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pdbfixer
Commit edd39ec2 by Peter Eastman
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Added option to add a water box

parent 907e7708
Showing with 94 additions and 18 deletions
html/addHydrogens.html
<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;
if (document.getElementById("addHydrogensCheckbox").checked) {
var ph = document.getElementById("phfield").value
if (!(ph > 0 && ph < 14)) {
alert("pH must be a number between 0 and 14.")
return false
}
}
if (document.getElementById("addWaterCheckbox").checked) {
var xsize = document.getElementById("boxxfield").value
var ysize = document.getElementById("boxyfield").value
var zsize = document.getElementById("boxzfield").value
var strength = document.getElementById("ionicstrengthfield").value
if (!(xsize > 0 && ysize > 0 && zsize > 0)) {
alert("Box dimensions must be positive numbers.")
return false
}
if (!(strength >= 0)) {
alert("Ionic strength must be a nonnegative number.")
return false
}
}
return true
}
</script>
<form id="mainform" method="post" action="/" onsubmit="return validateForm()">
<form id="mainform" method="post" action="/">
<h1>Delete Heterogens</h1>
A heterogen is any residue other than a standard amino acid or nucleotide. Do you want to delete heterogens?
<p>
......@@ -21,12 +36,31 @@ A heterogen is any residue other than a standard amino acid or nucleotide. Do y
<h1>Add Missing Hydrogens</h1>
Add missing hydrogen atoms?
<p>
<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">
<input type="checkbox" id="addHydrogensCheckbox" name="addhydrogens" onchange="document.getElementById('phfield').disabled=!document.getElementById('addHydrogensCheckbox').checked" checked> Add hydrogens appropriate for pH <input type="text" id="phfield" name="ph" value="7.0" size="5">
<h1>Add Water</h1>
Add a water box surrounding the model?
<p>
<input type="checkbox" id="addWaterCheckbox" name="addwater" onchange="enableControls(document.getElementById('waterInputs'), document.getElementById('addWaterCheckbox').checked)"> Add water
<div id="waterInputs" style="margin-left:50px">
<table style="text-align:right">
<tr><td>Box dimensions (in nm):</td><td><input type="text" id="boxxfield" name="boxx" size="8"></td><td><input type="text" id="boxyfield" name="boxy" size="8"></td><td><input type="text" id="boxzfield" name="boxz" size="8"></td></tr>
%s
</table>
<p>
Ions will be added to neutralize the model. You can optionally add more ions based on a desired bulk ionic strength.
<p>
<table>
<tr><td style="text-align:right">Ionic strength (molar):</td><td><input type="text" id="ionicstrengthfield" name="ionicstrength" size="8" value="0.0"></td></tr>
<tr><td style="text-align:right">Positive ion:</td><td><select name="positiveion"><option value="Cs">Cs+</option><option value="K">K+</option><option value="Li">Li+</option><option value="Na" selected>Na+</option><option value="Rb">Rb+</option></select></td></tr>
<tr><td style="text-align:right">Negative ion:</td><td><select name="negativeion"><option value="Cl" selected>Cl-</option><option value="Br">Br-</option><option value="F">F-</option><option value="I">I-</option></select></td></tr>
</table>
</div>
<p>
<input type="button" value="Continue" onclick="submitWithSpinner()"/>
<input type="button" value="Continue" onclick="if (validateForm()) submitWithSpinner()"/>
</form>
<script>
setCurrentStep(6)
enableControls(document.getElementById('waterInputs'), false)
</script>
</body>
<html>
\ No newline at end of file
<html>
html/header.html
......@@ -16,6 +16,14 @@ function setCheckboxes(selected) {
for (var i = 0; i < checkboxes.length; i++)
checkboxes[i].checked = selected
}
function enableControls(container, enabled) {
tags = ["input", "select"]
for (var i = 0; i < tags.length; i++) {
controls = container.getElementsByTagName(tags[i])
for (var j = 0; j < controls.length; j++)
controls[j].disabled = !enabled
}
}
function submitWithSpinner() {
animateSpinner.animateIndex = 0
setTimeout(function() {animateSpinner();document.getElementById('overlay').style.visibility='visible';}, 1500)
......@@ -83,7 +91,7 @@ body {font-family:sans-serif}
<p id="step3">Add Residues</p>
<p id="step4">Convert Residues</p>
<p id="step5">Add Heavy Atoms</p>
<p id="step6">Add Hydrogens</p>
<p id="step6">Add Water/Hydrogens</p>
<p id="step7">Save File</p>
</span>
<p/>
\ No newline at end of file
pdbfixer.py
......@@ -36,6 +36,7 @@ import simtk.openmm.app as app
import simtk.unit as unit
from simtk.openmm.app.internal.pdbstructure import PdbStructure
from simtk.openmm.app.element import hydrogen, oxygen
from simtk.openmm.app.forcefield import NonbondedGenerator
import numpy as np
import numpy.linalg as lin
import sys
......@@ -401,7 +402,7 @@ class PDBFixer(object):
# Create a System for energy minimizing it.
res = list(newTopology.residues())
forcefield = self._createForceField(newTopology)
forcefield = self._createForceField(newTopology, False)
system = forcefield.createSystem(newTopology)
# Set any previously existing atoms to be massless, they so won't move.
......@@ -479,8 +480,21 @@ class PDBFixer(object):
self.topology = modeller.topology
self.positions = modeller.positions
def _createForceField(self, newTopology):
forcefield = app.ForceField(os.path.join(os.path.dirname(__file__), 'soft.xml'))
def addSolvent(self, boxSize, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*unit.molar):
modeller = app.Modeller(self.topology, self.positions)
forcefield = self._createForceField(self.topology, True)
modeller.addSolvent(forcefield, boxSize=boxSize, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength)
self.topology = modeller.topology
self.positions = modeller.positions
def _createForceField(self, newTopology, water):
if water:
forcefield = app.ForceField('amber10.xml', 'tip3p.xml')
nonbonded = [f for f in forcefield._forces if isinstance(f, NonbondedGenerator)][0]
radii = {'H':0.198, 'Li':0.203, 'C':0.340, 'N':0.325, 'O':0.299, 'F':0.312, 'Na':0.333, 'Mg':0.141,
'P':0.374, 'S':0.356, 'Cl':0.347, 'K':0.474, 'Br':0.396, 'Rb':0.527, 'I':0.419, 'Cs':0.605}
else:
forcefield = app.ForceField(os.path.join(os.path.dirname(__file__), 'soft.xml'))
# The Topology may contain residues for which the ForceField does not have a template.
# If so, we need to create new templates for them.
......@@ -513,6 +527,14 @@ class PDBFixer(object):
if element not in atomTypes:
atomTypes[element] = (typeName, 0.0, element)
forcefield._atomTypes[typeName] = atomTypes[element]
if water:
# Select a reasonable vdW radius for this atom type.
if element.symbol in radii:
sigma = radii[element.symbol]
else:
sigma = 0.5
nonbonded.typeMap[typeName] = (0.0, sigma, 0.0)
indexInResidue[atom.index] = len(template.atoms)
template.atoms.append(app.ForceField._TemplateAtomData(atom.name, typeName, element))
for atom in residue.atoms():
......
ui.py
import simtk.openmm.app as app
from simtk.openmm.app.internal.pdbstructure import PdbStructure
import simtk.unit as unit
from pdbfixer import PDBFixer, substitutions, proteinResidues, dnaResidues, rnaResidues
import uiserver
import webbrowser
......@@ -69,9 +70,15 @@ def addHydrogensPageCallback(parameters, handler):
fixer.removeHeterogens(False)
elif heterogens == 'water':
fixer.removeHeterogens(True)
if 'add' in parameters:
if 'addhydrogens' in parameters:
pH = float(parameters.getfirst('ph'))
fixer.addMissingHydrogens(pH)
if 'addwater' in parameters:
boxSize = (float(parameters.getfirst('boxx')), float(parameters.getfirst('boxy')), float(parameters.getfirst('boxz')))*unit.nanometer
ionicStrength = float(parameters.getfirst('ionicstrength'))*unit.molar
positiveIon = parameters.getfirst('positiveion')+'+'
negativeIon = parameters.getfirst('negativeion')+'-'
fixer.addSolvent(boxSize, positiveIon, negativeIon, ionicStrength)
displaySaveFilePage()
def saveFilePageCallback(parameters, handler):
......@@ -171,11 +178,16 @@ 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(header+loadHtmlFile("addHeavyAtoms.html")% table)
uiserver.setContent(header+loadHtmlFile("addHeavyAtoms.html") % table)
def displayAddHydrogensPage():
uiserver.setCallback(addHydrogensPageCallback)
uiserver.setContent(header+loadHtmlFile("addHydrogens.html"))
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 displaySaveFilePage():
uiserver.setCallback(saveFilePageCallback)
......
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