mmLib.TLS.TLSGroupDesc

Package mmLib :: Module TLS :: Class TLSGroupDesc

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Type TLSGroupDesc

object --+
         |
        TLSGroupDesc

Description of one TLS Group.

Method Summary
	`__init__(self)`
	`add_range(self, chain_id1, frag_id1, chain_id2, frag_id2, selection)` Adds a segment of residues to the TLS group.
	`calc_tls_name(self)` Creates a name for the TLS group using the selected residue ranges.
	`construct_tls_group(self)` Creates a TLSGroup() object with the origin, T, L, and S tensors set according to the TLS description.
	`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, the add the Atoms to the TLSGroup from the given argument Structure.
	`is_null(self)` Returns True if the T,L,S tensors are not set, or are set with values of zero.
	`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.
	`set_L(self, l11, l22, l33, l12, l13, l23)` Sets the L tensor from the component arguments.
	`set_L_deg2(self, l11, l22, l33, l12, l13, l23)` Sets the L tensor from the component arguments.
	`set_name(self, name)` Sets the TLS group name.
	`set_origin(self, x, y, z)` Sets the TLS group origin of calculations.
	`set_S(self, s2211, s1133, s12, s13, s23, s21, s31, s32)` Sets the S tensor from the component arguments.
	`set_S_deg(self, s2211, s1133, s12, s13, s23, s21, s31, s32)` Sets the S tensor from the component arguments.
	`set_T(self, t11, t22, t33, t12, t13, t23)` Sets the T tensor from the component arguments.
	`set_tls_group(self, tls_group)` Sets the TLSGroupDesc tensor values from the TLSGroup instance.
Inherited from object
	`__delattr__(...)` x.__delattr__('name') <==> del x.name
	`__getattribute__(...)` x.__getattribute__('name') <==> x.name
	`__hash__(x)` x.__hash__() <==> hash(x)
	`__new__(T, S, ...)` T.__new__(S, ...) -> a new object with type S, a subtype of T
	`__reduce__(...)` helper for pickle
	`__reduce_ex__(...)` helper for pickle
	`__repr__(x)` x.__repr__() <==> repr(x)
	`__setattr__(...)` x.__setattr__('name', value) <==> x.name = value
	`__str__(x)` x.__str__() <==> str(x)

Method Details

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

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

calc_tls_name(self)

Creates a name for the TLS group using the selected residue ranges.

construct_tls_group(self)

Creates a TLSGroup() object with the origin, T, L, and S tensors set according to the TLS description.

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, the add the Atoms to the TLSGroup from the given argument Structure.

is_null(self)

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

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.

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

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

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

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

set_name(self, name)

Sets the TLS group name.

set_origin(self, x, y, z)

Sets the TLS group origin of calculations.

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

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)

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

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

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

set_tls_group(self, tls_group)

Sets the TLSGroupDesc tensor values from the TLSGroup instance.

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