mmLib.TLS

Package mmLib :: Module TLS

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Module mmLib.TLS

Utility classes for loading, manipulating, and analyzing TLS parameters.

Classes
`GLTLSAtomList`	OpenGL visualizations of TLS group atoms.
`GLTLSChain`	Collects a list of GLTLSGroup instances which are all in the same chain.
`GLTLSGroup`	Top level visualization object for a TLS group.
`TLSFile`	Read/Write a TLS files containing one or more TLSGroupDesc objects.
`TLSFileFormat`	Base class for TLS file types.
`TLSFileFormatPDB`	Reads TLS descriptions from the REMARK records in PDB files.
`TLSFileFormatTLSOUT`	Read/Write REFMAC5 TLSIN/TLSOUT files.
`TLSGroup`	A subclass of AtomList implementing methods for performing TLS calculations on the contained Atom instances.
`TLSGroupDesc`	Description of one TLS Group.
`TLSStructureAnalysis`	Algorithm object for rigid body searches on Structure objects.

Exceptions
`TLSError`	Base exception class for TLS module exceptions.
`TLSFileFormatError`	Raised when a file format error is encountered while loading a TLS group description file.

Function Summary
	`calc_itls_center_of_reaction(iT, iL, iS, origin)` iT is a single float; iL[3,3]; iS[3]
	`calc_itls_uiso(T, L, S, position)` Calculate the TLS predicted uiso from the isotropic TLS model for the atom at position.
	`calc_LS_displacement(cor, Lval, Lvec, Lrho, Lpitch, position, prob)` Returns the amount of rotational displacement from L for a atom at the given position.
	`calc_rmsd(msd)` Calculate RMSD from a given MSD.
	`calc_s11_s22_s33(s2211, s1133)` Calculates s11, s22, s33 based on s22-s11 and s11-s33 using the constraint s11+s22+s33=0
	`calc_TLS_center_of_reaction(T0, L0, S0, origin)` Calculate new tensors based on the center for reaction.
	`calc_TLS_least_squares_fit(atom_list, origin, weight_dict)` Perform a LSQ-TLS fit on the given AtomList.
	`calc_TLS_plus_b_least_squares_fit(atom_list, origin, weight_dict)` Perform a LSQ-TLS fit on the given Segment object using the TLS model with amino acid side chains which can pivot about the CA atom.
	`calc_TLSCA_least_squares_fit(segment, origin)` Perform a LSQ-TLS fit on the given Segment object using the TLS model with amino acid side chains which can pivot about the CA atom.
	`calc_Utls(T, L, S, position)` Returns the calculated value for the anisotropic U tensor for the given position.
	`goodness_color(x)` x in range 0.0->1.0
	`iter_itls_uiso(atom_iter, T, L, S, O)` Iterates the pair (atom, u_iso)
	`set_L_A(A, i, j, x, y, z, w)` Sets coefficents of a L tensor in matrix A for a atom at position x,y,z and weight w.
	`set_TLS_A(A, i, j, x, y, z, w)` Sets the six rows of matrix A starting at A[i,j] with the TLS coefficents for a atom located at position x,y,z with least-squares weight w.
	`set_TLS_b(b, i, u11, u22, u33, u12, u13, u23, w)` Sets the six rows of vector b with the experimental/target anisotropic ADP values U starting at index b[i] and ending at b[i+6] with weight w.
	`set_TLSiso_A(A, i, j, x, y, z, w)` Sets the one row of matrix A starting at A[i,j] with the istropic TLS model coefficents for a atom located at t position x, y, z with least-squares weight w.
	`set_TLSiso_b(b, i, Uiso, w)` Sets the six rows of vector b with the experimental/target anisotropic ADP values U starting at index b[i] and ending at b[i+6] with weight w.
	`solve_TLS_Ab(A, b)` Sove a overdetermined TLS system by singular value decomposition.
	`test_module()`

Variable Summary
`dict`	`CA_PIVOT_ATOMS` = `{'CYS': 'CA', 'GLN': 'CA', 'ILE': 'CA',...`

Function Details

calc_itls_center_of_reaction(iT, iL, iS, origin)

iT is a single float; iL[3,3]; iS[3]

calc_itls_uiso(T, L, S, position)

Calculate the TLS predicted uiso from the isotropic TLS model for the atom at position.

calc_LS_displacement(cor, Lval, Lvec, Lrho, Lpitch, position, prob)

Returns the amount of rotational displacement from L for a atom at the given position.

calc_rmsd(msd)

Calculate RMSD from a given MSD.

calc_s11_s22_s33(s2211, s1133)

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

calc_TLS_center_of_reaction(T0, L0, S0, origin)

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_TLS_least_squares_fit(atom_list, origin, weight_dict=None)

Perform a LSQ-TLS fit on the given AtomList. The TLS tensors are calculated at the given origin, with weights of weight_dict[atm]. Return values are T, L, S, lsq_residual.

calc_TLS_plus_b_least_squares_fit(atom_list, origin, weight_dict=None)

Perform a LSQ-TLS fit on the given Segment object using the TLS model with amino acid side chains which can pivot about the CA atom. This model uses 20 TLS parameters and 6 libration parameters per side chain.

calc_TLSCA_least_squares_fit(segment, origin)

calc_Utls(T, L, S, position)

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

goodness_color(x)

x in range 0.0->1.0

iter_itls_uiso(atom_iter, T, L, S, O)

Iterates the pair (atom, u_iso)

set_L_A(A, i, j, x, y, z, w)

Sets coefficents of a L tensor in matrix A for a atom at position x,y,z and weight w. This starts at A[i,j] and ends at A[i+6,j+6] Using weight w.

set_TLS_A(A, i, j, x, y, z, w)

Sets the six rows of matrix A starting at A[i,j] with the TLS coefficents for a atom located at position x,y,z with least-squares weight w. Matrix A is filled to row i+6 and column j+20.

set_TLS_b(b, i, u11, u22, u33, u12, u13, u23, w)

Sets the six rows of vector b with the experimental/target anisotropic ADP values U starting at index b[i] and ending at b[i+6] with weight w.

set_TLSiso_A(A, i, j, x, y, z, w)

Sets the one row of matrix A starting at A[i,j] with the istropic TLS model coefficents for a atom located at t position x, y, z with least-squares weight w. Matrix A is filled to coumn j+12.

set_TLSiso_b(b, i, Uiso, w)

Sets the six rows of vector b with the experimental/target anisotropic ADP values U starting at index b[i] and ending at b[i+6] with weight w.

solve_TLS_Ab(A, b)

Sove a overdetermined TLS system by singular value decomposition.

Variable Details

CA_PIVOT_ATOMS

Type:: dict
Value:: {'ALA': None, 'ARG': 'CA', 'ASN': 'CA', 'ASP': 'CA', 'CYS': 'CA', 'GLN': 'CA', 'GLU': 'CA', 'GLY': None, ...

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