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pdbfixer
Commit 892470c1 by Peter Eastman
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Preliminary support for adding missing residues

parent f8d71ec9
Showing with 15 additions and 18 deletions
ui.py
import simtk.openmm.app as app
from simtk.openmm.app.internal.pdbstructure import PdbStructure
from pdbfixer import PDBFixer, substitutions
import uiserver
import webbrowser
......@@ -7,19 +8,17 @@ from cStringIO import StringIO
def startPageCallback(parameters, handler):
if 'pdbfile' in parameters:
global fixer
pdb = app.PDBFile(parameters['pdbfile'].value.splitlines())
pdb = PdbStructure(parameters['pdbfile'].value.splitlines())
fixer = PDBFixer(pdb)
displayConvertResiduesPage()
def convertResiduesPageCallback(parameters, handler):
global nonstandard
nonstandard = [residue for i, residue in enumerate(nonstandard) if 'convert'+str(i) in parameters]
fixer.replaceNonstandardResidues(nonstandard)
nonstandard = []
fixer.nonstandardResidues = [residue for i, residue in enumerate(fixer.nonstandardResidues) if 'convert'+str(i) in parameters]
fixer.replaceNonstandardResidues()
displayMissingAtomsPage()
def missingAtomsPageCallback(parameters, handler):
fixer.addMissingAtoms(missingAtoms, missingTerminals)
fixer.addMissingAtoms()
displayDownloadPage()
def downloadPageCallback(parameters, handler):
......@@ -50,9 +49,9 @@ PDB File: <input type="file" name="pdbfile"/>
def displayConvertResiduesPage():
uiserver.setCallback(convertResiduesPageCallback)
global nonstandard
nonstandard = fixer.findNonstandardResidues()
if len(nonstandard) == 0:
fixer.findMissingResidues()
fixer.findNonstandardResidues()
if len(fixer.nonstandardResidues) == 0:
displayMissingAtomsPage()
return
indexInChain = {}
......@@ -60,7 +59,7 @@ def displayConvertResiduesPage():
for i, residue in enumerate(chain.residues()):
indexInChain[residue] = i+1
table = ""
for i, residue in enumerate(nonstandard):
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)
uiserver.setContent("""
<html>
......@@ -82,10 +81,8 @@ This PDB file contains non-standard residues. Do you want to convert them to th
def displayMissingAtomsPage():
uiserver.setCallback(missingAtomsPageCallback)
global missingAtoms
global missingTerminals
missingAtoms, missingTerminals = fixer.findMissingAtoms()
allResidues = list(set(missingAtoms.iterkeys()).union(missingTerminals.iterkeys()))
fixer.findMissingAtoms()
allResidues = list(set(fixer.missingAtoms.iterkeys()).union(fixer.missingTerminals.iterkeys()))
allResidues.sort(key=lambda x: x.index)
if len(allResidues) == 0:
displayDownloadPage()
......@@ -97,10 +94,10 @@ def displayMissingAtomsPage():
table = ""
for residue in allResidues:
atoms = []
if residue in missingAtoms:
atoms.extend(atom.name for atom in missingAtoms[residue])
if residue in missingTerminals:
atoms.extend(atom for atom in missingTerminals[residue])
if residue in fixer.missingAtoms:
atoms.extend(atom.name for atom in fixer.missingAtoms[residue])
if residue in fixer.missingTerminals:
atoms.extend(atom for atom in fixer.missingTerminals[residue])
table += ' <tr><td>%d</td><td>%s %d</td><td>%s</td></tr>\n' % (residue.chain.index+1, residue.name, indexInChain[residue], ', '.join(atoms))
uiserver.setContent("""
<html>
......
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