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- Target_relax_function(in_param, ifp)
- 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
- 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)
- estimate_Dxyz(in_data, omega_1)
- 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 #
# INPUT: #
# data_in is a list of realx_datum structures which is generated by readInRelaxData #
# Fr is spectrometr 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 is optional list of initial guess parameters for fitting routine #
# which shoud 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 DiffPot facilities #
# inc_sel specifies the residues which will which will be included into the fit #
# when relaxation data are available in data_in #
# Err_calc is 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. #
# RETURN: #
# 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. #
- get_InG(dT_e)
- 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. #
- readInRelaxData(file=0, pattern=['resid', 'ratio', 'ratio_err'])
# 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
- 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)
- showFitResults(results)
- show_realx_datum(datum)
# debugging subroutine printing out the content of realx_datum structure
- sqrt(...)
sqrt(x)
Return the square root of x.
- str2num(line=None)
- 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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