Package mmLib :: Module TLS :: Class TLSGroup
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Type TLSGroup

object --+        
         |        
      list --+    
             |    
      AtomList --+
                 |
                TLSGroup


A subclass of AtomList implementing methods for performing TLS calculations on the contained Atom instances.
Method Summary
  __init__(self, *args)
  calc_COR(self)
Returns the calc_COR() return information for this TLS Group.
  calc_s11_s22_s33(self, s2211, s1133)
Calculates s11, s22, s33 based on s22-s11 and s11-s33 using the constraint s11+s22+s33=0
  calc_tls_info(self)
Calculates a number of statistics about the TLS group tensors, goodness of fit, various parameter averages, center of reaction tensors, etc...
  calc_TLS_least_squares_fit(self, weight_dict)
Perform a least-squares fit of the atoms contained in self to the three TLS tensors: self.T, self.L, and self.S using the origin given by self.origin.
  is_null(self)
Returns True if the T,L,S tensors are not set, or are set with values of zero.
  iter_atm_Utls(self)
Iterates all the atoms in the TLS object, returning the 2-tuple (atm, U) where U is the calcuated U value from the current values of the TLS object's T,L,S, tensors and origin.
  set_L(self, l11, l22, l33, l12, l13, l23)
Sets the components of the symmetric L tensor from arguments.
  set_origin(self, x, y, z)
Sets the x, y, z components of the TLS origin vector.
  set_S(self, s2211, s1133, s12, s13, s23, s21, s31, s32)
Sets the componets of the asymmetric S tenssor.
  set_T(self, t11, t22, t33, t12, t13, t23)
Sets the components of the symmetric T tensor.
  shift_COR(self)
Shift the TLS group to the center of reaction.
  str_old(self)
    Inherited from AtomList
  calc_adv_anisotropy(self)
Calculates the adverage anisotropy for all Atoms in the AtomList.
  calc_adv_anisotropy3(self)
Calculates the adverage anisotropy 3-tuple for all Atoms in the AtomList.
  calc_adv_temp_factor(self)
Calculates the adverage temperature factor of all contained Atom instances and returns the adverage temperature factor.
  calc_adv_U(self)
Calculates the adverage U matrix of all contained Atom instances and returns the 3x3 symmetric U matrix of that adverage.
  calc_centroid(self)
Calculates the centroid of all contained Atom instances and returns a Vector to the centroid.
    Inherited from list
  __add__(x, y)
x.__add__(y) <==> x+y
  __contains__(x, y)
x.__contains__(y) <==> y in x
  __delitem__(x, y)
x.__delitem__(y) <==> del x[y]
  __delslice__(x, i, j)
Use of negative indices is not supported.
  __eq__(x, y)
x.__eq__(y) <==> x==y
  __ge__(x, y)
x.__ge__(y) <==> x>=y
  __getattribute__(...)
x.__getattribute__('name') <==> x.name
  __getitem__(x, y)
x.__getitem__(y) <==> x[y]
  __getslice__(x, i, j)
Use of negative indices is not supported.
  __gt__(x, y)
x.__gt__(y) <==> x>y
  __hash__(x)
x.__hash__() <==> hash(x)
  __iadd__(x, y)
x.__iadd__(y) <==> x+=y
  __imul__(x, y)
x.__imul__(y) <==> x*=y
  __iter__(x)
x.__iter__() <==> iter(x)
  __le__(x, y)
x.__le__(y) <==> x<=y
  __len__(x)
x.__len__() <==> len(x)
  __lt__(x, y)
x.__lt__(y) <==> x<y
  __mul__(x, n)
x.__mul__(n) <==> x*n
  __ne__(x, y)
x.__ne__(y) <==> x!=y
  __new__(T, S, ...)
T.__new__(S, ...) -> a new object with type S, a subtype of T
  __repr__(x)
x.__repr__() <==> repr(x)
  __reversed__(...)
L.__reversed__() -- return a reverse iterator over the list
  __rmul__(x, n)
x.__rmul__(n) <==> n*x
  __setitem__(x, i, y)
x.__setitem__(i, y) <==> x[i]=y
  __setslice__(x, i, j, y)
Use of negative indices is not supported.
  append(...)
L.append(object) -- append object to end
  count(L, value)
L.count(value) -> integer -- return number of occurrences of value
  extend(...)
L.extend(iterable) -- extend list by appending elements from the iterable
  index(...)
L.index(value, [start, [stop]]) -> integer -- return first index of value
  insert(...)
L.insert(index, object) -- insert object before index
  pop(L, index)
L.pop([index]) -> item -- remove and return item at index (default last)
  remove(...)
L.remove(value) -- remove first occurrence of value
  reverse(...)
L.reverse() -- reverse *IN PLACE*
  sort(...)
L.sort(cmp=None, key=None, reverse=False) -- stable sort *IN PLACE*; cmp(x, y) -> -1, 0, 1
    Inherited from object
  __delattr__(...)
x.__delattr__('name') <==> del x.name
  __reduce__(...)
helper for pickle
  __reduce_ex__(...)
helper for pickle
  __setattr__(...)
x.__setattr__('name', value) <==> x.name = value
  __str__(x)
x.__str__() <==> str(x)

Method Details

calc_COR(self)

Returns the calc_COR() return information for this TLS Group.

calc_s11_s22_s33(self, s2211, s1133)

Calculates s11, s22, s33 based on s22-s11 and s11-s33 using the constraint s11+s22+s33=0

calc_tls_info(self)

Calculates a number of statistics about the TLS group tensors, goodness of fit, various parameter averages, center of reaction tensors, etc...

calc_TLS_least_squares_fit(self, weight_dict=None)

Perform a least-squares fit of the atoms contained in self to the three TLS tensors: self.T, self.L, and self.S using the origin given by self.origin.

is_null(self)

Returns True if the T,L,S tensors are not set, or are set with values of zero.

iter_atm_Utls(self)

Iterates all the atoms in the TLS object, returning the 2-tuple (atm, U) where U is the calcuated U value from the current values of the TLS object's T,L,S, tensors and origin.

set_L(self, l11, l22, l33, l12, l13, l23)

Sets the components of the symmetric L tensor from arguments. Units should be in square radians.

set_origin(self, x, y, z)

Sets the x, y, z components of the TLS origin vector.

set_S(self, s2211, s1133, s12, s13, s23, s21, s31, s32)

Sets the componets of the asymmetric S tenssor. The trace of the S tensor is set with the standard convention of the Trace(S) = 0. Units in Radians*Angstroms.

set_T(self, t11, t22, t33, t12, t13, t23)

Sets the components of the symmetric T tensor. Units in square Angstroms.

shift_COR(self)

Shift the TLS group to the center of reaction.

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