def dihedral(self, p1, p2, p3, p4, conf = None):
"""Returns the dihedral angle between the plane containing the
distance vectors |p1|-|p2| and |p3|-|p2| and the plane containing the
distance vectors |p2|-|p3| and |p4|-|p3|."""
v1 = self.distanceVector(p2, p1, conf)
v2 = self.distanceVector(p3, p2, conf)
v3 = self.distanceVector(p3, p4, conf)
a = v1.cross(v2).normal()
b = v3.cross(v2).normal()
cos = a*b
sin = b.cross(a)*v2/v2.length()
return Transformation.angleFromSineAndCosine(sin, cos)
def __init__(self, attr, point1, point2):
center = 0.5 * (point1 + point2)
axis = point2 - point1
self.height = axis.length()
if self.height > 0:
axis = axis / self.height
rot_axis = ey.cross(axis)
sine = rot_axis.length()
cosine = ey * axis
angle = Transformation.angleFromSineAndCosine(sine, cosine)
if abs(angle) < 1.e-4 or abs(angle - 2. * N.pi) < 1.e-4:
rotation = None
else:
if abs(sine) < 1.e-4:
rot_axis = ex
rotation = (rot_axis, angle)
else:
rotation = None
ShapeObject.__init__(self, attr, rotation, center, center)
def __init__(self, attr, point1, point2): center = 0.5*(point1+point2) axis = point2-point1 self.height = axis.length() if self.height > 0: axis = axis/self.height rot_axis = VectorModule.ey.cross(axis) sine = rot_axis.length() cosine = VectorModule.ey*axis angle = Transformation.angleFromSineAndCosine(sine, cosine) if abs(angle) < 1.e-4 or abs(angle-2.*Numeric.pi) < 1.e-4: rotation = None else: if abs(sine) < 1.e-4: rot_axis = VectorModule.ex rotation = (rot_axis, angle) else: rotation = None ShapeObject.__init__(self, attr, rotation, center, center)
def addImproperTerm(self, data, improper, object, global_data):
if not self.arguments[2]:
return
a1 = improper.a1
a2 = improper.a2
a3 = improper.a3
a4 = improper.a4
i1 = a1.index
i2 = a2.index
i3 = a3.index
i4 = a4.index
t1 = global_data.atom_type[a1]
t2 = global_data.atom_type[a2]
t3 = global_data.atom_type[a3]
t4 = global_data.atom_type[a4]
terms = self.dataset.improperParameters(t1, t2, t3, t4)
if terms is not None:
atoms = [(t2,i2,a2), (t3,i3,a3), (t4,i4,a4)]
atoms.sort(_order)
i2, i3, i4 = tuple(map(lambda t: t[1], atoms))
a2, a3, a4 = tuple(map(lambda t: t[2], atoms))
v1 = a2.position()-a3.position()
v2 = a3.position()-a1.position()
v3 = a4.position()-a1.position()
a = v1.cross(v2).normal()
b = v3.cross(v2).normal()
cos = a*b
sin = b.cross(a)*v2/v2.length()
dihedral = Transformation.angleFromSineAndCosine(sin, cos)
if dihedral > Numeric.pi:
dihedral = dihedral - 2.*Numeric.pi
for p in terms:
if p[2] != 0.:
mult = p[0]
phase = Numeric.fmod(Numeric.pi-mult*dihedral,
2.*Numeric.pi)
if phase < 0.:
phase = phase + 2.*Numeric.pi
data.add('dihedrals', (i2, i3, i1, i4,
p[0], phase) + p[2:])
def addImproperTerm(self, data, improper, object, global_data):
if not self.arguments[2]:
return
a1 = improper.a1
a2 = improper.a2
a3 = improper.a3
a4 = improper.a4
i1 = a1.index
i2 = a2.index
i3 = a3.index
i4 = a4.index
t1 = global_data.atom_type[a1]
t2 = global_data.atom_type[a2]
t3 = global_data.atom_type[a3]
t4 = global_data.atom_type[a4]
terms = self.dataset.improperParameters(t1, t2, t3, t4)
if terms is not None:
atoms = [(t2,i2,a2), (t3,i3,a3), (t4,i4,a4)]
atoms.sort(_order)
i2, i3, i4 = tuple(map(lambda t: t[1], atoms))
a2, a3, a4 = tuple(map(lambda t: t[2], atoms))
v1 = a2.position()-a3.position()
v2 = a3.position()-a1.position()
v3 = a4.position()-a1.position()
a = v1.cross(v2).normal()
b = v3.cross(v2).normal()
cos = a*b
sin = b.cross(a)*v2/v2.length()
dihedral = Transformation.angleFromSineAndCosine(sin, cos)
if dihedral > Numeric.pi:
dihedral = dihedral - 2.*Numeric.pi
for p in terms:
if p[2] != 0.:
mult = p[0]
phase = Numeric.fmod(Numeric.pi-mult*dihedral,
2.*Numeric.pi)
if phase < 0.:
phase = phase + 2.*Numeric.pi
data.add('dihedrals', (i2, i3, i1, i4,
p[0], phase) + p[2:])
def addDihedralTerm(self, data, dihedral, object, global_data):
if not self.arguments[2]:
return
a1 = dihedral.a1
a2 = dihedral.a2
a3 = dihedral.a3
a4 = dihedral.a4
i1 = a1.index
i2 = a2.index
i3 = a3.index
i4 = a4.index
global_data.add('1_4_pairs', (i1, i4))
t1 = global_data.atom_type[a1]
t2 = global_data.atom_type[a2]
t3 = global_data.atom_type[a3]
t4 = global_data.atom_type[a4]
terms = self.dataset.dihedralParameters(t1, t2, t3, t4)
if terms is not None:
v1 = a1.position()-a2.position()
v2 = a2.position()-a3.position()
v3 = a4.position()-a3.position()
a = v1.cross(v2).normal()
b = v3.cross(v2).normal()
cos = a*b
sin = b.cross(a)*v2/v2.length()
dihedral = Transformation.angleFromSineAndCosine(sin, cos)
if dihedral > Numeric.pi:
dihedral = dihedral - 2.*Numeric.pi
for p in terms:
if p[2] != 0.:
mult = p[0]
phase = Numeric.fmod(Numeric.pi-mult*dihedral,
2.*Numeric.pi)
if phase < 0.:
phase = phase + 2.*Numeric.pi
data.add('dihedrals', (i1, i2, i3, i4,
p[0], phase) + p[2:])
def addDihedralTerm(self, data, dihedral, object, global_data):
if not self.arguments[2]:
return
a1 = dihedral.a1
a2 = dihedral.a2
a3 = dihedral.a3
a4 = dihedral.a4
i1 = a1.index
i2 = a2.index
i3 = a3.index
i4 = a4.index
global_data.add('1_4_pairs', (i1, i4))
t1 = global_data.atom_type[a1]
t2 = global_data.atom_type[a2]
t3 = global_data.atom_type[a3]
t4 = global_data.atom_type[a4]
terms = self.dataset.dihedralParameters(t1, t2, t3, t4)
if terms is not None:
v1 = a1.position()-a2.position()
v2 = a2.position()-a3.position()
v3 = a4.position()-a3.position()
a = v1.cross(v2).normal()
b = v3.cross(v2).normal()
cos = a*b
sin = b.cross(a)*v2/v2.length()
dihedral = Transformation.angleFromSineAndCosine(sin, cos)
if dihedral > Numeric.pi:
dihedral = dihedral - 2.*Numeric.pi
for p in terms:
if p[2] != 0.:
mult = p[0]
phase = Numeric.fmod(Numeric.pi-mult*dihedral,
2.*Numeric.pi)
if phase < 0.:
phase = phase + 2.*Numeric.pi
data.add('dihedrals', (i1, i2, i3, i4,
p[0], phase) + p[2:])