Package mmLib :: Module TLS :: Class TLSGroupDesc
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Class TLSGroupDesc

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object --+
         |
        TLSGroupDesc

Description of one TLS Group.

Instance Methods [hide private]
 
__init__(self)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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set_name(self, name)
Sets the TLS group name.
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set_origin(self, x, y, z)
Sets the TLS group origin of calculations.
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add_range(self, chain_id1, frag_id1, chain_id2, frag_id2, selection)
Adds a segment of residues to the TLS group.
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set_T(self, t11, t22, t33, t12, t13, t23)
Sets the T tensor from the component arguments.
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set_L(self, l11, l22, l33, l12, l13, l23)
Sets the L tensor from the component arguments.
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set_L_deg2(self, l11, l22, l33, l12, l13, l23)
Sets the L tensor from the component arguments.
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set_S(self, s2211, s1133, s12, s13, s23, s21, s31, s32)
Sets the S tensor from the component arguments.
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set_S_deg(self, s2211, s1133, s12, s13, s23, s21, s31, s32)
Sets the S tensor from the component arguments.
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set_tls_group(self, tls_group)
Sets the TLSGroupDesc tensor values from the TLSGroup instance.
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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_name(self)
Creates a name for the TLS group using the selected residue ranges.
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iter_atoms(self, struct)
Uses the TLS definition and the given Structure object to iterate over all atoms which should be included in the TLS group according to the range_list definitions.
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construct_tls_group(self)
Creates a TLSGroup() object with the origin, T, L, and S tensors set according to the TLS description.
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construct_tls_group_with_atoms(self, struct)
Creates a TLSGroup() object with the origin, T, L, and S tensors set according to the TLS description, then add the Atoms to the TLSGroup from the given argument Structure.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

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

Overrides: object.__init__
(inherited documentation)

add_range(self, chain_id1, frag_id1, chain_id2, frag_id2, selection)

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Adds a segment of residues to the TLS group. Not too sure how to handle segments which span chains, so assert on that condition.

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

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Sets the T tensor from the component arguments. Units are in square Angstroms.

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

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Sets the L tensor from the component arguments. Units are in square Radians.

set_L_deg2(self, l11, l22, l33, l12, l13, l23)

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Sets the L tensor from the component arguments. Units are in square Degrees.

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

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Sets the S tensor from the component arguments. Units are in Radians*Angstroms. The trace of S is set to 0.0.

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

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Sets the S tensor from the component arguments. Units are in Degrees*Angstroms. The trace of S is set to 0.0.