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

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    object --+        
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          list --+    
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Structure.AtomList --+
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                    TLSGroup

A subclass of AtomList implementing methods for performing TLS calculations on the contained Atom instances.

Instance Methods [hide private]
new empty list
__init__(self, *args)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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str_old(self) source code
 
set_origin(self, x, y, z)
Sets the x, y, z components of the TLS origin vector.
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set_T(self, t11, t22, t33, t12, t13, t23)
Sets the components of the symmetric T tensor.
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set_L(self, l11, l22, l33, l12, l13, l23)
Sets the components of the symmetric L tensor from arguments.
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set_S(self, s2211, s1133, s12, s13, s23, s21, s31, s32)
Sets the componets of the asymmetric S tenssor.
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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
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is_null(self)
Returns True if the T,L,S tensors are not set, or are set with values of zero.
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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.
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iter_atm_Utls(self)
Iterates over 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.
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calc_COR(self)
Returns the calc_COR() return information for this TLS Group.
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shift_COR(self)
Shift the TLS group to the center of reaction.
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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...
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Inherited from Structure.AtomList: calc_adv_U, calc_adv_anisotropy, calc_adv_anisotropy3, calc_adv_temp_factor, calc_centroid

Inherited from list: __add__, __contains__, __delitem__, __delslice__, __eq__, __ge__, __getattribute__, __getitem__, __getslice__, __gt__, __iadd__, __imul__, __iter__, __le__, __len__, __lt__, __mul__, __ne__, __new__, __repr__, __reversed__, __rmul__, __setitem__, __setslice__, __sizeof__, append, count, extend, index, insert, pop, remove, reverse, sort

Inherited from object: __delattr__, __format__, __reduce__, __reduce_ex__, __setattr__, __str__, __subclasshook__

Class Variables [hide private]

Inherited from list: __hash__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, *args)
(Constructor)

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x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Returns: new empty list
Overrides: object.__init__
(inherited documentation)

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

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

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

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

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

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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.