| | |
- Qfactor(term)
term can be a single potential term, or a list of terms
- addClockAtoms(resid=None, segid=None, tcOatom=None, tcXatom=None, tcYatom=None, ttOatom=None, ttXatom=None, ttYatom=None, tiOatom=None, tiXatom=None, tiYatom=None)
create psf and initial coordinates for all clock atoms used for optimizing
correlation times tau_c, tau_t and tau_i
- analyze(potList)
perform analysis of PREPot terms and return nicely formatted summary
- create_PREPot(name, file=0, assignType='normal', frequency=500, esim=0, restraints='', eSpinQuantumNumber=2.5, rlxType='r2dd', tauc=3.0, taut=0.5, taui=0.050000000000000003, fixTau=False, clockResid=None, clockSegid=None)
create an prePot.PREPot with given name, given the filename of an
PRE assignment table and/or a string of assignments, and an
ensemble simulation.
Specify the NMR Larmor frequency (in MHz) using the frequency argument.
eSpinQuantumNumber specifies the electron spin quantum number of the
spin label.
rlxType specifies the type of paramagnetic relaxation mechanism and can
be one of r2dd, r2curie, r2mix, r1dd, r1curie, or r1mix.
tauc, taut, and taui specify correlation times in ns. By default, tauc is
optimized along with atomic coordinates in the range 0.5tc .. 2tc, where
tc is the specified value.
Changing fixTau to True will disable correlation-time optimization
(clock pseudo atoms will not be added).
clockResid and clockSegid can be set if clock pseudo atoms preexist.
- getNucleusType(pre)
determine the nucleous involved in the experiment
- massSetup(list=[], axisMass=300)
appropriately setup clock masses to axisMass
if list is not specified, then pseudoatoms associated with
all registered PREPot objects are configured.
- registerTerm(term)
add the given PrePot object to a list associated with its Simulation.
These objects will be automatically processed by topologySetup and
massSetup.
- setupSBMFmode(term)
configure the given potential term to use modified model-free
Solomon-Bloembergen equation to calculate PREs.
- setupSBmode(term)
configure the given potential term to use Solomon-Bloembergen equation
to calculate PREs.
- topologySetup(ivm, list=[])
configure the given ivm.IVM object's topology setup using the
freedom string for each PREPot in list.
This function should be called prior to
ivm.IVM.autoTorsion() or protocol.torsionTopology()
|