="boxyfield" name="boxy" size="8"></td>
         <td><input type="text" id="boxzfield" name="boxz" size="8"></td>
         <td><input type="text" id="boxzfield" name="boxz" size="8"></td>
-        <td>Padding:</td>
+        </tr>
+        <tr>
+        <td>... or set them from padding:</td>
         <td><input type="text" id="xyzpadding" name="xyzpad" size="8" oninput="applyPaddingToWaterBox(this.value)"></td>
         <td><input type="text" id="xyzpadding" name="xyzpad" size="8" oninput="applyPaddingToWaterBox(this.value)"></td>
+        <td colspan="2"><input type="checkbox" id="cubicPaddingCheckBox" name="cubicPaddingCheckBox" checked>Force cubic geometry <span title="All sides are equal to the biggest dimension plus padding" style="border-bottom: 1px dotted black; cursor: help">?</span></td>
         </tr>
         </tr>
         %s
         %s
     </table>
     </table>
@@ -75,7 +86,7 @@ Add a water box surrounding the model?
 <script>
 <script>
 setCurrentStep(6);
 setCurrentStep(6);
 enableControls(document.getElementById('waterInputs'), false);
 enableControls(document.getElementById('waterInputs'), false);
-var molxyz = [].slice.call(document.getElementById('waterInputs').getElementsByTagName('tr')[1].getElementsByTagName('td')).splice(1,3).map(function(td){ return parseFloat(td.textContent)});
+var molxyz = [].slice.call(document.getElementById('boxContainingAllAtoms').getElementsByTagName('td')).splice(1,3).map(function(td){ return parseFloat(td.textContent)});
 var pbcxyz = [document.getElementById('boxxfield'), document.getElementById('boxyfield'), document.getElementById('boxzfield')];
 var pbcxyz = [document.getElementById('boxxfield'), document.getElementById('boxyfield'), document.getElementById('boxzfield')];
 </script>
 </script>
 </body>
 </body>

pdbfixer/ui.py

@@ -219,7 +219,7 @@ def displayAddHydrogensPage():
     if fixer.topology.getUnitCellDimensions() is not None:
     if fixer.topology.getUnitCellDimensions() is not None:
         dimensions = "<tr><td>Crystallographic unit cell:</td><td>%.3f</td><td>%.3f</td><td>%.3f</td></tr>" % fixer.topology.getUnitCellDimensions().value_in_unit(unit.nanometer)
         dimensions = "<tr><td>Crystallographic unit cell:</td><td>%.3f</td><td>%.3f</td><td>%.3f</td></tr>" % fixer.topology.getUnitCellDimensions().value_in_unit(unit.nanometer)
     sizeRange = tuple(max((pos[i] for pos in fixer.positions))-min((pos[i] for pos in fixer.positions)) for i in range(3))
     sizeRange = tuple(max((pos[i] for pos in fixer.positions))-min((pos[i] for pos in fixer.positions)) for i in range(3))
-    dimensions += "<tr><td>Box containing all atoms:</td><td>%.3f</td><td>%.3f</td><td>%.3f</td></tr>" % tuple(x.value_in_unit(unit.nanometer) for x in sizeRange)
+    dimensions += "<tr id='boxContainingAllAtoms'><td>Box containing all atoms:</td><td>%.3f</td><td>%.3f</td><td>%.3f</td></tr>" % tuple(x.value_in_unit(unit.nanometer) for x in sizeRange)
     uiserver.setContent(header+loadHtmlFile("addHydrogens.html") % dimensions)
     uiserver.setContent(header+loadHtmlFile("addHydrogens.html") % dimensions)
 
 
 def displaySaveFilePage():
 def displaySaveFilePage():