mmLib.Extensions.TLS.TLSGroup

Package mmLib :: Package Extensions :: Module TLS :: Class TLSGroup

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Class 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)` Calculate new tensors based on the center for reaction.
	`calc_mean_DP2(self)` Calculates the mean dP2 and standard deviation of U vs.
	`calc_mean_S(self)` Calculates the mean Suij of U vs.
	`calc_R(self)` Calculate the R factor of U vs.
	`calc_sum_DP2(self)` Calculates the sum of DP2(U,Utls) for all Atoms in the TLSGroup.
	`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)` 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.
	`calc_Utls(self, T, L, S, vec)` Returns the calculated value for the anisotropic U tensor for the given position.
	`check_valid_model(self)` Returns True if the TLS model is mathmatically valid.
	`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, T, L, S, o)` 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)`
	`verify_equivalent_models(self)` XXX: Fixme
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
	`__repr__(x)` x.__repr__() <==> repr(x)
	`__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(cmpfunc=None) -- stable sort IN PLACE; cmpfunc(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)
Inherited from type
	`__new__(T, S, ...)` T.__new__(S, ...) -> a new object with type S, a subtype of T

Method Details

calc_COR(self)

Calculate new tensors based on the center for reaction.
This method returns a dictionary of the calculations:

T^: T tensor in the coordinate system of L
L^: L tensor in the coordinate system of L
S^: S tensor in the coordinate system of L

COR: Center of Reaction

T',S',L': T,L,S tensors in origonal coordinate system
          with the origin shifted to the center of reaction.

calc_mean_DP2(self)

Calculates the mean dP2 and standard deviation of U vs. Utls for every atom in the TLS group. Returns the 2-tuple. (mean DP2, rmsd)

calc_mean_S(self)

Calculates the mean Suij of U vs. Utls.

calc_R(self)

Calculate the R factor of U vs. Utls.

calc_sum_DP2(self)

Calculates the sum of DP2(U,Utls) for all Atoms in the TLSGroup.

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... If tls_info["valid_model"] is not None, then the TLS group parameters are invalid.

calc_TLS_least_squares_fit(self)

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.

calc_Utls(self, T, L, S, vec)

Returns the calculated value for the anisotropic U tensor for the given position.

check_valid_model(self)

Returns True if the TLS model is mathmatically valid. This requires the eigenvalues of the L and T tensor to be positive, and the Utls calculated anisotropic ADPs must must also have positive eigenvalues.

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, T=None, L=None, S=None, o=None)

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.

verify_equivalent_models(self)

XXX: Fixme

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