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- Da(potTerm)
- DaMax(type, dist=0)
return scale factor to scale other experiments to the NNH norm
convention.
- DaScale(term, dist=0)
return scale factor to scale other experiments to the current
convention, set by calling either scale_toNH or scale_toCH.
- RDC_analyze(potList)
perform analysis of RDCPot terms and return nicely formatted summary
- Rfactor(rdc)
R-factor (in percent).
Eq. 5 from Clore+Garrett, JACS 121, 9008 (1999).
Da is scaled using the current scaling convention.
- Rfactor_infinite(rdc)
R-factor (in percent) for an infinite number of
randomly distributed vectors.
Eq. 3 from Clore+Garrett, JACS 121, 9008 (1999).
- Rh(potTerm)
- correctGyromagneticSigns()
use the correct (negative) sign for 15N's gyromagnetic ratio.
Call this function before any other in this module.
- create_DaRatioPot(name, rdc1, rdc2, ratio)
NOTE: needs to be updated and transfered to varTensorTools.
create a potential term which restrains the ratio of
rdc1.Da/rdc2.Da to be ratio
- create_RDCPot(name, file=0, oTensor=0, esim=0, restraints='')
create an rdcPot.RDCPot1 with given name, given orientational
varTensor.VarTensor, the filename of an rdc assignment table and/or
a string of assignments, and an ensemble simulation.
The file argument can optionally be a sequence of filenames.
- create_twoDaRatiosPot(name, rdc1, rdc2, rdc3, rdc4)
NOTE: needs to be updated and transfered to varTensorTools.
create a potential term which restrains the ratio of
rdc1.Da/rdc2.Da to be that of rdc3.Da/rdc4.Da
For EnsembleSimulations, three terms are returned in a PotList. These
are named 'inter', 'ratio1', and 'ratio2'. The first restrains the
ensemble average of the two ratios to be the same. The 'ratio' terms
restrain the ratio of each ensemble member to be the same. The terms
can be weighted separately using the scale member.
- deviation_percent(rdc)
deviation as a percent of total range of dipolar coupling values.
Da is scaled using the current scaling convention.
- getRDCType(rdc)
determine the atoms involved in the RDC experiment - from the
atom selections.
- makeTable(rdc)
given an rdcPot, generate the associated assignment
table. Return this as a string.
- orderParameter(aSel, bSel, simulation=0)
calculate the order parameter S^2 given two atom selections defining
a bond vector. The simulation parameter specifies an EnsembleSimulation
and defaults to the current simulation. It is assumed that the atomSels
correspond to single atoms: averaging is not performed
- recalculatePrefactors()
recalculate gamma_A * gamma_B / rAB^3 prefactors.
Call this function after changing gyromagnetic ratios or bond distance
values.
- scale_toCH(rdc, type=0)
scales the given expression for dipolar coupling such that
given Da = scale * Da_CH
For thymine, methyl RDCs are detected, and the
appropriate -3.17 D_CC value [Ottinger and Bax JACS 121, 4690 (1999)] is
used. If this behavior is not desired please manually specify the type
argument.
Also, for proton 'HH' experiments, enables the rdc distance dependence.
Valid types are:
'NHN', 'NCO', 'HNCO', 'CACO', 'CACB', 'CAHA', 'HH', 'HP'
- scale_toNH(rdc, type=0)
scales the given expression for dipolar coupling such that
given Da = scale * Da_NHN
For thymine, methyl RDCs are detected, and the
appropriate -3.17 D_CC value [Ottinger and Bax JACS 121, 4690 (1999)] is
used. If this behavior is not desired please manually specify the type
argument.
Also, for proton 'HH' experiments, enables the rdc distance dependence.
Valid types are:
'NHN', 'NCO', 'HNCO', 'CACO', 'CACB', 'CAHA', 'HH', 'HP'
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