Added option to delete heterogens

html/addHydrogens.html

@@ -9,9 +9,18 @@ function validateForm() {
     }
 }
 </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?
 <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">
 <p>
 <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'
 }
 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):
     """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.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):
         modeller = app.Modeller(self.topology, self.positions)
         modeller.addHydrogens(pH=pH)

ui.py

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