def displayMissingAtomsPage():
uiserver.setCallback(missingAtomsPageCallback)
fixer.findMissingAtoms()
allResidues = list(
set(fixer.missingAtoms.keys()).union(fixer.missingTerminals.keys()))
allResidues.sort(key=lambda x: x.index)
if len(allResidues) == 0:
fixer.addMissingAtoms()
displayAddHydrogensPage()
return
indexInChain = {}
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 residue in allResidues:
atoms = []
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(header + loadHtmlFile("addHeavyAtoms.html") % table)
def launchUI():
global header
header = loadHtmlFile("header.html")
uiserver.beginServing()
uiserver.setCallback(controlsCallback, "/controls")
displayStartPage()
webbrowser.open('http://localhost:'+str(uiserver.server.server_address[1]))
def displayConvertResiduesPage():
uiserver.setCallback(convertResiduesPageCallback)
fixer.findNonstandardResidues()
if len(fixer.nonstandardResidues) == 0:
displayMissingAtomsPage()
return
indexInChain = {}
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 = ''
nucleotides = ['DA', 'DC', 'DG', 'DT', 'A', 'C', 'G', 'T']
for i in range(len(fixer.nonstandardResidues)):
residue, replaceWith = fixer.nonstandardResidues[i]
if replaceWith in proteinResidues:
replacements = proteinResidues
else:
replacements = nucleotides
options = ''
for res in replacements:
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)
def displayConvertResiduesPage():
uiserver.setCallback(convertResiduesPageCallback)
fixer.findNonstandardResidues()
if len(fixer.nonstandardResidues) == 0:
displayMissingAtomsPage()
return
indexInChain = {}
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 = ''
nucleotides = ['DA', 'DC', 'DG', 'DT', 'A', 'C', 'G', 'T']
for i in range(len(fixer.nonstandardResidues)):
residue, replaceWith = fixer.nonstandardResidues[i]
if replaceWith in proteinResidues:
replacements = proteinResidues
else:
replacements = nucleotides
options = ''
for res in replacements:
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)
def displayAddHydrogensPage():
uiserver.setCallback(addHydrogensPageCallback)
dimensions = ""
if fixer.topology.getUnitCellDimensions() is not None:
dimensions = "<tr><td>Crystallographic unit cell:</td><td>%.3f</td><td>%.3f</td><td>%.3f</td></tr>" % fixer.topology.getUnitCellDimensions().value_in_unit(unit.nanometer)
sizeRange = tuple(max((pos[i] for pos in fixer.positions))-min((pos[i] for pos in fixer.positions)) for i in range(3))
dimensions += "<tr><td>Box containing all atoms:</td><td>%.3f</td><td>%.3f</td><td>%.3f</td></tr>" % tuple(x.value_in_unit(unit.nanometer) for x in sizeRange)
uiserver.setContent(header+loadHtmlFile("addHydrogens.html") % dimensions)
def displayAddHydrogensPage():
uiserver.setCallback(addHydrogensPageCallback)
dimensions = ""
if fixer.topology.getUnitCellDimensions() is not None:
dimensions = "<tr><td>Crystallographic unit cell:</td><td>%.3f</td><td>%.3f</td><td>%.3f</td></tr>" % fixer.topology.getUnitCellDimensions().value_in_unit(unit.nanometer)
sizeRange = tuple(max((pos[i] for pos in fixer.positions))-min((pos[i] for pos in fixer.positions)) for i in range(3))
dimensions += "<tr><td>Box containing all atoms:</td><td>%.3f</td><td>%.3f</td><td>%.3f</td></tr>" % tuple(x.value_in_unit(unit.nanometer) for x in sizeRange)
uiserver.setContent(header+loadHtmlFile("addHydrogens.html") % dimensions)
def launchUI():
global header
header = loadHtmlFile("header.html")
uiserver.beginServing()
uiserver.setCallback(controlsCallback, "/controls")
displayStartPage()
webbrowser.open('http://localhost:' +
str(uiserver.server.server_address[1]))
def displayAddResiduesPage():
uiserver.setCallback(addResiduesPageCallback)
fixer.findMissingResidues()
if len(fixer.missingResidues) == 0:
displayConvertResiduesPage()
return
table = ""
for i, key in enumerate(sorted(fixer.missingResidues)):
residues = fixer.missingResidues[key]
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)
def displayAddResiduesPage():
uiserver.setCallback(addResiduesPageCallback)
fixer.findMissingResidues()
if len(fixer.missingResidues) == 0:
displayConvertResiduesPage()
return
table = ""
for i, key in enumerate(sorted(fixer.missingResidues)):
residues = fixer.missingResidues[key]
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)
def launchUI():
global header
header = loadHtmlFile("header.html")
uiserver.beginServing()
uiserver.setCallback(controlsCallback, "/controls")
displayStartPage()
url = 'http://localhost:'+str(uiserver.server.server_address[1])
print("PDBFixer running: %s " % url)
webbrowser.open(url)
# the uiserver is running in a background daemon thread that dies whenever
# the main thread exits. So, to keep the whole process alive, we just sleep
# here in the main thread. When Control-C is called, the main thread shuts
# down and then the uiserver exits. Without this daemon/sleep combo, the
# process cannot be killed with Control-C. Reference stack overflow link:
# http://stackoverflow.com/a/11816038/1079728
while True:
time.sleep(0.5)
def displayDeleteChainsPage():
uiserver.setCallback(deleteChainsPageCallback)
numChains = len(list(fixer.topology.chains()))
if numChains < 2:
displayAddResiduesPage()
return
table = ""
for i, chain in enumerate(fixer.topology.chains()):
residues = list(r.name for r in chain.residues())
if any(r in proteinResidues for r in residues):
content = "Protein"
elif any(r in rnaResidues for r in residues):
content = "RNA"
elif any(r in dnaResidues for r in residues):
content = "DNA"
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(header+loadHtmlFile("removeChains.html") % (numChains, table))
def displayDeleteChainsPage():
uiserver.setCallback(deleteChainsPageCallback)
numChains = len(list(fixer.topology.chains()))
if numChains < 2:
displayAddResiduesPage()
return
table = ""
for i, chain in enumerate(fixer.topology.chains()):
residues = list(r.name for r in chain.residues())
if any(r in proteinResidues for r in residues):
content = "Protein"
elif any(r in rnaResidues for r in residues):
content = "RNA"
elif any(r in dnaResidues for r in residues):
content = "DNA"
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(header+loadHtmlFile("removeChains.html") % (numChains, table))
def launchUI():
global header
header = loadHtmlFile("header.html")
uiserver.beginServing()
uiserver.setCallback(controlsCallback, "/controls")
displayStartPage()
url = 'http://localhost:' + str(uiserver.server.server_address[1])
print("PDBFixer running: %s " % url)
webbrowser.open(url)
# the uiserver is running in a background daemon thread that dies whenever
# the main thread exits. So, to keep the whole process alive, we just sleep
# here in the main thread. When Control-C is called, the main thread shuts
# down and then the uiserver exits. Without this daemon/sleep combo, the
# process cannot be killed with Control-C. Reference stack overflow link:
# http://stackoverflow.com/a/11816038/1079728
global uiIsRunning
uiIsRunning = True
while uiIsRunning:
time.sleep(0.5)
def displayMissingAtomsPage():
uiserver.setCallback(missingAtomsPageCallback)
fixer.findMissingAtoms()
allResidues = list(set(fixer.missingAtoms.keys()).union(fixer.missingTerminals.keys()))
allResidues.sort(key=lambda x: x.index)
if len(allResidues) == 0:
fixer.addMissingAtoms()
displayAddHydrogensPage()
return
indexInChain = {}
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 residue in allResidues:
atoms = []
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(header+loadHtmlFile("addHeavyAtoms.html") % table)
def displayStartPage():
uiserver.setCallback(startPageCallback)
uiserver.setContent(header+loadHtmlFile("start.html"))
def displayStartPage():
uiserver.setCallback(startPageCallback)
uiserver.setContent(header+loadHtmlFile("start.html"))
def displaySaveFilePage():
uiserver.setCallback(saveFilePageCallback)
uiserver.setContent(header+loadHtmlFile("saveFile.html"))
def displaySaveFilePage():
uiserver.setCallback(saveFilePageCallback)
uiserver.setContent(header+loadHtmlFile("saveFile.html"))