def test_getUnmatchedResidues(self):
"""Test retrieval of list of residues for which no templates are available."""
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
# Create a ForceField object.
forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
# Get list of unmatched residues.
unmatched_residues = forcefield.getUnmatchedResidues(pdb.topology)
# Check results.
self.assertEqual(len(unmatched_residues), 1)
self.assertEqual(unmatched_residues[0].name, 'TMP')
self.assertEqual(unmatched_residues[0].id, '163')
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'ala_ala_ala.pdb'))
# Create a ForceField object.
forcefield = ForceField('tip3p.xml')
# Get list of unmatched residues.
unmatched_residues = forcefield.getUnmatchedResidues(pdb.topology)
# Check results.
self.assertEqual(len(unmatched_residues), 3)
self.assertEqual(unmatched_residues[0].name, 'ALA')
self.assertEqual(unmatched_residues[0].chain.id, 'X')
self.assertEqual(unmatched_residues[0].id, '1')
def test_getUnmatchedResidues(self):
"""Test retrieval of list of residues for which no templates are available."""
# Load the PDB file.
pdb = PDBFile(
os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
# Create a ForceField object.
forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
# Get list of unmatched residues.
unmatched_residues = forcefield.getUnmatchedResidues(pdb.topology)
# Check results.
self.assertEqual(len(unmatched_residues), 1)
self.assertEqual(unmatched_residues[0].name, 'TMP')
self.assertEqual(unmatched_residues[0].id, '163')
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'ala_ala_ala.pdb'))
# Create a ForceField object.
forcefield = ForceField('tip3p.xml')
# Get list of unmatched residues.
unmatched_residues = forcefield.getUnmatchedResidues(pdb.topology)
# Check results.
self.assertEqual(len(unmatched_residues), 3)
self.assertEqual(unmatched_residues[0].name, 'ALA')
self.assertEqual(unmatched_residues[0].chain.id, 'X')
self.assertEqual(unmatched_residues[0].id, '1')
def test_ggenerateTemplatesForUnmatchedResidues(self):
"""Test generation of blank forcefield residue templates for unmatched residues."""
#
# Test where we generate parameters for only a ligand.
#
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'nacl-water.pdb'))
# Create a ForceField object.
forcefield = ForceField('tip3p.xml')
# Get list of unmatched residues.
unmatched_residues = forcefield.getUnmatchedResidues(pdb.topology)
[templates, residues] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
# Check results.
self.assertEqual(len(unmatched_residues), 24)
self.assertEqual(len(residues), 2)
self.assertEqual(len(templates), 2)
unique_names = set([ residue.name for residue in residues ])
self.assertTrue('HOH' not in unique_names)
self.assertTrue('NA' in unique_names)
self.assertTrue('CL' in unique_names)
template_names = set([ template.name for template in templates ])
self.assertTrue('HOH' not in template_names)
self.assertTrue('NA' in template_names)
self.assertTrue('CL' in template_names)
# Define forcefield parameters using returned templates.
# NOTE: This parameter definition file will currently only work for residues that either have
# no external bonds or external bonds to other residues parameterized by the simpleTemplateGenerator.
simple_ffxml_contents = """
<ForceField>
<AtomTypes>
<Type name="XXX" class="XXX" element="C" mass="12.0"/>
</AtomTypes>
<HarmonicBondForce>
<Bond type1="XXX" type2="XXX" length="0.1409" k="392459.2"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="XXX" type2="XXX" type3="XXX" angle="2.09439510239" k="527.184"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<Atom type="XXX" charge="0.000" sigma="0.315" epsilon="0.635"/>
</NonbondedForce>
</ForceField>"""
#
# Test the pre-geenration of missing residue template for a ligand.
#
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
# Create a ForceField object.
forcefield = ForceField('amber99sb.xml', 'tip3p.xml', StringIO(simple_ffxml_contents))
# Get list of unique unmatched residues.
[templates, residues] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
# Add residue templates to forcefield.
for template in templates:
# Replace atom types.
for atom in template.atoms:
atom.type = 'XXX'
# Register the template.
forcefield.registerResidueTemplate(template)
# Parameterize system.
system = forcefield.createSystem(pdb.topology, nonbondedMethod=NoCutoff)
def test_ggenerateTemplatesForUnmatchedResidues(self):
"""Test generation of blank forcefield residue templates for unmatched residues."""
#
# Test where we generate parameters for only a ligand.
#
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'nacl-water.pdb'))
# Create a ForceField object.
forcefield = ForceField('tip3p.xml')
# Get list of unmatched residues.
unmatched_residues = forcefield.getUnmatchedResidues(pdb.topology)
[templates, residues
] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
# Check results.
self.assertEqual(len(unmatched_residues), 24)
self.assertEqual(len(residues), 2)
self.assertEqual(len(templates), 2)
unique_names = set([residue.name for residue in residues])
self.assertTrue('HOH' not in unique_names)
self.assertTrue('NA' in unique_names)
self.assertTrue('CL' in unique_names)
template_names = set([template.name for template in templates])
self.assertTrue('HOH' not in template_names)
self.assertTrue('NA' in template_names)
self.assertTrue('CL' in template_names)
# Define forcefield parameters using returned templates.
# NOTE: This parameter definition file will currently only work for residues that either have
# no external bonds or external bonds to other residues parameterized by the simpleTemplateGenerator.
simple_ffxml_contents = """
<ForceField>
<AtomTypes>
<Type name="XXX" class="XXX" element="C" mass="12.0"/>
</AtomTypes>
<HarmonicBondForce>
<Bond type1="XXX" type2="XXX" length="0.1409" k="392459.2"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="XXX" type2="XXX" type3="XXX" angle="2.09439510239" k="527.184"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<Atom type="XXX" charge="0.000" sigma="0.315" epsilon="0.635"/>
</NonbondedForce>
</ForceField>"""
#
# Test the pre-geenration of missing residue template for a ligand.
#
# Load the PDB file.
pdb = PDBFile(
os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
# Create a ForceField object.
forcefield = ForceField('amber99sb.xml', 'tip3p.xml',
StringIO(simple_ffxml_contents))
# Get list of unique unmatched residues.
[templates, residues
] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
# Add residue templates to forcefield.
for template in templates:
# Replace atom types.
for atom in template.atoms:
atom.type = 'XXX'
# Register the template.
forcefield.registerResidueTemplate(template)
# Parameterize system.
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=NoCutoff)