def phiPsi(self, conf = None):
"""
:returns: a list of the (phi, psi) backbone angles for each residue
:rtype: list of tuple of float
"""
universe = self.universe()
if universe is None:
universe = Universe.InfiniteUniverse()
angles = []
for i in range(len(self)):
r = self[i]
if i == 0:
phi = None
else:
phi = universe.dihedral(r.peptide.C, r.peptide.C_alpha,
r.peptide.N,
self[i-1].peptide.C, conf)
if i == len(self)-1:
psi = None
else:
psi = universe.dihedral(self[i+1].peptide.N,
r.peptide.C, r.peptide.C_alpha,
r.peptide.N, conf)
angles.append((phi, psi))
return angles
def __init__(self,
universe,
force_field,
subset1=None,
subset2=None,
threads=None,
mpi_communicator=None):
if not Universe.isUniverse(universe):
raise TypeError("energy evaluator defined only for universes")
self.universe = universe
self.universe_version = self.universe._version
self.ff = force_field
self.configuration = self.universe.configuration()
self.global_data = ForceFieldData()
if subset1 is not None and subset2 is None:
subset2 = subset1
terms = self.ff.evaluatorTerms(self.universe, subset1, subset2,
self.global_data)
if not isinstance(terms, type([])):
raise ValueError("evaluator term list not a list")
from MMTK_forcefield import Evaluator
if threads is None:
import MMTK.ForceFields
threads = MMTK.ForceFields.default_energy_threads
self.evaluator = Evaluator(Numeric.array(terms), threads,
mpi_communicator)
def phiPsi(self, conf = None):
"""
:returns: the values of the backbone dihedral angles phi and psi.
:rtype: tuple (float, float)
"""
universe = self.universe()
if universe is None:
universe = Universe.InfiniteUniverse()
C = None
for a in self.peptide.N.bondedTo():
if a.parent.parent != self:
C = a
break
if C is None:
phi = None
else:
phi = universe.dihedral(self.peptide.C, self.peptide.C_alpha,
self.peptide.N, C, conf)
N = None
for a in self.peptide.C.bondedTo():
if a.parent.parent != self:
N = a
break
if N is None:
psi = None
else:
psi = universe.dihedral(N, self.peptide.C, self.peptide.C_alpha,
self.peptide.N, conf)
return phi, psi
def createUnitCellUniverse(self):
"""
Constructs an empty universe (OrthrhombicPeriodicUniverse or
ParallelepipedicPeriodicUniverse) representing the
unit cell of the crystal. If the PDB file does not define
a unit cell at all, an InfiniteUniverse is returned.
:returns: a universe
:rtype: :class:~MMTK.Universe.Universe
"""
if self.from_fractional is None:
return Universe.InfiniteUniverse()
e1 = self.from_fractional(Vector(1., 0., 0.))
e2 = self.from_fractional(Vector(0., 1., 0.))
e3 = self.from_fractional(Vector(0., 0., 1.))
if abs(e1.normal()*Vector(1., 0., 0.)-1.) < 1.e-15 \
and abs(e2.normal()*Vector(0., 1., 0.)-1.) < 1.e-15 \
and abs(e3.normal()*Vector(0., 0., 1.)-1.) < 1.e-15:
return \
Universe.OrthorhombicPeriodicUniverse((e1.length(),
e2.length(),
e3.length()))
return Universe.ParallelepipedicPeriodicUniverse((e1, e2, e3))
def viewConfigurationVMD(object, configuration=None, format='pdb', label=None):
from MMTK import Universe
format = format.lower()
if format != 'pdb':
return genericViewConfiguration(object, configuration, format)
tempfile.tempdir = tempdir
filename = tempfile.mktemp()
filename_tcl = filename.replace('\\', '\\\\')
script = tempfile.mktemp()
script_tcl = script.replace('\\', '\\\\')
tempfile.tempdir = None
object.writeToFile(filename, configuration, format)
file = open(script, 'w')
file.write('mol load pdb ' + filename_tcl + '\n')
if isCalpha(object):
file.write('mol modstyle 0 all trace\n')
file.write('color Name 1 white\n')
file.write('color Name 2 white\n')
file.write('color Name 3 white\n')
if Universe.isUniverse(object):
# add a box around periodic universes
basis = object.basisVectors()
if basis is not None:
v1, v2, v3 = basis
p = -0.5 * (v1 + v2 + v3)
for p1, p2 in [(p, p + v1), (p, p + v2), (p + v1, p + v1 + v2),
(p + v2, p + v1 + v2), (p, p + v3),
(p + v1, p + v1 + v3), (p + v2, p + v2 + v3),
(p + v1 + v2, p + v1 + v2 + v3),
(p + v3, p + v1 + v3), (p + v3, p + v2 + v3),
(p + v1 + v3, p + v1 + v2 + v3),
(p + v2 + v3, p + v1 + v2 + v3)]:
file.write('graphics 0 line {%f %f %f} {%f %f %f}\n' %
(tuple(p1 / Units.Ang) + tuple(p2 / Units.Ang)))
file.write('file delete ' + filename_tcl + '\n')
if sys.platform != 'win32':
# Under Windows, it seems to be impossible to delete
# the script file while it is still in use. For the moment
# we just don't delete it at all.
file.write('file delete ' + script_tcl + '\n')
file.close()
subprocess.Popen([viewer['pdb'][1], '-nt', '-e', script])
def __init__(self, universe, force_field, subset1=None, subset2=None,
threads=None, mpi_communicator=None):
if not Universe.isUniverse(universe):
raise TypeError, "energy evaluator defined only for universes"
self.universe = universe
self.universe_version = self.universe._version
self.ff = force_field
self.configuration = self.universe.configuration()
self.global_data = ForceFieldData()
if subset1 is not None and subset2 is None:
subset2 = subset1
terms = self.ff.evaluatorTerms(self.universe,
subset1, subset2,
self.global_data)
from MMTK_forcefield import Evaluator
if threads is None:
import MMTK.ForceFields
threads = MMTK.ForceFields.default_energy_threads;
self.evaluator = Evaluator(Numeric.array(terms), threads,
mpi_communicator)
def viewConfigurationVMD(object, configuration = None, format = 'pdb',
label = None):
from MMTK import Universe
format = format.lower()
if format != 'pdb':
return genericViewConfiguration(object, configuration, format)
tempfile.tempdir = tempdir
filename = tempfile.mktemp()
filename_tcl = filename.replace('\\', '\\\\')
script = tempfile.mktemp()
script_tcl = script.replace('\\', '\\\\')
tempfile.tempdir = None
object.writeToFile(filename, configuration, format)
file = open(script, 'w')
file.write('mol load pdb ' + filename_tcl + '\n')
if isCalpha(object):
file.write('mol modstyle 0 all trace\n')
file.write('color Name 1 white\n')
file.write('color Name 2 white\n')
file.write('color Name 3 white\n')
if Universe.isUniverse(object):
# add a box around periodic universes
basis = object.basisVectors()
if basis is not None:
v1, v2, v3 = basis
p = -0.5*(v1+v2+v3)
for p1, p2 in [(p, p+v1), (p, p+v2), (p+v1, p+v1+v2),
(p+v2, p+v1+v2), (p, p+v3), (p+v1, p+v1+v3),
(p+v2, p+v2+v3), (p+v1+v2, p+v1+v2+v3),
(p+v3, p+v1+v3), (p+v3, p+v2+v3),
(p+v1+v3, p+v1+v2+v3), (p+v2+v3, p+v1+v2+v3)]:
file.write('graphics 0 line {%f %f %f} {%f %f %f}\n' %
(tuple(p1/Units.Ang) + tuple(p2/Units.Ang)))
file.write('file delete ' + filename_tcl + '\n')
if sys.platform != 'win32':
# Under Windows, it seems to be impossible to delete
# the script file while it is still in use. For the moment
# we just don't delete it at all.
file.write('file delete ' + script_tcl + '\n')
file.close()
subprocess.Popen([viewer['pdb'][1], '-nt', '-e', script])
def graphicsObjects(self, **options):
"""
:keyword configuration: the configuration in which the objects
are drawn (default: the current configuration)
:type configuration: :class:`~MMTK.ParticleProperties.Configuration`
:keyword model: the graphical representation to be used (one of
"wireframe", "tube", "ball_and_stick", "vdw" and
"vdw_and_stick"). The vdw models use balls
with the radii taken from the atom objects.
Default is "wireframe".
:type model: str
:keyword ball_radius: the radius of the balls representing the atoms
in a ball_and_stick model, default: 0.03
This is also used in vdw and vdw_and_stick when
an atom does not supply a radius.
:type ball_radius: float
:keyword stick_radius: the radius of the sticks representing the bonds
in a ball_and_stick, vdw_and_stick or tube model.
Default: 0.02 for the tube model, 0.01 for the
ball_and_stick and vdw_and_stick models
:type stick_radius: float
:keyword graphics_module: the module in which the elementary graphics
objects are defined
(default: Scientific.Visualization.VRML)
:type graphics_module: module
:keyword color_values: a color value for each atom which defines
the color via the color scale object specified
by the option color_scale. If no value is
given, the atoms' colors are taken from the
attribute 'color' of each atom object (default
values for each chemical element are provided
in the chemical database).
:type color_values: :class:`~MMTK.ParticleProperties.ParticleScalar`
:keyword color_scale: an object that returns a color object (as defined
in the module Scientific.Visualization.Color)
when called with a number argument. Suitable
objects are defined by
Scientific.Visualization.Color.ColorScale and
Scientific.Visualization.Color.SymmetricColorScale.
The object is used only when the option
color_values is specified as well. The default
is a blue-to-red color scale that covers the
range of the values given in color_values.
:type color_scale: callable
:keyword color: a color name predefined in the module
Scientific.Visualization.Color. The corresponding
color is applied to all graphics objects that are
returned.
:returns: a list of graphics objects that represent
the object for which the method is called.
:rtype: list
"""
conf = options.get('configuration', None)
model = options.get('model', 'wireframe')
if model == 'tube':
model = 'ball_and_stick'
radius = options.get('stick_radius', 0.02)
options['stick_radius'] = radius
options['ball_radius'] = radius
try:
module = options['graphics_module']
except KeyError:
from Scientific.Visualization import VRML
module = VRML
color = options.get('color', None)
if color is None:
color_values = options.get('color_values', None)
if color_values is not None:
lower = N.minimum.reduce(color_values.array)
upper = N.maximum.reduce(color_values.array)
options['color_scale'] = module.ColorScale((lower, upper))
try:
distance_fn = self.universe().distanceVector
except AttributeError:
from MMTK import Universe
distance_fn = Universe.InfiniteUniverse().distanceVector
return self._graphics(conf, distance_fn, model, module, options)