Displayed residue numbers match the ones in the PDB file. User can select what…

Displayed residue numbers match the ones in the PDB file.  User can select what amino acid to convert nonstandard ones to

html/convertResidues.html

-This PDB file contains non-standard residues.  Do you want to convert them to the corresponding standard residues?
+This PDB file contains non-standard residues.  Do you want to convert them to standard residues?
 <p>
 <p>
 <form method="post" action="/">
 <form method="post" action="/">
 <table border="1" id="table">
 <table border="1" id="table">

pdbfixer.py

@@ -98,7 +98,7 @@ class PDBFixer(object):
         self.topology = self.pdb.topology
         self.topology = self.pdb.topology
         self.positions = self.pdb.positions
         self.positions = self.pdb.positions
         self.centroid = unit.sum(self.positions)/len(self.positions)
         self.centroid = unit.sum(self.positions)/len(self.positions)
-        self._structureChains = list(self.structure.iter_chains())
+        self.structureChains = list(self.structure.iter_chains())
         
         
         # Load the templates.
         # Load the templates.
         
         
@@ -248,10 +248,10 @@ class PDBFixer(object):
         modeller.delete(allChains[i] for i in chainIndices)
         modeller.delete(allChains[i] for i in chainIndices)
         self.topology = modeller.topology
         self.topology = modeller.topology
         self.positions = modeller.positions
         self.positions = modeller.positions
-        self._structureChains = [self._structureChains[i] for i in range(len(self._structureChains)) if i not in chainIndices]
+        self.structureChains = [self.structureChains[i] for i in range(len(self.structureChains)) if i not in chainIndices]
     
     
     def findNonstandardResidues(self):
     def findNonstandardResidues(self):
-        self.nonstandardResidues = [r for r in self.topology.residues() if r.name in substitutions]
+        self.nonstandardResidues = [(r, substitutions[r.name]) for r in self.topology.residues() if r.name in substitutions]
     
     
     def replaceNonstandardResidues(self):
     def replaceNonstandardResidues(self):
         if len(self.nonstandardResidues) > 0:
         if len(self.nonstandardResidues) > 0:
@@ -259,9 +259,9 @@ class PDBFixer(object):
 
 
             # Find atoms that should be deleted.
             # Find atoms that should be deleted.
             
             
-            for residue in self.nonstandardResidues:
-                residue.name = substitutions[residue.name]
-                template = self.templates[residue.name]
+            for residue, replaceWith in self.nonstandardResidues:
+                residue.name = replaceWith
+                template = self.templates[replaceWith]
                 standardAtoms = set(atom.name for atom in template.topology.atoms())
                 standardAtoms = set(atom.name for atom in template.topology.atoms())
                 for atom in residue.atoms():
                 for atom in residue.atoms():
                     if atom.element in (None, hydrogen) or atom.name not in standardAtoms:
                     if atom.element in (None, hydrogen) or atom.name not in standardAtoms:
@@ -275,7 +275,7 @@ class PDBFixer(object):
             self.positions = modeller.positions
             self.positions = modeller.positions
     
     
     def findMissingResidues(self):
     def findMissingResidues(self):
-        chains = [c for c in self._structureChains if any(atom.record_name == 'ATOM' for atom in c.iter_atoms())]
+        chains = [c for c in self.structureChains if any(atom.record_name == 'ATOM' for atom in c.iter_atoms())]
         chainWithGaps = {}
         chainWithGaps = {}
         
         
         # Find the sequence of each chain, with gaps for missing residues.
         # Find the sequence of each chain, with gaps for missing residues.
@@ -309,7 +309,7 @@ class PDBFixer(object):
         # Now build the list of residues to add.
         # Now build the list of residues to add.
         
         
         self.missingResidues = {}
         self.missingResidues = {}
-        for structChain, topChain in zip(self._structureChains, self.pdb.topology.chains()):
+        for structChain, topChain in zip(self.structureChains, self.topology.chains()):
             if structChain in chainSequence:
             if structChain in chainSequence:
                 offset = chainOffset[structChain]
                 offset = chainOffset[structChain]
                 sequence = chainSequence[structChain].residues
                 sequence = chainSequence[structChain].residues

ui.py

@@ -6,6 +6,10 @@ import webbrowser
 import os.path
 import os.path
 from cStringIO import StringIO
 from cStringIO import StringIO
 
 
+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']
+
 def loadHtmlFile(name):
 def loadHtmlFile(name):
     htmlPath = os.path.join(os.path.dirname(__file__), 'html')
     htmlPath = os.path.join(os.path.dirname(__file__), 'html')
     file = os.path.join(htmlPath, name)
     file = os.path.join(htmlPath, name)
@@ -39,7 +43,9 @@ def addResiduesPageCallback(parameters, handler):
     displayMissingAtomsPage()
     displayMissingAtomsPage()
 
 
 def convertResiduesPageCallback(parameters, handler):
 def convertResiduesPageCallback(parameters, handler):
-    fixer.nonstandardResidues = [residue for i, residue in enumerate(fixer.nonstandardResidues) if 'convert'+str(i) in parameters]
+    for i in range(len(fixer.nonstandardResidues)):
+        if 'convert'+str(i) in parameters:
+            fixer.nonstandardResidues[i] = (fixer.nonstandardResidues[i][0], parameters.getfirst('residue'+str(i)))
     fixer.replaceNonstandardResidues()
     fixer.replaceNonstandardResidues()
     displayMissingAtomsPage()
     displayMissingAtomsPage()
 
 
@@ -72,9 +78,6 @@ def displayDeleteChainsPage():
         displayAddResiduesPage()
         displayAddResiduesPage()
         return
         return
     table = ""
     table = ""
-    proteinResidues = ['ALA', 'ASN', 'CYS', 'GLU', 'HIS', 'LEU', 'MET', 'PRO', 'THR', 'TYR.pdb ARG', 'ASP', 'GLN', 'GLY', 'ILE', 'LYS', 'PHE', 'SER', 'TRP', 'VAL']
-    rnaResidues = ['A', 'G', 'C', 'U']
-    dnaResidues = ['DA', 'DG', 'DC', 'DT']
     for i, chain in enumerate(fixer.topology.chains()):
     for i, chain in enumerate(fixer.topology.chains()):
         residues = list(r.name for r in chain.residues())
         residues = list(r.name for r in chain.residues())
         if any(r in proteinResidues for r in residues):
         if any(r in proteinResidues for r in residues):
@@ -97,7 +100,12 @@ def displayAddResiduesPage():
     table = ""
     table = ""
     for i, key in enumerate(sorted(fixer.missingResidues)):
     for i, key in enumerate(sorted(fixer.missingResidues)):
         residues = fixer.missingResidues[key]
         residues = fixer.missingResidues[key]
-        table += '    <tr><td>%d</td><td>%d to %d</td><td>%s</td><td><input type="checkbox" name="add%d" checked></td></tr>\n' % (key[0]+1, key[1]+1, key[1]+len(residues), ', '.join(residues), i)
+        chain = fixer.structureChains[key[0]]
+        if key[1] < len(chain.residues):
+            offset = chain.residues[key[1]].number-len(residues)-1
+        else:
+            offset = chain.residues[-1].number
+        table += '    <tr><td>%d</td><td>%d to %d</td><td>%s</td><td><input type="checkbox" name="add%d" checked></td></tr>\n' % (key[0]+1, offset+1, offset+len(residues), ', '.join(residues), i)
     uiserver.setContent(header+loadHtmlFile("addResidues.html") % table)
     uiserver.setContent(header+loadHtmlFile("addResidues.html") % table)
 
 
 def displayConvertResiduesPage():
 def displayConvertResiduesPage():
@@ -107,12 +115,19 @@ def displayConvertResiduesPage():
         displayMissingAtomsPage()
         displayMissingAtomsPage()
         return
         return
     indexInChain = {}
     indexInChain = {}
-    for chain in fixer.topology.chains():
-        for i, residue in enumerate(chain.residues()):
-            indexInChain[residue] = i+1
-    table = ""
-    for i, residue in enumerate(fixer.nonstandardResidues):
-        table += '    <tr><td>%d</td><td>%s %d</td><td>%s</td><td><input type="checkbox" name="convert%d" checked></td></tr>\n' % (residue.chain.index+1, residue.name, indexInChain[residue], substitutions[residue.name], i)
+    for structChain, topChain in zip(fixer.structureChains, fixer.topology.chains()):
+        for structResidue, topResidue in zip(structChain.iter_residues(), topChain.residues()):
+            indexInChain[topResidue] = structResidue.number
+    table = ''
+    for i in range(len(fixer.nonstandardResidues)):
+        residue, replaceWith = fixer.nonstandardResidues[i]
+        options = ''
+        for res in proteinResidues:
+            selected = ''
+            if res == replaceWith:
+                selected = ' selected'
+            options += '<option value="%s"%s>%s</option>' % (res, selected, res)
+        table += '    <tr><td>%d</td><td>%s %d</td><td><select name="residue%d">%s</select></td><td><input type="checkbox" name="convert%d" checked></td></tr>\n' % (residue.chain.index+1, residue.name, indexInChain[residue], i, options, i)
     uiserver.setContent(header+loadHtmlFile("convertResidues.html") % table)
     uiserver.setContent(header+loadHtmlFile("convertResidues.html") % table)
 
 
 def displayMissingAtomsPage():
 def displayMissingAtomsPage():
@@ -124,9 +139,9 @@ def displayMissingAtomsPage():
         displayAddHydrogensPage()
         displayAddHydrogensPage()
         return
         return
     indexInChain = {}
     indexInChain = {}
-    for chain in fixer.topology.chains():
-        for i, residue in enumerate(chain.residues()):
-            indexInChain[residue] = i+1
+    for structChain, topChain in zip(fixer.structureChains, fixer.topology.chains()):
+        for structResidue, topResidue in zip(structChain.iter_residues(), topChain.residues()):
+            indexInChain[topResidue] = structResidue.number
     table = ""
     table = ""
     for residue in allResidues:
     for residue in allResidues:
         atoms = []
         atoms = []