prePot
index
/home/schwitrs/bzr-repo/xplor-python3/bin.Linux_x86_64/prePot.py


PREPot Object - potential of restraints for PRE 
 
reference:
J. Iwahara, C. Schwieters and G.M. Clore, JACS 126, 5879-5896 (2004).
(programed by Junji Iwahara)
 
Please use prePotTools.create_PREPot to create this potential term.
 
constructor: PREPot(instanceName,
                    restraintList,
                    dummy,
                    sel1Filter,
                    sel2Filter,
                    simulation)
 
  instanceName : user-specified identifier
  restraintList: optional XPLOR-style restraint table 
  dummy        : optional unused legacy argument.
  sel1Filter   : set the sel1Filter member. See below for description.
  sel2Filter   : set the sel2Filter member. See below for description.
  simulation   : simulation.Simulation specification (optional)
 
Restraint Table Syntax:
 
    -for normal-
      ASSIgn (selection 1) (selection 2) Gobs error
 
    -for nonstereo -
      ASSIgn (selection 1) (selection 2) (selection 3) Gobs1 err1 Gobs2 err2
 
    where Gobs is the PRE expressed in hertz. For nonstereo, the paramagnetic
    center must be selection 1. The presence of selection 3 will toggle
    the restraint's isStereoAssigned flag to False. This sort of restraint
    is used for CH2 or NH2 protons that exhibit two resolved peaks but are not
    stereospecifically assigned.
 
    For  either restraint type the numerical entries can be replaced by
    the literal SUM:
      ASSign (selection 1) (selection 2) SUM [weight]
 
    then SUM-type restraints are indicated, with the Gobs and error
    given by the subsequent ASSIgn statement. SUM restraints can also
    take an optional weight after the SUM literal. The optional weight
    can also be specified in the final entry, after the error value.
 
methods
  addRestraints(restraintList) - add the specified XPLOR-style restraints
 
  calcEnergy()                 - calc energy, returns the energy value.
  calcEnergyAndDerivs(derivs)  - calc energy, derivs, returns the energy value.
 
  rms()         - return the restraint violation
  qFactor()     - return Q-factor
  rFactor()     - return R-factor
  correlation() - return correlation between calculated and observed PRE values.
  violations()  - return number of violations
  simulation()  - return the associated ensembleSimulation.EnsembleSimulation
  showRestraints(violated)  - return info on restraints. Argument violated is
                              boolean specifying whether to return only 
                              violated restraints.
  restraints() - return a sequence of restraints. See the description of the
                     Restraint class below.
  ensWeight(index) - return the ensemble weight associated with the
                     specified member.
  setEnsWeights(vals) - use the specified ensemble weights instead of those
                        in the underlying EnsembleSimulation.
  mkSumRestraints(paraCenter,
                  weights)  - convert restraints which have a selection which 
                              matches paraCenter to SUM restraints- one for
                              each atom in a restraint selection which 
                              matches paraCenter. The weights is an array
                              of weights to given these terms. If it is empty
                              weights of 1 are given.
 
 
The following parameters can be set [defaults in square brackets]
 
  equType    - Type of back-calculation of PRE
               "sb"      : the SB equation   (SB mode)   [default]
               "sbmf"    : the SBMF equation (SBMF mode)
 
  aveType    - Type of averaging
               "r-6"     : averaging with <r^(-6)>
               "sum"     : sum over r^(-6) terms, dividing by aveSize, or:
                           1/aveSize \sum r^{-6}
 
  aveSize    - used only for aveType=="sum". See previous entry.
 
  rlxType    - Type of paramagnetic relaxation mechanism
               "r2dd"    : R2 relaxation enhancement by dipolar mechanism 
               "r2curie" :                           by Curie spin relaxation
               "r2mix"   :     r2dd + r2curie
               "r1dd"    : R1 relaxation enhancement by dipolar mechanism
               "r1curie" :                           by Curie spin relaxation
               "r1mix"   :     r1dd + r1curie
               For the SBMF mode, only r2dd and r1dd are supported.
 
  funType    - Type of penalty function
               "correlation" : optimize correlation between calculated and
                               observed values
               "square"      : Squared well potential
               "harmonic"    : Harmonic potential [default]
               "onesixth"    : ((Gcal)^(-1/6)-(Gobs)^(-1/6))^2
 
  potType    - Energy form for large violations
               "hard"    : quadratic penalty for large errors [default]
               "soft"    : switchover to linear penalty function for large errors
 
               For potType="soft", the asympotic energy function becomes:
 
                    ret *= A + B / pow(r,softExp) + asympSlope * r;
 
               where r = calcd - obs PRE value, and A and B are determined
               such that the energy and its first derivative are continuous at
               r = rSwitch.
 
  sclType    - Type of scaling
               "const"   : Constant scaling. 
                             1.0 for all
               "sigma"   : Scaling based on error. 
                             1.0/(error)^2
               "obsig"   : Scaling based on Gobs and error
                             Gobs/Gmax/(error)^2
 
  sbmfType   - Which correlation time to specify
               "taut"    : specify taut [default]
               "taui"    : specify taui
               The time which is not specified is computed via the equation:
                1/tau_t = 1/tau_c + 1/tau_i
 
  sel1Filter - used to filter the restraints specified in input restraint
               specifications. The first set of atoms used become the
               intersection of those specified in the restraint and sel1Filter.
               The setting of this member only affects restraints read after
               applying the setting.
 
  sel1Filter - same for the second (and third, if specified) set of atoms.
 
  fixTauc    - whether tau_c is fixed (True) or optimized (False) [True].
               If False, clock atoms must be set with setTaucAtoms().
 
  tcMin      - bounds for tauc, when TcType "opt" is specified.
  tcMax
 
  fixTaut    - whether tau_t is fixed (True) or optimized (False) [True]
               If False, clock atoms must be set with setTautAtoms().
  fixTaui    - whether tau_i is fixed (True) or optimized (False) [True]
               If False, clock atoms must be set with setTauiAtoms().
 
  tiMin      - bounds for taui when TiType "opt" is specified.
  tiMax
 
  ensInterconvert - how to treat averaging over EnsembleSimulation members-
                    for SBMF mode. [Default: fast]
                "fast"   : include average over EnsembleSimulation members in
                           calculation of order parameters and distance ave.
                "slow"   : for each EnsembleSimulation member, calculate the
                           averages over ensemble of tags, and then perform
                           a linear EnsembleSimulation-weighted sum to compute
                           Gamma.
 
  rSwitch    - for soft potType, value of calcd-obs PRE for which to switch 
               over to the asymptotic form of the energy function.
  softExp    - exponent for asymptotic form of the energy function.
  asympSlope - slope for asymptotic form of the energy function.
 
  verbose    - if true, sporadically spit out info [False]
  threshold  - threshold in violation calculation [0.1]
  showAllRestraints - boolean which changes the behavior of showViolations. If 
                      this parameter is set to True, the behavior of
                      showViolations is modified such that all restraints are
                      printed. Violated restraints are indicated by an
                      asterisk in the first column. [1]
  useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights
                    or to use those of the underlying EnsembleSimulation.
  npc        - number of paramagnetic centers [1]
               (This is NOT the number of tag conformers)
               For instance, ncp=2 for a homodimer in which the individual
               subunits each have a single paramagentic center. This is, 
               rather, a multiplicative prefactor in the calculation of the
               1/r^6 sum to account for summing due to the presence of
               multiple paramagnetic centers, or equivalent nuclei undergoing
               paramagnetic relaxation.
  rho0       - constant prefactor used for scaling PRE values when tauc is not
               fit [1].
  expTemp    - temperature (only for r2curie, r2mix, r1curie, r1mix) [300]
  taur       - rotational correlation time 
                  (only for r2curie, r2mix, r1curie, r1mix)
  tauc       - correlation time (1/tc = 1/tr + 1/ts)
  taut       - overall correlation time in the SBMF equation (1/tt=1/tc+1/ti)
  freqI      - NMR frequency (MHz)          [500.0]
  gfac       - electron g-factor            [2.0]
  sqn        - electron spin quantum number [2.5]
  gammaI     - nuclear gyromagnetic ratio   [26.752196]
  useDistMultMat - boolean specifying whether to use distMultMat [False].
  distMultMat    - a row-major matrix (or 2D list) of dimension len(sel1)x
                   len(sel2) specifying multipiers of the i,j 1/r^6 distance
                   contributions to the PRE.
 
  Unit of correlation times are nano-seconds.
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
 
Restraint class
 
members/methods:
  name()    - the restraint name
  comment() - the restraint comment (entered after the ! in the PRE table)
 
  sel1      - an atomSel.AtomSel corresponding to the first selection
              in the restraint table. This member is identical to
                selPairs()[0].a
  sel2      - an atomSel.AtomSel corresponding to the second selection
              in the restraint table. This member is identical to
                selPairs()[0].a
  sel3      - an atomSel.AtomSel corresponding to the second selection
              in the restraint table. This member is identical to
                selPairs()[0].a
 
  asString() - a string representation of the restraint.
 
 
  gamma()    - return calculated Gamma
  g()      - observed PRE (Gamma)
  gSigma() - error in observed PRE (Gamma)
  weight() - weight on this restraint - depends on sclType()
 
 
  sumTerms() - for non-sum terms: 0
               for sum terms: -1 for all but last: the number of sum terms.
  sumWeight()- weight of contribution of this sum term.
  contrib()  - return Gamma contribution from this SUM term
 
  status() - return LESS, INSIDE or GREATER for position in square well.
 
  isStereoAssigned() - whether a third selection is present in the assignment
                       statement. See above.
 
 
  vectors
    i6contrib;
    sri6_contrib;
    s2ang_contrib;
    s2rad_contrib;
    sri6_contribB;
    s2ang_contribB;
    s2rad_contribB;
 
  float numbers
    s2angular()
    s2radial() 
    reff();
 
  for NONSTEREO
  vector:
    i6contribB
  floats
    contribB()
    gammaB()
    gB()    
    gBSigma()
    reffB()
    s2angularB()
    s2radialB() 
    s2B()
    sumCalc()
    sumObs() 
    difCalc()
    difObs() 
    smallObs() 
    largeObs() 
    smallCalc()
    largeCalc()
 
    emstatus() - returns EM1 EM2 or EM3 in analogy to status()
 
 
 
 
 
# This file was automatically generated by SWIG (http://www.swig.org).
# Version 4.0.2
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.

 
Classes
       
builtins.object
CDSList_PRERestraint
EnsemblePot
PREPot_LetterClass
Modified
ModifiedBase
PREPot
Restraint_PREPot
PRERestraint
VarEnsWeights
rc_EnsemblePot
rc_ptr_PRERestraint

 
class CDSList_PRERestraint(builtins.object)
    CDSList_PRERestraint(*args)
 

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< CDS::rc_ptr< PRERestraint > >'
__getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< PRERestraint > >'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__len__(self, *args, **kwargs) -> 'int'
__repr__ = _swig_repr(self)
__setitem__(self, *args, **kwargs) -> 'void'
append(self, *args, **kwargs) -> 'void'
help(self, *args, **kwargs) -> 'String'
remove(self, *args, **kwargs) -> 'void'
removeAll(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_CDSList_PRERestraint(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

 
class EnsemblePot(builtins.object)
    EnsemblePot(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
addEnsWeights(self, *args, **kwargs) -> 'void'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcWDerivs(self, *args, **kwargs) -> 'bool const'
clearEnsWeights(self, *args, **kwargs) -> 'void'
energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs2(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs3(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs4(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivsPost(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivsPre(self, *args, **kwargs) -> 'float_type'
ensWeight(self, *args, **kwargs) -> 'float_type'
ensWeights(self, *args, **kwargs) -> 'CDSList< float_type >'
ensWeightsInfo(self, *args, **kwargs) -> 'String'
getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
simulation(self, *args) -> 'EnsembleSimulation const *'
updateEnsWeights(self, *args, **kwargs) -> 'void'
useSimEnsWeights(self, *args, **kwargs) -> 'bool const'

Static methods defined here:
__swig_destroy__ = delete_EnsemblePot(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

 
class Modified(builtins.object)
    Modified(*args, **kwargs)
 

 
  Methods defined here:
__call__(self, *args, **kwargs) -> 'int'
Call self as a function.
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
clear(self, *args, **kwargs) -> 'void'
set(self, *args, **kwargs) -> 'void'
update(self, *args, **kwargs) -> 'void'
value(self, *args, **kwargs) -> 'int'

Static methods defined here:
__swig_destroy__ = delete_Modified(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

Data and other attributes defined here:
MOD_SELF = 1
MOD_SIMULATION = 2

 
class ModifiedBase(builtins.object)
    ModifiedBase(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
registerTo(self, *args, **kwargs) -> 'void'
unRegister(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_ModifiedBase(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
modified

 
registeredSimulations

 
thisown

 
The membership flag

 
class PREPot_LetterClass(EnsemblePot)
    PREPot_LetterClass(*args, **kwargs)
 

 
 
Method resolution order:
PREPot_LetterClass
EnsemblePot
builtins.object

Methods defined here:
AveSqObs(self, *args, **kwargs) -> 'float_type'
Qfactor(self, *args, **kwargs) -> 'float_type'
Rfactor(self, *args, **kwargs) -> 'float_type'
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
addRestraints(self, *args, **kwargs) -> 'void'
assignType(self)
for backwards compatibility
asympSlope(self, *args, **kwargs) -> 'float_type const'
aveS2(self, *args, **kwargs) -> 'float_type'
aveSize(self, *args, **kwargs) -> 'float_type const'
aveType(self, *args, **kwargs) -> 'PREPot::PREAveType'
checkClockAtoms(self, *args, **kwargs) -> 'void'
coeff(self, *args, **kwargs) -> 'double'
coeff2(self, *args, **kwargs) -> 'double'
correlation(self, *args, **kwargs) -> 'float_type'
distMult(self, *args, **kwargs) -> 'CDSMatrix< float_type >'
energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs2(self, *args, **kwargs) -> 'float_type'
ensInterconvert(self, *args, **kwargs) -> 'PREPot::PREEnsInterconvert const'
equType(self, *args, **kwargs) -> 'PREPot::PREEquType'
expTemp(self, *args, **kwargs) -> 'float_type const'
fixTauc(self, *args, **kwargs) -> 'bool const'
fixTaui(self, *args, **kwargs) -> 'bool const'
fixTaut(self, *args, **kwargs) -> 'bool const'
force(self)
freqI(self, *args, **kwargs) -> 'float_type const'
funType(self, *args, **kwargs) -> 'PREPot::PREFunType const'
gammaI(self, *args, **kwargs) -> 'float_type const'
gfac(self, *args, **kwargs) -> 'float_type const'
hardExp(self, *args, **kwargs) -> 'float_type const'
iaAtom(self, *args, **kwargs) -> 'Atom const'
ibAtom(self, *args, **kwargs) -> 'Atom const'
info(self, *args, **kwargs) -> 'String'
ioAtom(self, *args, **kwargs) -> 'Atom const'
kForOpt(self, *args, **kwargs) -> 'double'
kaAtom(self, *args, **kwargs) -> 'Atom const'
kbAtom(self, *args, **kwargs) -> 'Atom const'
koAtom(self, *args, **kwargs) -> 'Atom const'
mScale(self, *args, **kwargs) -> 'float_type const'
minS2(self, *args, **kwargs) -> 'float_type'
mkSumRestraints(self, *args, **kwargs) -> 'void'
npc(self, *args, **kwargs) -> 'int const'
numRestraints(self, *args, **kwargs) -> 'int'
potType(self, *args, **kwargs) -> 'PREPot::PREPotType'
pyXplorHelp(self, *args, **kwargs) -> 'String'
qFactor(self, *args, **kwargs) -> 'float_type'
rFactor(self, *args, **kwargs) -> 'float_type'
rSwitch(self, *args, **kwargs) -> 'float_type const'
restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< PRERestraint > >'
restraintsSize(self, *args, **kwargs) -> 'int'
rho0(self, *args, **kwargs) -> 'float_type const'
rlxType(self, *args, **kwargs) -> 'PREPot::PRERlxType'
rms(self, *args, **kwargs) -> 'float_type'
sbmfType(self, *args, **kwargs) -> 'PREPot::PRESbmfType'
sclType(self, *args, **kwargs) -> 'PREPot::PRESclType'
sel1Filter(self, *args, **kwargs) -> 'AtomSel const'
sel2Filter(self, *args, **kwargs) -> 'AtomSel const'
setAsympSlope(self, *args, **kwargs) -> 'void'
setAveSize(self, *args, **kwargs) -> 'void'
setAveType(self, *args, **kwargs) -> 'void'
setCoeff(self, *args, **kwargs) -> 'void'
setDistMult(self, *args, **kwargs) -> 'void'
setEnsInterconvert(self, *args, **kwargs) -> 'void'
setEquType(self, *args, **kwargs) -> 'void'
setExpTemp(self, *args, **kwargs) -> 'void'
setFixTauc(self, *args, **kwargs) -> 'void'
setFixTaui(self, *args, **kwargs) -> 'void'
setFixTaut(self, *args, **kwargs) -> 'void'
setForce(self, val)
setFreqI(self, *args, **kwargs) -> 'void'
setFunType(self, *args, **kwargs) -> 'void'
setGammaI(self, *args, **kwargs) -> 'void'
setGfac(self, *args, **kwargs) -> 'void'
setHardExp(self, *args, **kwargs) -> 'void'
setIaAtom(self, *args, **kwargs) -> 'void'
setIbAtom(self, *args, **kwargs) -> 'void'
setIoAtom(self, *args, **kwargs) -> 'void'
setKaAtom(self, *args, **kwargs) -> 'void'
setKbAtom(self, *args, **kwargs) -> 'void'
setKoAtom(self, *args, **kwargs) -> 'void'
setMScale(self, *args, **kwargs) -> 'void'
setNpc(self, *args, **kwargs) -> 'void'
setPotType(self, *args, **kwargs) -> 'void'
setRSwitch(self, *args, **kwargs) -> 'void'
setRho0(self, *args, **kwargs) -> 'void'
setRlxType(self, *args, **kwargs) -> 'void'
setSbmfType(self, *args, **kwargs) -> 'void'
setSclType(self, *args, **kwargs) -> 'void'
setSel1Filter(self, *args, **kwargs) -> 'void'
setSel2Filter(self, *args, **kwargs) -> 'void'
setShowAllRestraints(self, *args, **kwargs) -> 'void'
setSoftExp(self, *args, **kwargs) -> 'void'
setSqn(self, *args, **kwargs) -> 'void'
setTaAtom(self, *args, **kwargs) -> 'void'
setTauC(self, val)
setTauI(self, val)
setTauR(self, *args, **kwargs) -> 'void'
setTauT(self, val)
setTauc(self, *args, **kwargs) -> 'void'
setTaucAtoms(self, *args, **kwargs) -> 'void'
setTaui(self, *args, **kwargs) -> 'void'
setTauiAtoms(self, *args, **kwargs) -> 'void'
setTaut(self, *args, **kwargs) -> 'void'
setTautAtoms(self, *args, **kwargs) -> 'void'
setTbAtom(self, *args, **kwargs) -> 'void'
setTcMax(self, *args, **kwargs) -> 'void'
setTcMin(self, *args, **kwargs) -> 'void'
setTcType(self, val)
setTiMax(self, *args, **kwargs) -> 'void'
setTiMin(self, *args, **kwargs) -> 'void'
setTiType(self, val)
setToAtom(self, *args, **kwargs) -> 'void'
setTtType(self, val)
setUseDistMult(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
setWeightMax(self, *args, **kwargs) -> 'void'
showAllRestraints(self, *args, **kwargs) -> 'bool const'
showCurrentTaui(self, *args, **kwargs) -> 'void'
showCurrentTaut(self, *args, **kwargs) -> 'void'
showRestraints(self, *args, **kwargs) -> 'String'
showViolations(self, *args, **kwargs) -> 'String'
softExp(self, *args, **kwargs) -> 'float_type const'
sqn(self, *args, **kwargs) -> 'float_type const'
taAtom(self, *args, **kwargs) -> 'Atom const'
tauc(self, *args, **kwargs) -> 'float_type'
taui(self, *args, **kwargs) -> 'float_type'
taur(self, *args, **kwargs) -> 'float_type const'
taut(self, *args, **kwargs) -> 'float_type'
tbAtom(self, *args, **kwargs) -> 'Atom const'
tc(self, *args, **kwargs) -> 'double'
tcMax(self, *args, **kwargs) -> 'float_type const'
tcMin(self, *args, **kwargs) -> 'float_type const'
tcOatom(self)
tcType(self)
tcXatom(self)
tcYatom(self)
ti(self, *args, **kwargs) -> 'double'
tiMax(self, *args, **kwargs) -> 'float_type const'
tiMin(self, *args, **kwargs) -> 'float_type const'
tiOatom(self)
tiType(self)
tiXatom(self)
tiYatom(self)
toAtom(self, *args, **kwargs) -> 'Atom const'
tt(self, *args, **kwargs) -> 'double'
ttOatom(self)
ttType(self)
ttXatom(self)
ttYatom(self)
useDistMult(self, *args, **kwargs) -> 'bool const'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'
weightMax(self, *args, **kwargs) -> 'float_type const'
weightedAveSqObs(self, *args, **kwargs) -> 'float_type'
weightedQFactor(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_PREPot_LetterClass(...)

Data descriptors defined here:
ave_calcd

 
ave_obs

 
corr

 
denom

 
distMult_

 
nCorr

 
num

 
sumCalcd2

 
sumObs2

 
thisown

 
The membership flag

Data and other attributes defined here:
CONST = 0
CORRELATION = 3
FAST = 0
HARD = 1
HARMONIC = 1
OBSIG = 2
ONESIXTH = 2
R1CURIE = 4
R1DD = 3
R1MIX = 5
R2CURIE = 1
R2DD = 0
R2MIX = 2
R_6 = 0
SB = 0
SBMF = 1
SIGMA = 1
SLOW = 1
SOFT = 0
SQUARE = 0
SUM = 1
TIMODE = 1
TTMODE = 0
ensembleSimulation = <module 'ensembleSimulation' from '/home/schwitr...-python3/bin.Linux_x86_64/ensembleSimulation.py'>
# This file was automatically generated by SWIG (http://www.swig.org).
# Version 4.0.2
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.

Methods inherited from EnsemblePot:
addEnsWeights(self, *args, **kwargs) -> 'void'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcWDerivs(self, *args, **kwargs) -> 'bool const'
clearEnsWeights(self, *args, **kwargs) -> 'void'
energyMaybeDerivs3(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs4(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivsPost(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivsPre(self, *args, **kwargs) -> 'float_type'
ensWeight(self, *args, **kwargs) -> 'float_type'
ensWeights(self, *args, **kwargs) -> 'CDSList< float_type >'
ensWeightsInfo(self, *args, **kwargs) -> 'String'
getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
simulation(self, *args) -> 'EnsembleSimulation const *'
updateEnsWeights(self, *args, **kwargs) -> 'void'
useSimEnsWeights(self, *args, **kwargs) -> 'bool const'

Data descriptors inherited from EnsemblePot:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

 
class PRERestraint(Restraint_PREPot)
    PRERestraint(*args)
 

 
 
Method resolution order:
PRERestraint
Restraint_PREPot
builtins.object

Methods defined here:
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
asString(self, *args, **kwargs) -> 'String'
calcContrib(self, *args, **kwargs) -> 'void'
calcGamma(self, *args, **kwargs) -> 'void'
calcd(self, *args, **kwargs) -> 'float_type'
calcd2(self, *args, **kwargs) -> 'float_type'
comment(self, *args, **kwargs) -> 'String'
contrib(self, *args, **kwargs) -> 'float_type'
contribB(self, *args, **kwargs) -> 'float_type'
deriv(self, *args, **kwargs) -> 'void'
difAB(self, *args, **kwargs) -> 'float_type'
dtdp(self, *args, **kwargs) -> 'void'
emstatus(self, *args, **kwargs) -> 'PRERestraint::EmStatus'
energy(self, *args, **kwargs) -> 'float_type'
energyNonStereo(self, *args, **kwargs) -> 'float_type'
err(self, *args, **kwargs) -> 'float_type'
err2(self, *args, **kwargs) -> 'float_type'
g(self)
gB(self)
gBSigma(self)
gSigma(self)
gamma(self)
gammaB(self)
isStereoAssigned(self, *args, **kwargs) -> 'bool const'
kdfsb(self, *args, **kwargs) -> 'float_type'
largeCalc(self, *args, **kwargs) -> 'float_type'
largeObs(self, *args, **kwargs) -> 'float_type'
obs(self, *args, **kwargs) -> 'float_type'
obs2(self, *args, **kwargs) -> 'float_type'
reff(self, *args, **kwargs) -> 'float_type'
reffB(self, *args, **kwargs) -> 'float_type'
s2(self, *args, **kwargs) -> 'float_type'
s2B(self, *args, **kwargs) -> 'float_type'
s2angular(self, *args, **kwargs) -> 'float_type'
s2angularB(self, *args, **kwargs) -> 'float_type'
s2radial(self, *args, **kwargs) -> 'float_type'
s2radialB(self, *args, **kwargs) -> 'float_type'
setClockDeriv(self, *args, **kwargs) -> 'void'
setEmStatus(self, *args, **kwargs) -> 'void'
setErr(self, *args, **kwargs) -> 'void'
setIsStereoAssigned(self, *args, **kwargs) -> 'void'
setMF(self, *args, **kwargs) -> 'void'
setMF_contrib(self, *args, **kwargs) -> 'void'
setObs(self, *args, **kwargs) -> 'void'
setWF(self, val)
setWeight(self, *args, **kwargs) -> 'void'
smallCalc(self, *args, **kwargs) -> 'float_type'
smallObs(self, *args, **kwargs) -> 'float_type'
status(self, *args, **kwargs) -> 'PRERestraint::Status'
sumAB(self, *args, **kwargs) -> 'float_type'
sumTerms(self, *args, **kwargs) -> 'int'
sumWeight(self, *args, **kwargs) -> 'float_type'
weight(self, *args, **kwargs) -> 'float_type const'

Static methods defined here:
__swig_destroy__ = delete_PRERestraint(...)

Data descriptors defined here:
sel1

 
sel2

 
sel3

 
sumList

 
thisown

 
The membership flag
verbose

 

Data and other attributes defined here:
EM1 = 0
EM2 = 1
EM3 = 2
FOR_TC = 0
FOR_TI = 2
FOR_TT = 1
GREATER = 1
INSIDE = 2
LESS = 0

Methods inherited from Restraint_PREPot:
diff(self, *args, **kwargs) -> 'float_type'
name(self, *args, **kwargs) -> 'String const'
setName(self, *args, **kwargs) -> 'void'
violated(self, *args, **kwargs) -> 'bool'

Data descriptors inherited from Restraint_PREPot:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

 
class Restraint_PREPot(builtins.object)
    Restraint_PREPot(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
diff(self, *args, **kwargs) -> 'float_type'
name(self, *args, **kwargs) -> 'String const'
setName(self, *args, **kwargs) -> 'void'
violated(self, *args, **kwargs) -> 'bool'

Static methods defined here:
__swig_destroy__ = delete_Restraint_PREPot(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

 
class VarEnsWeights(builtins.object)
    VarEnsWeights(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)

Static methods defined here:
__swig_destroy__ = delete_VarEnsWeights(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
ensWeights

 
mult

 
thisown

 
The membership flag

 
class rc_EnsemblePot(builtins.object)
    rc_EnsemblePot(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)

Static methods defined here:
__swig_destroy__ = delete_rc_EnsemblePot(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

 
class rc_ptr_PRERestraint(builtins.object)
    rc_ptr_PRERestraint(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'PRERestraint *'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__ref__(self, *args, **kwargs) -> 'PRERestraint &'
__repr__ = _swig_repr(self)
asString(self, *args, **kwargs) -> 'String'
calcContrib(self, *args, **kwargs) -> 'void'
calcGamma(self, *args, **kwargs) -> 'void'
calcd(self, *args, **kwargs) -> 'float_type'
calcd2(self, *args, **kwargs) -> 'float_type'
comment(self, *args, **kwargs) -> 'String'
contrib(self, *args, **kwargs) -> 'float_type'
contribB(self, *args, **kwargs) -> 'float_type'
count(self, *args, **kwargs) -> 'int'
decr(self, *args, **kwargs) -> 'void'
deriv(self, *args, **kwargs) -> 'void'
difAB(self, *args, **kwargs) -> 'float_type'
diff(self, *args, **kwargs) -> 'float_type'
dtdp(self, *args, **kwargs) -> 'void'
emstatus(self, *args, **kwargs) -> 'PRERestraint::EmStatus'
energy(self, *args, **kwargs) -> 'float_type'
energyNonStereo(self, *args, **kwargs) -> 'float_type'
err(self, *args, **kwargs) -> 'float_type'
err2(self, *args, **kwargs) -> 'float_type'
forceDelete(self, *args, **kwargs) -> 'void'
g(self)
gB(self)
gBSigma(self)
gSigma(self)
gamma(self)
gammaB(self)
incr(self, *args, **kwargs) -> 'void'
isStereoAssigned(self, *args, **kwargs) -> 'bool const'
kdfsb(self, *args, **kwargs) -> 'float_type'
largeCalc(self, *args, **kwargs) -> 'float_type'
largeObs(self, *args, **kwargs) -> 'float_type'
name(self, *args, **kwargs) -> 'String const'
obs(self, *args, **kwargs) -> 'float_type'
obs2(self, *args, **kwargs) -> 'float_type'
ptr(self, *args, **kwargs) -> 'PRERestraint *'
reff(self, *args, **kwargs) -> 'float_type'
reffB(self, *args, **kwargs) -> 'float_type'
release(self, *args, **kwargs) -> 'PRERestraint *'
reset(self, *args, **kwargs) -> 'void'
s2(self, *args, **kwargs) -> 'float_type'
s2B(self, *args, **kwargs) -> 'float_type'
s2angular(self, *args, **kwargs) -> 'float_type'
s2angularB(self, *args, **kwargs) -> 'float_type'
s2radial(self, *args, **kwargs) -> 'float_type'
s2radialB(self, *args, **kwargs) -> 'float_type'
setClockDeriv(self, *args, **kwargs) -> 'void'
setEmStatus(self, *args, **kwargs) -> 'void'
setErr(self, *args, **kwargs) -> 'void'
setIsStereoAssigned(self, *args, **kwargs) -> 'void'
setMF(self, *args, **kwargs) -> 'void'
setMF_contrib(self, *args, **kwargs) -> 'void'
setName(self, *args, **kwargs) -> 'void'
setObs(self, *args, **kwargs) -> 'void'
setWF(self, val)
setWeight(self, *args, **kwargs) -> 'void'
smallCalc(self, *args, **kwargs) -> 'float_type'
smallObs(self, *args, **kwargs) -> 'float_type'
status(self, *args, **kwargs) -> 'PRERestraint::Status'
sumAB(self, *args, **kwargs) -> 'float_type'
sumTerms(self, *args, **kwargs) -> 'int'
sumWeight(self, *args, **kwargs) -> 'float_type'
violated(self, *args, **kwargs) -> 'bool'
weight(self, *args, **kwargs) -> 'float_type const'

Static methods defined here:
__swig_destroy__ = delete_rc_ptr_PRERestraint(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
sel1

 
sel2

 
sel3

 
sumList

 
thisown

 
The membership flag
verbose

 

 
realPREPot = class PREPot(builtins.object)
    realPREPot(*args)
 

 
  Methods defined here:
AveSqObs(self, *args, **kwargs) -> 'float_type'
Qfactor(self, *args, **kwargs) -> 'float_type'
Rfactor(self, *args, **kwargs) -> 'float_type'
__deref__(self, *args, **kwargs) -> 'PREPot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'PREPot &'
__repr__ = _swig_repr(self)
addEnsWeights(self, *args, **kwargs) -> 'void'
addRestraints(self, *args, **kwargs) -> 'void'
assignType(self)
for backwards compatibility
asympSlope(self, *args, **kwargs) -> 'float_type const'
aveS2(self, *args, **kwargs) -> 'float_type'
aveSize(self, *args, **kwargs) -> 'float_type const'
aveType(self, *args, **kwargs) -> 'PREPot::PREAveType'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcWDerivs(self, *args, **kwargs) -> 'bool const'
checkClockAtoms(self, *args, **kwargs) -> 'void'
clearEnsWeights(self, *args, **kwargs) -> 'void'
coeff(self, *args, **kwargs) -> 'double'
coeff2(self, *args, **kwargs) -> 'double'
correlation(self, *args, **kwargs) -> 'float_type'
decrRefCnt(self, *args, **kwargs) -> 'void'
distMult(self, *args, **kwargs) -> 'CDSMatrix< float_type >'
energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs2(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs3(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs4(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivsPost(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivsPre(self, *args, **kwargs) -> 'float_type'
ensInterconvert(self, *args, **kwargs) -> 'PREPot::PREEnsInterconvert const'
ensWeight(self, *args, **kwargs) -> 'float_type'
ensWeights(self, *args, **kwargs) -> 'CDSList< float_type >'
ensWeightsInfo(self, *args, **kwargs) -> 'String'
equType(self, *args, **kwargs) -> 'PREPot::PREEquType'
expTemp(self, *args, **kwargs) -> 'float_type const'
fixTauc(self, *args, **kwargs) -> 'bool const'
fixTaui(self, *args, **kwargs) -> 'bool const'
fixTaut(self, *args, **kwargs) -> 'bool const'
force(self)
freqI(self, *args, **kwargs) -> 'float_type const'
funType(self, *args, **kwargs) -> 'PREPot::PREFunType const'
gammaI(self, *args, **kwargs) -> 'float_type const'
getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &'
gfac(self, *args, **kwargs) -> 'float_type const'
hardExp(self, *args, **kwargs) -> 'float_type const'
iaAtom(self, *args, **kwargs) -> 'Atom const'
ibAtom(self, *args, **kwargs) -> 'Atom const'
incrRefCnt(self, *args, **kwargs) -> 'void'
info(self, *args, **kwargs) -> 'String'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
ioAtom(self, *args, **kwargs) -> 'Atom const'
kForOpt(self, *args, **kwargs) -> 'double'
kaAtom(self, *args, **kwargs) -> 'Atom const'
kbAtom(self, *args, **kwargs) -> 'Atom const'
koAtom(self, *args, **kwargs) -> 'Atom const'
mScale(self, *args, **kwargs) -> 'float_type const'
minS2(self, *args, **kwargs) -> 'float_type'
mkSumRestraints(self, *args, **kwargs) -> 'void'
npc(self, *args, **kwargs) -> 'int const'
numRestraints(self, *args, **kwargs) -> 'int'
potName(self, *args, **kwargs) -> 'char const *'
potType(self, *args, **kwargs) -> 'PREPot::PREPotType'
pyXplorHelp(self, *args, **kwargs) -> 'String'
qFactor(self, *args, **kwargs) -> 'float_type'
rFactor(self, *args, **kwargs) -> 'float_type'
rSwitch(self, *args, **kwargs) -> 'float_type const'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< PRERestraint > >'
restraintsSize(self, *args, **kwargs) -> 'int'
rho0(self, *args, **kwargs) -> 'float_type const'
rlxType(self, *args, **kwargs) -> 'PREPot::PRERlxType'
rms(self, *args, **kwargs) -> 'float_type'
sbmfType(self, *args, **kwargs) -> 'PREPot::PRESbmfType'
scale(self, *args, **kwargs) -> 'float_type const'
sclType(self, *args, **kwargs) -> 'PREPot::PRESclType'
sel1Filter(self, *args, **kwargs) -> 'AtomSel const'
sel2Filter(self, *args, **kwargs) -> 'AtomSel const'
setAsympSlope(self, *args, **kwargs) -> 'void'
setAveSize(self, *args, **kwargs) -> 'void'
setAveType(self, *args, **kwargs) -> 'void'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setCoeff(self, *args, **kwargs) -> 'void'
setDistMult(self, *args, **kwargs) -> 'void'
setEnsInterconvert(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setEquType(self, *args, **kwargs) -> 'void'
setExpTemp(self, *args, **kwargs) -> 'void'
setFixTauc(self, *args, **kwargs) -> 'void'
setFixTaui(self, *args, **kwargs) -> 'void'
setFixTaut(self, *args, **kwargs) -> 'void'
setForce(self, val)
setFreqI(self, *args, **kwargs) -> 'void'
setFunType(self, *args, **kwargs) -> 'void'
setGammaI(self, *args, **kwargs) -> 'void'
setGfac(self, *args, **kwargs) -> 'void'
setHardExp(self, *args, **kwargs) -> 'void'
setIaAtom(self, *args, **kwargs) -> 'void'
setIbAtom(self, *args, **kwargs) -> 'void'
setIoAtom(self, *args, **kwargs) -> 'void'
setKaAtom(self, *args, **kwargs) -> 'void'
setKbAtom(self, *args, **kwargs) -> 'void'
setKoAtom(self, *args, **kwargs) -> 'void'
setMScale(self, *args, **kwargs) -> 'void'
setNpc(self, *args, **kwargs) -> 'void'
setPotType(self, *args, **kwargs) -> 'void'
setRSwitch(self, *args, **kwargs) -> 'void'
setRho0(self, *args, **kwargs) -> 'void'
setRlxType(self, *args, **kwargs) -> 'void'
setSbmfType(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setSclType(self, *args, **kwargs) -> 'void'
setSel1Filter(self, *args, **kwargs) -> 'void'
setSel2Filter(self, *args, **kwargs) -> 'void'
setShowAllRestraints(self, *args, **kwargs) -> 'void'
setSoftExp(self, *args, **kwargs) -> 'void'
setSqn(self, *args, **kwargs) -> 'void'
setTaAtom(self, *args, **kwargs) -> 'void'
setTauC(self, val)
setTauI(self, val)
setTauR(self, *args, **kwargs) -> 'void'
setTauT(self, val)
setTauc(self, *args, **kwargs) -> 'void'
setTaucAtoms(self, *args, **kwargs) -> 'void'
setTaui(self, *args, **kwargs) -> 'void'
setTauiAtoms(self, *args, **kwargs) -> 'void'
setTaut(self, *args, **kwargs) -> 'void'
setTautAtoms(self, *args, **kwargs) -> 'void'
setTbAtom(self, *args, **kwargs) -> 'void'
setTcMax(self, *args, **kwargs) -> 'void'
setTcMin(self, *args, **kwargs) -> 'void'
setTcType(self, val)
setThreshold(self, *args, **kwargs) -> 'void'
setTiMax(self, *args, **kwargs) -> 'void'
setTiMin(self, *args, **kwargs) -> 'void'
setTiType(self, val)
setToAtom(self, *args, **kwargs) -> 'void'
setTtType(self, val)
setUseDistMult(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
setWeightMax(self, *args, **kwargs) -> 'void'
showAllRestraints(self, *args, **kwargs) -> 'bool const'
showCurrentTaui(self, *args, **kwargs) -> 'void'
showCurrentTaut(self, *args, **kwargs) -> 'void'
showRestraints(self, *args, **kwargs) -> 'String'
showViolations(self, *args, **kwargs) -> 'String'
simulation(self, *args) -> 'EnsembleSimulation const *'
softExp(self, *args, **kwargs) -> 'float_type const'
sqn(self, *args, **kwargs) -> 'float_type const'
taAtom(self, *args, **kwargs) -> 'Atom const'
tauc(self, *args, **kwargs) -> 'float_type'
taui(self, *args, **kwargs) -> 'float_type'
taur(self, *args, **kwargs) -> 'float_type const'
taut(self, *args, **kwargs) -> 'float_type'
tbAtom(self, *args, **kwargs) -> 'Atom const'
tc(self, *args, **kwargs) -> 'double'
tcMax(self, *args, **kwargs) -> 'float_type const'
tcMin(self, *args, **kwargs) -> 'float_type const'
tcOatom(self)
tcType(self)
tcXatom(self)
tcYatom(self)
threshold(self, *args, **kwargs) -> 'float_type const'
ti(self, *args, **kwargs) -> 'double'
tiMax(self, *args, **kwargs) -> 'float_type const'
tiMin(self, *args, **kwargs) -> 'float_type const'
tiOatom(self)
tiType(self)
tiXatom(self)
tiYatom(self)
toAtom(self, *args, **kwargs) -> 'Atom const'
tt(self, *args, **kwargs) -> 'double'
ttOatom(self)
ttType(self)
ttXatom(self)
ttYatom(self)
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateEnsWeights(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
useDistMult(self, *args, **kwargs) -> 'bool const'
useSimEnsWeights(self, *args, **kwargs) -> 'bool const'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'
weightMax(self, *args, **kwargs) -> 'float_type const'
weightedAveSqObs(self, *args, **kwargs) -> 'float_type'
weightedQFactor(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_PREPot(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
ave_calcd

 
ave_obs

 
corr

 
denom

 
distMult_

 
instanceDataCleanup

 
instanceDataCreate

 
instanceData_

 
modified

 
nCorr

 
num

 
registeredSimulations

 
sumCalcd2

 
sumObs2

 
thisown

 
The membership flag

Data and other attributes defined here:
ensembleSimulation = <module 'ensembleSimulation' from '/home/schwitr...-python3/bin.Linux_x86_64/ensembleSimulation.py'>
# This file was automatically generated by SWIG (http://www.swig.org).
# Version 4.0.2
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.

 
Functions
       
PREPot(*args)
pyXplorHelp(*args) -> 'String'