def test_hydrogen_bonds(self):
# Test `hydrogen_bonds` function
sel = Selection('noh')
result = [
HydrogenBond(Atom(18), Atom(19), Atom(9)),
HydrogenBond(Atom(9), Atom(11), Atom(6)),
HydrogenBond(Atom(6), Atom(7), Atom(15))
]
self.assertEqual(list(hydrogen_bonds(sel)), result)
self.assertEqual(list(hydrogen_bonds(sel, sel)), result)
result = [
HydrogenBond(Atom(18), Atom(19), Atom(9)),
HydrogenBond(Atom(9), Atom(11), Atom(6)),
HydrogenBond(Atom(6), Atom(7), Atom(9)),
HydrogenBond(Atom(6), Atom(7), Atom(15))
]
self.assertEqual(list(hydrogen_bonds(sel, angle=75)), result)
self.assertEqual(list(hydrogen_bonds(sel, angle=180)), [])
self.assertEqual(list(hydrogen_bonds(sel, distance=2)), [])
# If the selections do not share same atoms, check the hydrogen bonds are returned only in correct direction
sel1 = Selection('index 6')
sel2 = Selection('index 9')
self.assertEqual(list(hydrogen_bonds(sel1, sel2, angle=75)),
[HydrogenBond(Atom(6), Atom(7), Atom(9))])
def test_properties(self):
# Test basic properties
VMD.molecule.load('psf', data('water.psf'), 'pdb', data('water.pdb'))
sel = Selection('resid 1 to 3')
# Test getters
self.assertEqual(sel.selection, 'resid 1 to 3')
# Test setters
with self.assertRaises(AttributeError):
sel.selection = 'none'
def test_selection_updates(self):
# Test selection updates if frame is changed
molid = VMD.molecule.load('psf', data('water.psf'), 'pdb',
data('water.pdb'))
VMD.molecule.read(molid, 'dcd', data('water.1.dcd'), waitfor=-1)
mol = Molecule(molid)
# Create selection linked to the molecule frame
sel = Selection('x < -1.4')
self.assertEqual(list(sel), [Atom(9), Atom(18), Atom(19), Atom(20)])
# Change the molecule frame, the selection should follow
mol.frame = 0
self.assertEqual(list(sel), [
Atom(0),
Atom(1),
Atom(9),
Atom(10),
Atom(18),
Atom(19),
Atom(20)
])
mol.frame = 4
self.assertEqual(
list(sel),
[Atom(0), Atom(1),
Atom(9), Atom(18),
Atom(19), Atom(20)])
# Define the selection's frame
result = [
Atom(0, frame=9),
Atom(1, frame=9),
Atom(9, frame=9),
Atom(18, frame=9),
Atom(19, frame=9),
Atom(20, frame=9)
]
sel.frame = 9
self.assertEqual(list(sel), result)
# Change the molecule frame, the selection keeps its frame
mol.frame = 11
self.assertEqual(list(sel), result)
# Set the selection's frame back to the molecule's frame
sel.frame = NOW
self.assertEqual(list(sel), [Atom(9), Atom(18), Atom(19), Atom(20)])
def test_rmsd_collector(self):
# Test RMSD collector
ref = Molecule.create()
ref.load(data('water.psf'))
ref.load(data('water.pdb'))
dset = DataSet()
dset.add_collector(RMSDCollector('all', Selection('all', ref)))
dset.add_collector(
RMSDCollector('all and name OH2',
Selection('all and name OH2', ref)))
dset.add_collector(
RMSDCollector('all and noh',
Selection('all and noh', ref),
name='noh'))
analyzer = Analyzer(self.mol, [data('water.1.dcd')])
analyzer.add_dataset(dset)
analyzer.analyze()
# Write data to check result
buf = StringIO()
dset.write(buf)
# Check the result
self.assertEqual(buf.getvalue(), open(data('rmsd.dat')).read())
def test_contacts(self):
# Test `contacts` method
VMD.molecule.load('psf', data('water.psf'), 'pdb', data('water.pdb'))
sel1 = Selection('resid 1 to 3 and noh')
sel2 = Selection('hydrogen')
self.assertEqual(list(sel1.contacts(sel2, 1.0)), [])
self.assertEqual(list(sel1.contacts(sel2, 2.0)), [(Atom(6), Atom(11))])
self.assertEqual(list(sel2.contacts(sel1, 2.0)), [(Atom(11), Atom(6))])
def test_center(self):
# Test `center` function.
sel = Selection('all')
# Center of selection
self.assertAlmostEqualSeqs(list(center(sel)),
[-0.0001906, 0.0004762, -0.0001429])
res = Residue(0)
# Center of residue
self.assertAlmostEqualSeqs(list(center(res)),
[-1.3403333, 2.1406667, 0.967])
atom = Atom(0)
# Center of atom - atom coordinates
self.assertAlmostEqualSeqs(list(center(atom)), [-1.493, 1.9, 1.28])
# Center of atom iterables
# The manuall computation seems to differ a bit from the `atomsel.center`
self.assertAlmostEqualSeqs(list(center(iter(sel))),
[-0.0001905, 0.0004762, -0.0001429])
self.assertAlmostEqualSeqs(list(center((Atom(i) for i in xrange(10)))),
[-0.146, 0.3756, 0.3972])
def _get_selection(self):
return Selection(
_molrep.get_selection(self._molecule.molid, self.repindex),
self._molecule)
import VMD
from pyvmd import measure
from pyvmd.atoms import Selection
from pyvmd.molecules import Molecule, FORMAT_PDB, FORMAT_PSF
TEMPLATE_PDB = '../structures/3j5p.pdb'
TMP_DIR = tempfile.mkdtemp(prefix='vmd_')
TOPOLOGY = '/usr/lib/vmd/plugins/noarch/tcl/readcharmmtop1.1/top_all27_prot_lipid_na.inp'
# Load template
template = Molecule.create()
template.load(TEMPLATE_PDB)
# Center the template
center = measure.center(Selection('all', template))
Selection('all', template).atomsel.moveby((-center[0], -center[1], -center[2]))
# Rotate the template, so model takes less space
VMD.evaltcl('[atomselect %d all] move [transaxis z -35]' % template.molid)
# Save individual chains
for chain in 'ABCD':
print "Saving monomer %s" % chain
Selection('chain {} and resid 393 to 502'.format(chain), template).atomsel.write(FORMAT_PDB, '{}/{}1.pdb'.format(TMP_DIR, chain))
Selection('chain {} and resid 508 to 719'.format(chain), template).atomsel.write(FORMAT_PDB, '{}/{}2.pdb'.format(TMP_DIR, chain))
# Load psfgen and topology
VMD.evaltcl("package require psfgen")
VMD.evaltcl("topology %s" % TOPOLOGY)
# Aliasing
VMD.evaltcl("pdbalias residue HIS HSE")
from pyvmd.atoms import Selection
from pyvmd.molecules import Molecule, FORMAT_PDB
PSF = 'initial.psf'
PDB = '00_minimize/00_minimize.coor'
# Lipid tail simulation constraint
LIPID_TAILS_PDB = 'tails_only.pdb'
# Protein fixed simulation constraint
PROTEIN_PDB = 'protein.pdb'
# Protein CA constraint
BACKBONE_CA_PDB = 'backbone_ca.pdb'
model = Molecule.create()
model.load(PSF)
model.load(PDB, FORMAT_PDB)
model_sel = Selection('all', model)
model_sel.atomsel.set('beta', 0)
# Lipid constraints
# Fix all and release only the lipid tails
model_sel.atomsel.set('occupancy', 1)
Selection('lipid and not name N "C1[1-5]" "H[1-5]\d" P1 "O."', model).atomsel.set('occupancy', 0)
model_sel.atomsel.write(FORMAT_PDB, LIPID_TAILS_PDB)
# Protein constraints
model_sel.atomsel.set('occupancy', 0)
Selection('protein and noh', model).atomsel.set('occupancy', 1)
model_sel.atomsel.write(FORMAT_PDB, PROTEIN_PDB)
# Protein CA constraints
model_sel.atomsel.set('occupancy', 0)