Skip to content

P
pdbfixer
Commit 3515f0da by Peter Eastman
Options

Improvements to the user interface

parent 8f391650
Showing with 173 additions and 120 deletions
README.md
pdbfixer
PDBFixer
========
PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation for simulating them. It can automatically fix the following problems:
- Add missing heavy atoms.
- Add missing hydrogen atoms.
- Build missing loops.
- Convert non-standard amino acids to their standard equivalents.
- Select a single position for atoms with multiple alternate positions listed.
- Delete unwanted chains from the model.
\ No newline at end of file
html/addHeavyAtoms.html 0 → 100644
<html>
<head><title>PDB Fixer</title></head>
<body>
The following residues are missing heavy atoms, which will be added.
<p>
<form method="post" 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>
html/addHydrogens.html 0 → 100644
<html>
<head><title>PDB Fixer</title>
<script>
function validateForm() {
if (document.getElementById("addCheckbox").checked) {
var ph = document.getElementById("phfield").value;
if (ph > 0 && ph < 14)
return true;
alert("pH must be a number between 0 and 14.")
return false;
}
}
</script>
</head>
<body>
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"/>
</form>
</body>
<html>
\ No newline at end of file
html/addResidues.html 0 → 100644
<html>
<head>
<title>PDB Fixer</title>
<script>
function setCheckboxes(selected) {
checkboxes = document.getElementById("table").getElementsByTagName("input");
for (var i = 0; i < checkboxes.length; i++)
checkboxes[i].checked = selected
}
</script>
</head>
<body>
The SEQRES records in this PDB file include residues that are missing from the atom data section. Do you want to add the missing residues?
<p>
<form method="post" action="/">
<table border="1" id="table">
<tr><th>Chain</th><th>Residue Positions</th><th>Sequence</th><th>Add?</th></tr>
%s
</table>
<input type="button" value="Select All" onclick="setCheckboxes(true);"/><input type="button" value="Select None" onclick="setCheckboxes(false);"/>
<p>
<input type="submit" value="Continue"/>
</form>
</body>
<html>
html/convertResidues.html 0 → 100644
<html>
<head>
<title>PDB Fixer</title>
<script>
function setCheckboxes(selected) {
checkboxes = document.getElementById("table").getElementsByTagName("input");
for (var i = 0; i < checkboxes.length; i++)
checkboxes[i].checked = selected
}
</script>
</head>
<body>
This PDB file contains non-standard residues. Do you want to convert them to the corresponding standard residues?
<p>
<form method="post" action="/">
<table border="1" id="table">
<tr><th>Chain</th><th>Residue</th><th>Convert To</th><th>Convert?</th></tr>
%s
</table>
<input type="button" value="Select All" onclick="setCheckboxes(true);"/><input type="button" value="Select None" onclick="setCheckboxes(false);"/>
<p>
<input type="submit" value="Continue"/>
</form>
</body>
<html>
\ No newline at end of file
html/removeChains.html 0 → 100644
<html>
<head>
<title>PDB Fixer</title>
<script>
function setCheckboxes(selected) {
checkboxes = document.getElementById("table").getElementsByTagName("input");
for (var i = 0; i < checkboxes.length; i++)
checkboxes[i].checked = selected
}
</script>
</head>
<body>
This PDB file contains %d chains. Select which ones to include.
<p>
<form method="post" action="/">
<table border="1" id="table">
<tr><th>Chain</th><th># Residues</th><th>Content</th><th>Include?</th></tr>
%s
</table>
<input type="button" value="Select All" onclick="setCheckboxes(true);"/><input type="button" value="Select None" onclick="setCheckboxes(false);"/>
<p>
<input type="submit" value="Continue"/>
</form>
</body>
<html>
\ No newline at end of file
html/saveFile.html 0 → 100644
<html>
<head><title>PDB Fixer</title></head>
<body>
The fixed PDB file is ready to save.
<p>
<form method="post" action="/">
<input type="submit" name="save" value="Save File"/>
<input type="submit" name="newfile" value="Process Another File"/>
</form>
</body>
<html>
html/start.html 0 → 100644
<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" onchange="document.getElementById('submit').disabled=false;"/>
<p>
<input type="submit" id="submit" value="Analyze File" disabled/>
</form>
</body>
</html>
ui.py
......@@ -3,8 +3,14 @@ from simtk.openmm.app.internal.pdbstructure import PdbStructure
from pdbfixer import PDBFixer, substitutions
import uiserver
import webbrowser
import os.path
from cStringIO import StringIO
def loadHtmlFile(name):
htmlPath = os.path.join(os.path.dirname(__file__), 'html')
file = os.path.join(htmlPath, name)
return open(file).read()
def startPageCallback(parameters, handler):
if 'pdbfile' in parameters:
global fixer
......@@ -38,10 +44,10 @@ def addHydrogensPageCallback(parameters, handler):
if 'add' in parameters:
pH = float(parameters.getfirst('ph'))
fixer.addMissingHydrogens(pH)
displayDownloadPage()
displaySaveFilePage()
def downloadPageCallback(parameters, handler):
if 'download' in parameters:
def saveFilePageCallback(parameters, handler):
if 'save' in parameters:
output = StringIO()
app.PDBFile.writeFile(fixer.topology, fixer.positions, output)
handler.sendDownload(output.getvalue(), 'output.pdb')
......@@ -50,21 +56,7 @@ def downloadPageCallback(parameters, handler):
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>
""")
uiserver.setContent(loadHtmlFile("start.html"))
def displayDeleteChainsPage():
uiserver.setCallback(deleteChainsPageCallback)
......@@ -87,23 +79,7 @@ def displayDeleteChainsPage():
else:
content = ', '.join(set(residues))
table += ' <tr><td>%d</td><td>%d</td><td>%s</td><td><input type="checkbox" name="include%d" checked></td></tr>\n' % (chain.index+1, len(residues), content, i)
uiserver.setContent("""
<html>
<head><title>PDB Fixer</title></head>
<body>
This PDB file contains %d chains. Select which ones to include.
<p>
<form method="post" action="/">
<table border="1">
<tr><th>Chain</th><th># Residues</th><th>Content</th><th>Include?</th></tr>
%s
</table>
<p>
<input type="submit" value="Continue"/>
</form>
</body>
<html>
""" % (numChains, table))
uiserver.setContent(loadHtmlFile("removeChains.html") % (numChains, table))
def displayAddResiduesPage():
uiserver.setCallback(addResiduesPageCallback)
......@@ -115,23 +91,7 @@ def displayAddResiduesPage():
for i, key in enumerate(sorted(fixer.missingResidues)):
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)
uiserver.setContent("""
<html>
<head><title>PDB Fixer</title></head>
<body>
The SEQRES records in this PDB file include residues that are missing from the atom data section. Do you want to add the missing residues?
<p>
<form method="post" action="/">
<table border="1">
<tr><th>Chain</th><th>Residue Positions</th><th>Sequence</th><th>Add?</th></tr>
%s
</table>
<p>
<input type="submit" value="Continue"/>
</form>
</body>
<html>
""" % table)
uiserver.setContent(loadHtmlFile("addResidues.html") % table)
def displayConvertResiduesPage():
uiserver.setCallback(convertResiduesPageCallback)
......@@ -146,23 +106,7 @@ def displayConvertResiduesPage():
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)
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="post" 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)
uiserver.setContent(loadHtmlFile("convertResidues.html") % table)
def displayMissingAtomsPage():
uiserver.setCallback(missingAtomsPageCallback)
......@@ -184,58 +128,17 @@ def displayMissingAtomsPage():
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>
<head><title>PDB Fixer</title></head>
<body>
The following residues are missing heavy atoms, which will be added.
<p>
<form method="post" 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)
uiserver.setContent(loadHtmlFile("addHeavyAtoms.html")% table)
def displayAddHydrogensPage():
uiserver.setCallback(addHydrogensPageCallback)
uiserver.setContent("""
<html>
<head><title>PDB Fixer</title></head>
<body>
Add missing hydrogen atoms?
<p>
<form method="post" action="/">
<input type="checkbox" name="add" checked> Add hydrogens appropriate for pH <input type="text" name="ph" value="7.0" size="5">
<p>
<input type="submit" value="Continue"/>
</form>
</body>
<html>
""")
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="post" action="/">
<input type="submit" name="download" value="Download"/>
<input type="submit" name="newfile" value="Process Another File"/>
</form>
</body>
<html>
""")
uiserver.setContent(loadHtmlFile("addHydrogens.html"))
def displaySaveFilePage():
uiserver.setCallback(saveFilePageCallback)
uiserver.setContent(loadHtmlFile("saveFile.html"))
def launchUI():
uiserver.beginServing()
displayStartPage()
webbrowser.open('http://'+uiserver.serverAddress)
\ No newline at end of file
webbrowser.open('http://localhost:'+str(uiserver.server.server_address[1]))
\ No newline at end of file
uiserver.py
......@@ -48,7 +48,6 @@ class _ThreadingHTTPServer(ThreadingMixIn, HTTPServer):
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()
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment