Package mmLib :: Module TLS
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Module TLS

source code

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

Classes [hide private]
  TLSError
Base exception class for TLS module exceptions.
  TLSFileFormatError
Raised when a file format error is encountered while loading a TLS group description file.
  TLSGroupDesc
Description of one TLS Group.
  TLSFile
Read/Write 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 REFMAC TLSIN/TLSOUT files.
  TLSFileFormatPureTLSOUT
Read/Write REFMAC5 TLSIN/TLSOUT files.
  TLSFileFormatPHENIXOUT
Write PHENIX-TLSOUT files.
  TLSFileFormatPHENIX
Read/Write PHENIX TLSIN/TLSOUT files.
  TLSGroup
A subclass of AtomList implementing methods for performing TLS calculations on the contained Atom instances.
  TLSStructureAnalysis
Algorithm object for rigid body searches on Structure objects.
  GLTLSAtomList
OpenGL visualizations of TLS group atoms.
  GLTLSGroup
Top level visualization object for a TLS group.
  GLTLSChain
Collects a list of GLTLSGroup instances which are all in the same chain.
Functions [hide private]
 
solve_TLS_Ab(A, b)
Solve an overdetermined TLS system by singular value decomposition.
source code
 
calc_rmsd(msd)
Calculate RMSD from a given MSD.
source code
 
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.
source code
 
set_TLSiso_A(A, i, j, x, y, z, w)
Sets the one row of matrix A starting at A[i,j] with the isotropic TLS model coefficients for an atom located at t position x, y, z with least-squares weight w.
source code
 
calc_itls_uiso(T, L, S, position)
Calculate the TLS predicted uiso from the isotropic TLS model for the atom at position.
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iter_itls_uiso(atom_iter, T, L, S, O)
Iterates the pair (atom, u_iso)
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calc_itls_center_of_reaction(iT, iL, iS, origin)
iT is a single float; iL[3,3]; iS[3]
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calc_s11_s22_s33(s2211, s1133)
Calculates s11, s22, s33 based on s22-s11 and s11-s33 using the constraint s11+s22+s33=0
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calc_Utls(T, L, S, position)
Returns the calculated value for the anisotropic U tensor for the given position.
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calc_LS_displacement(cor, Lval, Lvec, Lrho, Lpitch, position, prob)
Returns the amount of rotational displacement from L for an atom at the given position.
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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 coefficients for an atom located at position x,y,z with least-squares weight w.
source code
 
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.
source code
 
calc_TLS_least_squares_fit(atom_list, origin, weight_dict=None)
Perform a LSQ-TLS fit on the given AtomList.
source code
 
calc_TLS_center_of_reaction(T0, L0, S0, origin)
Calculate new tensors based on the center for reaction.
source code
 
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.
source code
 
set_L_A(A, i, j, x, y, z, w)
Sets coefficients of a L tensor in matrix A for an atom at position x,y,z and weight w.
source code
 
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.
source code
 
goodness_color(x)
x in range 0.0->1.0
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test_module() source code
Variables [hide private]
  CA_PIVOT_ATOMS = {'ALA': None, 'ARG': 'CA', 'ASN': 'CA', 'ASP'...
  __package__ = 'mmLib'
Function Details [hide private]

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

source code 

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

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

source code 

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

calc_TLS_least_squares_fit(atom_list, origin, weight_dict=None)

source code 

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_center_of_reaction(T0, L0, S0, origin)

source code 
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 original coordinate system
          with the origin shifted to the center of reaction.

calc_TLS_plus_b_least_squares_fit(atom_list, origin, weight_dict=None)

source code 

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.

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

source code 

Sets coefficients of a L tensor in matrix A for an 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.

calc_TLSCA_least_squares_fit(segment, origin)

source code 

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.


Variables Details [hide private]

CA_PIVOT_ATOMS

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