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Package mmLib ::
Module TLS


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  

iT is a single float; iL[3,3]; iS[3]  
Calculate the TLS predicted uiso from the isotropic TLS model for the atom at position.  
Returns the amount of rotational displacement from L for a atom at the given position.  
Calculate RMSD from a given MSD.  
Calculates s11, s22, s33 based on s22s11 and s11s33 using the constraint s11+s22+s33=0  
Calculate new tensors based on the center for reaction.  
Perform a LSQTLS fit on the given AtomList.  
Perform a LSQTLS fit on the given Segment object using the TLS model with amino acid side chains which can pivot about the CA atom.  
Perform a LSQTLS fit on the given Segment object using the TLS model with amino acid side chains which can pivot about the CA atom.  
Returns the calculated value for the anisotropic U tensor for the given position.  
x in range 0.0>1.0  
Iterates the pair (atom, u_iso)  
Sets coefficents of a L tensor in matrix A for a atom at position x,y,z and weight 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 leastsquares weight 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.  
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 leastsquares weight 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.  
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 s22s11 and s11s33 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 LSQTLS 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 LSQTLS 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)Perform a LSQTLS 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_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 leastsquares 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 leastsquares 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

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