Added option to delete heterogens

html/addHydrogens.html

@@ -9,9 +9,18 @@ function validateForm() {
     }
     }
 }
 }
 </script>
 </script>
+<form method="post" action="/" onsubmit="return validateForm()">
+<h1>Delete Heterogens</h1>
+A heterogen is any residue other than a standard amino acid or nucleotide.  Do you want to delete heterogens?
+<p>
+<select name="heterogens">
+    <option value="all" selected>Keep all heterogens</option>
+    <option value="water">Delete heterogens except water</option>
+    <option value="none">Delete all heterogens</option>
+</select>
+<h1>Add Missing Hyrogens</h1>
 Add missing hydrogen atoms?
 Add missing hydrogen atoms?
 <p>
 <p>
-<form method="post" action="/" onsubmit="return validateForm()">
 <input type="checkbox" id="addCheckbox" name="add" checked> Add hydrogens appropriate for pH <input type="text" id="phfield" name="ph" value="7.0" size="5">
 <input type="checkbox" id="addCheckbox" name="add" checked> Add hydrogens appropriate for pH <input type="text" id="phfield" name="ph" value="7.0" size="5">
 <p>
 <p>
 <input type="submit" value="Continue"/>
 <input type="submit" value="Continue"/>

pdbfixer.py

@@ -61,8 +61,8 @@ substitutions = {
     'TPL':'TRP', 'TPO':'THR', 'TPQ':'ALA', 'TRG':'LYS', 'TRO':'TRP', 'TYB':'TYR', 'TYI':'TYR', 'TYQ':'TYR', 'TYS':'TYR', 'TYY':'TYR'
     'TPL':'TRP', 'TPO':'THR', 'TPQ':'ALA', 'TRG':'LYS', 'TRO':'TRP', 'TYB':'TYR', 'TYI':'TYR', 'TYQ':'TYR', 'TYS':'TYR', 'TYY':'TYR'
 }
 }
 proteinResidues = ['ALA', 'ASN', 'CYS', 'GLU', 'HIS', 'LEU', 'MET', 'PRO', 'THR', 'TYR', 'ARG', 'ASP', 'GLN', 'GLY', 'ILE', 'LYS', 'PHE', 'SER', 'TRP', 'VAL']
 proteinResidues = ['ALA', 'ASN', 'CYS', 'GLU', 'HIS', 'LEU', 'MET', 'PRO', 'THR', 'TYR', 'ARG', 'ASP', 'GLN', 'GLY', 'ILE', 'LYS', 'PHE', 'SER', 'TRP', 'VAL']
-rnaResidues = ['A', 'G', 'C', 'U']
-dnaResidues = ['DA', 'DG', 'DC', 'DT']
+rnaResidues = ['A', 'G', 'C', 'U', 'I']
+dnaResidues = ['DA', 'DG', 'DC', 'DT', 'DI']
 
 
 def _overlayPoints(points1, points2):
 def _overlayPoints(points1, points2):
     """Given two sets of points, determine the translation and rotation that matches them as closely as possible.
     """Given two sets of points, determine the translation and rotation that matches them as closely as possible.
@@ -434,6 +434,21 @@ class PDBFixer(object):
             self.topology = newTopology2
             self.topology = newTopology2
             self.positions = newPositions2
             self.positions = newPositions2
     
     
+    def removeHeterogens(self, keepWater):
+        keep = set(proteinResidues).union(dnaResidues).union(rnaResidues)
+        keep.add('N')
+        keep.add('UNK')
+        if keepWater:
+            keep.add('HOH')
+        toDelete = []
+        for residue in self.topology.residues():
+            if residue.name not in keep:
+                toDelete.append(residue)
+        modeller = app.Modeller(self.topology, self.positions)
+        modeller.delete(toDelete)
+        self.topology = modeller.topology
+        self.positions = modeller.positions
+    
     def addMissingHydrogens(self, pH):
     def addMissingHydrogens(self, pH):
         modeller = app.Modeller(self.topology, self.positions)
         modeller = app.Modeller(self.topology, self.positions)
         modeller.addHydrogens(pH=pH)
         modeller.addHydrogens(pH=pH)

ui.py

@@ -50,6 +50,11 @@ def missingAtomsPageCallback(parameters, handler):
     displayAddHydrogensPage()
     displayAddHydrogensPage()
 
 
 def addHydrogensPageCallback(parameters, handler):
 def addHydrogensPageCallback(parameters, handler):
+    heterogens = parameters.getfirst('heterogens')
+    if heterogens == 'none':
+        fixer.removeHeterogens(False)
+    elif heterogens == 'water':
+        fixer.removeHeterogens(True)
     if 'add' in parameters:
     if 'add' in parameters:
         pH = float(parameters.getfirst('ph'))
         pH = float(parameters.getfirst('ph'))
         fixer.addMissingHydrogens(pH)
         fixer.addMissingHydrogens(pH)