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- Target_relax_function(in_param, ifp)
- target function for fitting
- addTmPAtoms(tpOatom=None, tpXatom=None, tpYatom=None, resid=None, segid=None, pot=None, mass=1000)
- create psf and initial coordinates for pseudo atoms used for optimizing
correlation times tau_c, tau_t and tau_i
- analyze(potList)
- perform analysis of DiffPot terms and return nicely formatted summary
- calcR2R1ratio(Freq=None, Ing=None, Rsel='resid 1:1000')
- Subrutine which simulates NMR relaxation data
INPUT:
Freq is spectrometer frequency in GHz
Ing is a vector of diffusion tensor parameters which will be used
for relaxation rates calculation
Ing=[Dx, Dy, Dz, alpha, betha, gamma]
for axial mode Ing=[Dxy, Dz, betha, alpha]
for iso mode Ing=[Dxyz]
Dx, Dy, Dz are in inverse nanoseconds, alpha, betha, and
gamma are in degrees
Ing is in the same format as results.Fit_vector
res_sel is selection of residues in a format 'resid N:M' where
integers N and M specify the range of residues used to
simulate relaxation data
RETURN:
out_dat list in format [resNum, R2/R1]
- calc_relax_data(Fr=None, InG=None, res_sel=None)
- # Subrutine which simulates NMR relaxation data
# INPUT:
# Fr is spectrometer frequency in GHz
# InG is a vector of diffusion tensor parameters which will be used
# for relaxation rates calculation
# InG=[Dx, Dy, Dz, alpha, betha, gamma]
# for axial mode InG=[Dxy, Dz, betha, alpha]
# for iso mode InG=[Dxyz]
# Dx, Dy, Dz are in inverse nanoseconds, alpha, betha, and gamma are in degrees
# InG is in the same format as results.Fit_vector
# res_sel is selection of residues in a format 'resid N:M' where integers N and M
# specify the range of residues used to simulate relaxation data
# RETURN:
# simulated_data list of realx_datum() structures containing R1, R2, and R2/R1
# for details see declaration of FitResults() class below.
- create_DiffPot(name, sel='known and (not PSEUDO)', temperature=293, addAtoms=False, mass=1000, link_to=None)
- create an instance of an diffPot.DiffPot object
Arguments:
name - is an instance name of a diffPot object.
sel - is selection of atoms which will be used to create
protein surface tessellation by surfTessellation object
This parameter is used only if the created relaxRatioPot
instance is not using a surfTessellation
borrowed from another potential, i.e. link_to=None, in
which case sel argument is omitted.
temperature - the nominal experimental temperature in Kelvins
addAtoms - flag wich specifies whether the pseudo atoms for
temperature optimization are created or not. Default
setting does not assume temperature optimization. The
state addAtoms=True creates pseudo atoms
mass - value for the mass of the pseudo atoms
link_to - used to link the potential to surfTessellation created
by another potential or to a standing alone
surfTessellation object. The default setting that
external surfTessellation is not given, and, therefore,
creates a new surfTessellation using sel atom selection.
returns a diffPot object
- diffValuesEuler(dT_e)
- given a diffusion tensor (in 100*[inverse ns]) return the
eigenvalues and Euler angles corresponding to the rotation matrix
formed from the eigenvectors
in a list:
[ a,b,c, gamma, beta, alpha ]
The eigenvalues are scaled by a factor of 0.1 such that they have
units of (10 * [inverse ns]).
- estimate_Dxyz(in_data, omega_1)
- Estimates eigenvalue of diffusion tensor for given set of initial data
using assumption of isotropic tumbling model
- fill_in_relax_datum(datum, datum_line, pattern)
- # service subroutine which distributes
# the list of given data into given
# rerealx_datum structure according given pattern
- fill_in_results(results, in_Fit_res_list, mode, dlina, dT_e)
- fitRelaxData(data_in=None, Fr=None, InG=None, mode='full', inc_sel='known', Err_calc=1)
- Function which fits NMR NH relaxation data using Nelder-Mead downhill
(amoeba) simplex method
Arguments:
data_in - list of relax_datum structures which is generated by
readInRelaxData
Fr - is the spectrometer frequency in MHz
mode - specifies the model for relaxation data fitting
the available options for mode are:
full - is fully anisotropic tensor
axial - is axially symmetric tensor
iso - is spherically symmetric tensor
InG - optional list of initial guess parameters for fitting
routine which should be compatiable with mode settings:
for full mode InG=[Dx, Dy, Dz, alpha, betha, gamma]
for axial mode InG=[Dxy, Dz, betha, alpha]
for iso mode InG-[Dxyz]
Dx, Dy, Dz are in inverse nanoseconds, alpha, betha, and gamma are
in degrees
if InG is not given then it is estimated for the loaded protein
coordinates using facilities in diffPot
inc_sel - specifies the residues which will which will be included
into the fit when relaxation data are available in data_in.
Could be either a text string or an atom selection object.
Err_calc - number of bootstrap cycles for error calculations
default settings Err_calc=1 which means that only the original data
is used: no synthetic data sets prepared and no confidence
intervals calculated. Bootstrap error estimations is lengthy. For
robust estimation of confidence intervals the number of bootstrap
cycles, Err_calc, should be equal to the number of R2/R1 relaxation
data points in the data set used for fitting, len(in_relax).
However to get an estimate of the order of magnitude for confidence
intervals one may use about 20% of this number.
Returns:
list_results[0], a python structure containing results of fitting
for the original data set of relaxation data
for details see declaration of FitResults() class below.
- make_ratio(datum)
- For given realx_datum structure constructs a ratio of relaxation
rates R2/R1.
- meanTemperature(term)
- term can be a single potential term, or a list of terms
- merge2values(value1, err1, value2, err2)
- mergeRelaxData(data_merged)
- # subroutine with analyzes give list of realx_datum structures,
# sorts the list according to the residue number,
# finds items with the same residue numbers,
# and merges them in a single relaxa_datum.
- readInRST(restraints=None)
- # routine like above which starts from reading restraints
# for use in test file
- readInRelaxData(file, pattern=['resid', 'ratio', 'ratio_err'], verbose=False)
- # pattern specifies the way the data given in the file
# possible keys for pattern are :
# resid - residue number
# ratio - ratio of relaxation rates
# ratio_err - errors in ration of relaxation rates
# R1 - longitudinal relaxation rate
# R1_err - error in longitudinal relaxation rate
# R2 - transverse relaxation rate
# R2_err - error in transverse relaxation rate
# skip - skip entry
# T1 - longitudinal relaxation time
# T1_err - error in longitudinal relaxation time
# T2 - transverse relaxation time
# T2_err - error in transverse relaxation time
# NOE - heteronuclear NOE
# NOE_err - error in heteronuclear NOE
- registerTerm(term)
- add the given DiffPot object to a list associated with its Simulation.
These objects will be automatically processed by topologySetup and
massSetup.
- remove_position_from_list(l_st, p_sn)
- reset_DiffPot_temp(pot=None, temperature=None)
- rms_relax_function(in_param, ifp)
- showFitResults(results)
- show_relax_datum(datum)
- debugging subroutine printing out the content of realx_datum structure
- sqrt(x, /)
- Return the square root of x.
- str2num(line=None)
- tensParams(Dx, Dy, Dz)
- Given eigenvalues of a diffusion tensor, return a tuple
containing (tau, anisotropy , rhombicity), where tau is the
correlation time in ns.
- topologySetup(ivm, list=[])
- configure the given ivm.IVM object's topology setup using the
freedom string for each DiffPot in list.
This function should be called prior to
ivm.IVM.autoTorsion() or protocol.torsionTopology()
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