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pdbfixer
Commit 7730f38d by Peter Eastman
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Lots of enhancements and bug fixes. Very early beginnings of a UI.

parent af019e18
Showing with 197 additions and 0 deletions
ui.py 0 → 100644
import simtk.openmm.app as app
from pdbfixer import PDBFixer, substitutions
import uiserver
import webbrowser
from cStringIO import StringIO
def startPageCallback(parameters, handler):
if 'pdbfile' in parameters:
global fixer
pdb = app.PDBFile(parameters['pdbfile'].value.splitlines())
fixer = PDBFixer(pdb)
displayConvertResiduesPage()
def convertResiduesPageCallback(parameters, handler):
global nonstandard
fixer.replaceNonstandardResidues(nonstandard)
nonstandard = []
displayMissingAtomsPage()
def missingAtomsPageCallback(parameters, handler):
fixer.addMissingAtoms(missingAtoms, missingTerminals)
displayDownloadPage()
def downloadPageCallback(parameters, handler):
if 'download' in parameters:
output = StringIO()
app.PDBFile.writeFile(fixer.processedTopology, fixer.processedPositions, output)
handler.sendDownload(output.getvalue(), 'output.pdb')
else:
displayStartPage()
def displayStartPage():
uiserver.setCallback(startPageCallback)
uiserver.setContent("""
<html>
<head><title>PDBFixer</title></head>
<body>
<h1>Welcome To PDBFixer!</h1>
Select a PDB file to load. It will be analyzed for problems.
<p>
<form method="post" action="/" enctype="multipart/form-data">
PDB File: <input type="file" name="pdbfile"/>
<p>
<input type="submit" value="Analyze File"/>
</form>
</body>
</html>
""")
def displayConvertResiduesPage():
uiserver.setCallback(convertResiduesPageCallback)
global nonstandard
nonstandard = fixer.findNonstandardResidues()
if len(nonstandard) == 0:
displayMissingAtomsPage()
return
table = ""
for i, residue in enumerate(nonstandard):
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, residue.index+1, substitutions[residue.name], i)
uiserver.setContent("""
<html>
<head><title>PDB Fixer</title></head>
<body>
This PDB file contains non-standard residues. Do you want to convert them to the corresponding standard residues?
<p>
<form method="get" action="/">
<table border="1">
<tr><th>Chain</th><th>Residue</th><th>Convert To</th><th>Convert?</th></tr>
%s
</table>
<p>
<input type="submit" value="Continue"/>
</form>
</body>
<html>
""" % table)
def displayMissingAtomsPage():
uiserver.setCallback(missingAtomsPageCallback)
global missingAtoms
global missingTerminals
missingAtoms, missingTerminals = fixer.findMissingAtoms()
allResidues = list(set(missingAtoms.iterkeys()).union(missingTerminals.iterkeys()))
allResidues.sort(key=lambda x: x.index)
if len(allResidues) == 0:
displayDownloadPage()
return
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])
table += ' <tr><td>%d</td><td>%s %d</td><td>%s</td></tr>\n' % (residue.chain.index+1, residue.name, residue.index+1, ', '.join(atoms))
uiserver.setContent("""
<html>
<head><title>PDB Fixer</title></head>
<body>
The following residues are missing heavy atoms, which will be added.
<p>
<form method="get" action="/">
<table border="1">
<tr><th>Chain</th><th>Residue</th><th>Missing Atoms</th></tr>
%s
</table>
<p>
<input type="submit" value="Continue"/>
</form>
</body>
<html>
""" % table)
def displayDownloadPage():
uiserver.setCallback(downloadPageCallback)
uiserver.setContent("""
<html>
<head><title>PDB Fixer</title></head>
<body>
The fixed PDB file is ready to download.
<p>
<form method="get" action="/">
<input type="submit" name="download" value="Download"/>
<input type="submit" name="newfile" value="Process Another File"/>
</form>
</body>
<html>
""")
def launchUI():
uiserver.beginServing()
displayStartPage()
webbrowser.open('http://'+uiserver.serverAddress)
\ No newline at end of file
uiserver.py 0 → 100644
from threading import Thread
from SocketServer import ThreadingMixIn
from BaseHTTPServer import HTTPServer, BaseHTTPRequestHandler
from urlparse import parse_qs
import cgi
class _Handler(BaseHTTPRequestHandler):
def do_GET(self):
self.hasSentResponse = False
if callback is not None:
queryStart = self.path.find('?')
if queryStart > -1:
parameters = parse_qs(self.path[queryStart+1:])
else:
parameters = {}
result = callback(parameters, self)
if not self.hasSentResponse:
self.sendResponse(content)
def do_POST(self):
self.hasSentResponse = False
if callback is not None:
parameters = cgi.FieldStorage(fp=self.rfile, headers=self.headers, environ={'REQUEST_METHOD':'POST', 'CONTENT_TYPE':self.headers['Content-Type']})
callback(parameters, self)
if not self.hasSentResponse:
self.sendResponse(content)
def sendResponse(self, response):
self.hasSentResponse = True
self.send_response(200)
self.send_header("Content-type", "text/html")
self.send_header("Content-length", str(len(content)))
self.end_headers()
self.wfile.write(content)
def sendDownload(self, download, filename):
self.hasSentResponse = True
self.send_response(200)
self.send_header("Content-type", "text/plain")
self.send_header("Content-length", str(len(download)))
self.send_header("Content-Disposition", 'attachment; filename="%s"' % filename)
self.end_headers()
self.wfile.write(download)
class _ThreadingHTTPServer(ThreadingMixIn, HTTPServer):
pass
content = ""
callback = None
server = _ThreadingHTTPServer(("localhost", 8000), _Handler)
serverAddress = server.server_address[0]+':'+str(server.server_address[1])
def beginServing():
Thread(target=server.serve_forever).start()
def setContent(newContent):
global content
content = newContent
def setCallback(newCallback):
global callback
callback = newCallback
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