Support for additional solvation boxes

pdbfixer/html/addHydrogens.html

@@ -8,14 +8,21 @@ function validateForm() {
         }
         }
     }
     }
     if (document.getElementById("addWaterCheckbox").checked) {
     if (document.getElementById("addWaterCheckbox").checked) {
+        var custombox = document.getElementById("customBoxRadio").checked
         var xsize = document.getElementById("boxxfield").value
         var xsize = document.getElementById("boxxfield").value
         var ysize = document.getElementById("boxyfield").value
         var ysize = document.getElementById("boxyfield").value
         var zsize = document.getElementById("boxzfield").value
         var zsize = document.getElementById("boxzfield").value
-        var strength = document.getElementById("ionicstrengthfield").value
-        if (!(xsize > 0 && ysize > 0 && zsize > 0)) {
+        if (custombox && !(xsize > 0 && ysize > 0 && zsize > 0)) {
             alert("Box dimensions must be positive numbers.")
             alert("Box dimensions must be positive numbers.")
             return false
             return false
         }
         }
+        var geombox = document.getElementById("geometricBoxRadio").checked
+        var padsize = document.getElementById("geomPadding").value
+        if (geombox && !(padsize > 0)) {
+            alert("Box padding must be a positive number.")
+            return false
+        }
+        var strength = document.getElementById("ionicstrengthfield").value
         if (!(strength >= 0)) {
         if (!(strength >= 0)) {
             alert("Ionic strength must be a nonnegative number.")
             alert("Ionic strength must be a nonnegative number.")
             return false
             return false
@@ -59,15 +66,28 @@ 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>Type box dimensions (in nm):</td>
+        <td style="text-align:left"><input id="customBoxRadio" type="radio" name="boxType" value="custom" checked>Custom box dimensions (in nm):</td>
+        <div id="customBoxDimensions">
         <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>
+        </div>
         </tr>
         </tr>
+
         <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 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>
+        <td style="text-align:left"><input id="geometricBoxRadio" type="radio" name="boxType" value="geometry">Geometry with padding (in nm):</td>
+        <div id="geometricBoxDimensions">
+        <td><input type="text" id="geomPadding" name="geomPadding" size="8">
+        </td>
+        <td colspan="2">
+            <select id="geometryDropdown" name="geometryDropdown">
+                <option value="cube" selected="selected">Cube</option>
+                <option value="truncatedOctahedron">Truncated octahedron</option>
+                <option value="rhombicDodecahedron">Rhombic dodecahedron</option>
+            </select>
+            <span title="The specified padding will be applied on the largest molecular axis, maintaining selected geometry" style="border-bottom: 1px dotted black; cursor: help">?</span>
+        </div>
+        </td>
         </tr>
         </tr>
         %s
         %s
     </table>
     </table>
@@ -87,7 +107,11 @@ Add a water box surrounding the model?
 setCurrentStep(6);
 setCurrentStep(6);
 enableControls(document.getElementById('waterInputs'), false);
 enableControls(document.getElementById('waterInputs'), false);
 var molxyz = [].slice.call(document.getElementById('boxContainingAllAtoms').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 hiddenInput = document.createElement("input");
+hiddenInput.setAttribute("type", "hidden");
+hiddenInput.setAttribute("name", "maxMolecularAxis");
+hiddenInput.setAttribute("value", Math.max.apply(Math, molxyz));
+document.getElementById("mainform").appendChild(hiddenInput);
 </script>
 </script>
 </body>
 </body>
 <html>
 <html>

pdbfixer/pdbfixer.py

@@ -1021,15 +1021,17 @@ class PDBFixer(object):
         self.topology = modeller.topology
         self.topology = modeller.topology
         self.positions = modeller.positions
         self.positions = modeller.positions
 
 
-    def addSolvent(self, boxSize=None, padding=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*unit.molar):
+    def addSolvent(self, boxSize=None, padding=None, boxVectors=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*unit.molar):
         """Add a solvent box surrounding the structure.
         """Add a solvent box surrounding the structure.
 
 
         Parameters
         Parameters
         ----------
         ----------
         boxSize : simtk.openmm.Vec3, optional, default=None
         boxSize : simtk.openmm.Vec3, optional, default=None
-            The size of the box to fill with water.  If specified, padding must not be specified.
+            The size of the box to fill with water.  If specified, padding and boxVectors must not be specified.
         padding : simtk.unit.Quantity compatible with nanometers, optional, default=None
         padding : simtk.unit.Quantity compatible with nanometers, optional, default=None
-            Padding around macromolecule for filling box with water.  If specified, boxSize must not be specified.
+            Padding around macromolecule for filling box with water.  If specified, boxSize and boxVectors must not be specified.
+        boxVectors : 3-tuple of simtk.openmm.Vec3, optional, default=None
+            Three vectors specifying the geometry of the box. If specified, padding and boxSize must not be specified.
         positiveIon : str, optional, default='Na+'
         positiveIon : str, optional, default='Na+'
             The type of positive ion to add.  Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'.
             The type of positive ion to add.  Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'.
         negativeIon : str, optional, default='Cl-'
         negativeIon : str, optional, default='Cl-'
@@ -1053,7 +1055,7 @@ class PDBFixer(object):
 
 
         modeller = app.Modeller(self.topology, self.positions)
         modeller = app.Modeller(self.topology, self.positions)
         forcefield = self._createForceField(self.topology, True)
         forcefield = self._createForceField(self.topology, True)
-        modeller.addSolvent(forcefield, padding=padding, boxSize=boxSize, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength)
+        modeller.addSolvent(forcefield, padding=padding, boxSize=boxSize, boxVectors=boxVectors, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength)
         chains = list(modeller.topology.chains())
         chains = list(modeller.topology.chains())
         if len(chains) == 1:
         if len(chains) == 1:
             chains[0].id = 'A'
             chains[0].id = 'A'

pdbfixer/ui.py

@@ -3,9 +3,11 @@ from __future__ import absolute_import
 import webbrowser
 import webbrowser
 import os.path
 import os.path
 import time
 import time
+from math import sqrt
 
 
 import simtk.openmm.app as app
 import simtk.openmm.app as app
 import simtk.unit as unit
 import simtk.unit as unit
+from simtk.openmm.vec3 import Vec3
 
 
 from .pdbfixer import PDBFixer, proteinResidues, dnaResidues, rnaResidues, _guessFileFormat
 from .pdbfixer import PDBFixer, proteinResidues, dnaResidues, rnaResidues, _guessFileFormat
 from . import uiserver
 from . import uiserver
@@ -111,11 +113,25 @@ def addHydrogensPageCallback(parameters, handler):
         pH = float(parameters.getfirst('ph'))
         pH = float(parameters.getfirst('ph'))
         fixer.addMissingHydrogens(pH)
         fixer.addMissingHydrogens(pH)
     if 'addwater' in parameters:
     if 'addwater' in parameters:
-        boxSize = (float(parameters.getfirst('boxx')), float(parameters.getfirst('boxy')), float(parameters.getfirst('boxz')))*unit.nanometer
+        padding, boxSize, boxVectors = None, None, None
+        if parameters.getfirst('boxType') == 'geometry':
+            geompadding = float(parameters.getfirst('geomPadding')) * unit.nanometer
+            geometry = parameters.getfirst('geometryDropdown')
+            base_size = float(parameters.getfirst('maxMolecularAxis')) * unit.nanometer
+            if geometry == 'cube':
+                padding = geompadding
+            elif geometry == 'truncatedOctahedron':
+                vectors = Vec3(1,0,0), Vec3(1/3,2*sqrt(2)/3,0), Vec3(-1/3,1/3,sqrt(6)/3)
+                boxVectors = [(base_size+geompadding)*v for v in vectors]
+            elif geometry == 'rhombicDodecahedron':
+                vectors = Vec3(1,0,0), Vec3(0,1,0), Vec3(0.5,0.5,sqrt(2)/2)
+                boxVectors = [(base_size+geompadding)*v for v in vectors]
+        else:
+            boxSize = (float(parameters.getfirst('boxx')), float(parameters.getfirst('boxy')), float(parameters.getfirst('boxz')))*unit.nanometer
         ionicStrength = float(parameters.getfirst('ionicstrength'))*unit.molar
         ionicStrength = float(parameters.getfirst('ionicstrength'))*unit.molar
         positiveIon = parameters.getfirst('positiveion')+'+'
         positiveIon = parameters.getfirst('positiveion')+'+'
         negativeIon = parameters.getfirst('negativeion')+'-'
         negativeIon = parameters.getfirst('negativeion')+'-'
-        fixer.addSolvent(boxSize, None, positiveIon, negativeIon, ionicStrength)
+        fixer.addSolvent(boxSize, padding, boxVectors, positiveIon, negativeIon, ionicStrength)
     displaySaveFilePage()
     displaySaveFilePage()
 
 
 def saveFilePageCallback(parameters, handler):
 def saveFilePageCallback(parameters, handler):
@@ -123,7 +139,10 @@ def saveFilePageCallback(parameters, handler):
         output = StringIO()
         output = StringIO()
         if fixer.source is not None:
         if fixer.source is not None:
             output.write("REMARK   1 PDBFIXER FROM: %s\n" % fixer.source)
             output.write("REMARK   1 PDBFIXER FROM: %s\n" % fixer.source)
-        app.PDBFile.writeFile(fixer.topology, fixer.positions, output, True)
+        try:
+            app.PDBFile.writeFile(fixer.topology, fixer.positions, output, True)
+        except AssertionError:
+            print
         handler.sendDownload(output.getvalue(), 'output.pdb')
         handler.sendDownload(output.getvalue(), 'output.pdb')
     else:
     else:
         displayStartPage()
         displayStartPage()