prePot
index
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)
 
constructor: PREPot(instanceName,
                    sim1,sim2,
                    restraintList,
                    assignType)
 
  instanceName : user-specified identifier
  sim1, sim2   : Simulation specifications (optional)
  assignType   : "normal"[defaul] or "nonstereo" (optional)
                 Use nonstereo for CH2 or NH2 protons that exhibit
                 two resolved peaks but are not stereospecifically assigned.
  restraintList: optional XPLOR-style restraint table
    -for normal-
      assign (selection 1) (selection 2) Gobs error
    -for nonstereo -
      assign (selection 1) (selection 2) (selection 3) Gobs1 err1 Gobs2 err2
      For nonstereo, paramagnetic center must be selection 1.
    for either of these type the numerical entries can be replaced by
    the literal SUM, and 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, or after the error
    entry.
 
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
  violations()  - return number of violations
  showRestraints(violated)  - return info on restraints. Argument violated is
                              boolean specifying whether to return only 
                              violated restraints.
 
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)>
               "r-3"     :                <r^(-3)>^2  (only for SB mode)
               "center"  : center of selected atoms   (only for SB mode)
 
  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 penaltiyy function
               "square"  : Squared well potential
               "harmonic": Harmonic potential [default]
               "onesixth": ((Gcal)^(-1/6)-(Gobs)^(-1/6))^2
 
  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   - Type of SBMF mode
               "taut"    : Optimize taut [default]
               "taui"    : Optimize taui
 
  TcType     - Type of tc 
               "opt"     : Optimized in range of tcmin < tc < tcmax
                           Clock atoms must be set with setTauCAtoms().
               "fix"     : fixed value ( tauc )
 
  TtType     - Type of tt
               "opt"     : Optimized in range of 0 < tt < tc
                           Clock atoms must be set with setTauTAtoms().
               "fix"     : fixed value ( taut )
 
  TiType     - Type of ti
               "opt"     : Optimized in range of timin < ti < timax
                           Clock atoms must be set with setTauIAtoms().
               "fix"     : fixed value ( taui )
 
 
  verbose    - if true, sporadically spit out info [False]
  force      - force constant
  threshold  - threshold in violation calculation [0.1]
  npc        - number of paramagnetic centers [1]
               (This is NOT the number of multi-conformer)
  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/te)
  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]
 
  Unit of correlation times are nano-second.
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 

 
Classes
       
__builtin__.object
CDSList_PRERestraint
CDSList_PRERestraintPtr
Modified
ModifiedPtr
ModifiedBase
ModifiedBasePtr
PREPot
PREPotPtr
PREPot_LetterClass
PREPot_LetterClassPtr
PRERestraint
PRERestraintPtr

 
class CDSList_PRERestraint(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_CDSList_PRERestraint>)
__delitem__(*args)
__getattr__ lambda self, name
__getitem__(*args)
__getslice__(*args)
__init__(self, *args)
__len__(*args)
__repr__(self)
__setattr__ lambda self, name, value
__setitem__(*args)
help(*args)

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x13a8ef8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_PRERestraint' objects>
list of weak references to the object (if defined)

 
class CDSList_PRERestraintPtr(CDSList_PRERestraint)
    
Method resolution order:
CDSList_PRERestraintPtr
CDSList_PRERestraint
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from CDSList_PRERestraint:
__del__(self, destroy=<built-in function delete_CDSList_PRERestraint>)
__delitem__(*args)
__getattr__ lambda self, name
__getitem__(*args)
__getslice__(*args)
__len__(*args)
__repr__(self)
__setattr__ lambda self, name, value
__setitem__(*args)
help(*args)

Data and other attributes inherited from CDSList_PRERestraint:
__dict__ = <dictproxy object at 0x13a8f30>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_PRERestraint' objects>
list of weak references to the object (if defined)

 
class Modified(__builtin__.object)
     Methods defined here:
__call__(*args)
__del__(self, destroy=<built-in function delete_Modified>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
clear(*args)
set(*args)
update(*args)
value(*args)

Data and other attributes defined here:
MOD_SELF = 1
MOD_SIMULATION = 2
__dict__ = <dictproxy object at 0x13d0088>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Modified' objects>
list of weak references to the object (if defined)

 
class ModifiedBase(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_ModifiedBase>)
__getattr__ lambda self, name
__init__(self)
__repr__(self)
__setattr__ lambda self, name, value
registerTo(*args)
unRegister(*args)
updateValues(*args)

Properties defined here:
modified
get = ModifiedBase_modified_get(...)
set = ModifiedBase_modified_set(...)
registeredSimulations
get = ModifiedBase_registeredSimulations_get(...)
set = ModifiedBase_registeredSimulations_set(...)

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x13a8d00>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'modified': <built-in function ModifiedBase_modified_get>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_get>}
__swig_setmethods__ = {'modified': <built-in function ModifiedBase_modified_set>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'ModifiedBase' objects>
list of weak references to the object (if defined)

 
class ModifiedBasePtr(ModifiedBase)
    
Method resolution order:
ModifiedBasePtr
ModifiedBase
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from ModifiedBase:
__del__(self, destroy=<built-in function delete_ModifiedBase>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
registerTo(*args)
unRegister(*args)
updateValues(*args)

Properties inherited from ModifiedBase:
modified
get = ModifiedBase_modified_get(...)
set = ModifiedBase_modified_set(...)
registeredSimulations
get = ModifiedBase_registeredSimulations_get(...)
set = ModifiedBase_registeredSimulations_set(...)

Data and other attributes inherited from ModifiedBase:
__dict__ = <dictproxy object at 0x13a8cc8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'modified': <built-in function ModifiedBase_modified_get>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_get>}
__swig_setmethods__ = {'modified': <built-in function ModifiedBase_modified_set>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'ModifiedBase' objects>
list of weak references to the object (if defined)

 
class ModifiedPtr(Modified)
    
Method resolution order:
ModifiedPtr
Modified
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from Modified:
__call__(*args)
__del__(self, destroy=<built-in function delete_Modified>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
clear(*args)
set(*args)
update(*args)
value(*args)

Data and other attributes inherited from Modified:
MOD_SELF = 1
MOD_SIMULATION = 2
__dict__ = <dictproxy object at 0x13a8cc8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Modified' objects>
list of weak references to the object (if defined)

 
class PREPot(__builtin__.object)
     Methods defined here:
AveSqObs(*args)
Qfactor(*args)
Rfactor(*args)
__del__(self, destroy=<built-in function delete_PREPot>)
__deref__(*args)
__getattr__ lambda self, name
__init__(self, *args)
__mul__(*args)
__oldinit__ = __init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
addRestraints(*args)
assignType(*args)
asympSlope(*args)
aveS2(*args)
aveType(*args)
calcDerivs(*args)
calcEnergy(*args)
calcEnergyAndDerivs(*args)
checkClockAtoms(*args)
coeff(*args)
coeff2(*args)
equType(*args)
expTemp(*args)
force(*args)
freqI(*args)
funType(*args)
gammaI(*args)
gfac(*args)
hardExp(*args)
help(*args)
iaAtom(*args)
ibAtom(*args)
incrRefCount(*args)
info(*args)
instanceData(*args)
instanceName(*args)
ioAtom(*args)
kForOpt(*args)
kaAtom(*args)
kbAtom(*args)
koAtom(*args)
mScale(*args)
minS2(*args)
npc(*args)
numRestraints(*args)
omegaRatio(*args)
pointer(*args)
potName(*args)
potType(*args)
qFactor(*args)
rFactor(*args)
rSwitch(*args)
registerInstanceData(*args)
registerTo(*args)
resetPotName(*args)
restraints(*args)
restraintsSize(*args)
rlxType(*args)
rms(*args)
sbmfType(*args)
scale(*args)
sclType(*args)
setAsympSlope(*args)
setAveType(*args)
setCoeff(*args)
setEquType(*args)
setExpTemp(*args)
setForce(*args)
setFreqI(*args)
setFunType(*args)
setGammaI(*args)
setGfac(*args)
setHardExp(*args)
setIaAtom(*args)
setIbAtom(*args)
setIoAtom(*args)
setKaAtom(*args)
setKbAtom(*args)
setKoAtom(*args)
setMScale(*args)
setNpc(*args)
setOmegaRatio(*args)
setPotType(*args)
setRSwitch(*args)
setRlxType(*args)
setSbmfType(*args)
setScale(*args)
setSclType(*args)
setSoftExp(*args)
setSqn(*args)
setTaAtom(*args)
setTauC(*args)
setTauI(*args)
setTauR(*args)
setTauT(*args)
setTaucAtoms(*args)
setTauiAtoms(*args)
setTautAtoms(*args)
setTbAtom(*args)
setTcMax(*args)
setTcMin(*args)
setTcType(*args)
setThreshold(*args)
setTiMax(*args)
setTiMin(*args)
setTiType(*args)
setToAtom(*args)
setTtType(*args)
setVerbose(*args)
setWeightMax(*args)
showCurrentTauc(*args)
showCurrentTaui(*args)
showCurrentTaut(*args)
showRestraints(*args)
showViolations(*args)
softExp(*args)
sqn(*args)
taAtom(*args)
tauc(*args)
taui(*args)
taur(*args)
taut(*args)
tbAtom(*args)
tc(*args)
tcType(*args)
tcmax(*args)
tcmin(*args)
threshold(*args)
ti(*args)
tiType(*args)
timax(*args)
timin(*args)
toAtom(*args)
tt(*args)
ttType(*args)
unRegister(*args)
updateValues(*args)
verbose(*args)
violations(*args)
weightMax(*args)
weightedAveSqObs(*args)
weightedQFactor(*args)

Properties defined here:
instanceData_
get = PREPot_instanceData__get(...)
set = PREPot_instanceData__set(...)
modified
get = PREPot_modified_get(...)
set = PREPot_modified_set(...)
registeredSimulations
get = PREPot_registeredSimulations_get(...)
set = PREPot_registeredSimulations_set(...)

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x13c51a0>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'instanceData_': <built-in function PREPot_instanceData__get>, 'modified': <built-in function PREPot_modified_get>, 'registeredSimulations': <built-in function PREPot_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function PREPot_instanceData__set>, 'modified': <built-in function PREPot_modified_set>, 'registeredSimulations': <built-in function PREPot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'PREPot' objects>
list of weak references to the object (if defined)

 
class PREPotPtr(PREPot)
    
Method resolution order:
PREPotPtr
PREPot
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from PREPot:
AveSqObs(*args)
Qfactor(*args)
Rfactor(*args)
__del__(self, destroy=<built-in function delete_PREPot>)
__deref__(*args)
__getattr__ lambda self, name
__mul__(*args)
__oldinit__ = __init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
addRestraints(*args)
assignType(*args)
asympSlope(*args)
aveS2(*args)
aveType(*args)
calcDerivs(*args)
calcEnergy(*args)
calcEnergyAndDerivs(*args)
checkClockAtoms(*args)
coeff(*args)
coeff2(*args)
equType(*args)
expTemp(*args)
force(*args)
freqI(*args)
funType(*args)
gammaI(*args)
gfac(*args)
hardExp(*args)
help(*args)
iaAtom(*args)
ibAtom(*args)
incrRefCount(*args)
info(*args)
instanceData(*args)
instanceName(*args)
ioAtom(*args)
kForOpt(*args)
kaAtom(*args)
kbAtom(*args)
koAtom(*args)
mScale(*args)
minS2(*args)
npc(*args)
numRestraints(*args)
omegaRatio(*args)
pointer(*args)
potName(*args)
potType(*args)
qFactor(*args)
rFactor(*args)
rSwitch(*args)
registerInstanceData(*args)
registerTo(*args)
resetPotName(*args)
restraints(*args)
restraintsSize(*args)
rlxType(*args)
rms(*args)
sbmfType(*args)
scale(*args)
sclType(*args)
setAsympSlope(*args)
setAveType(*args)
setCoeff(*args)
setEquType(*args)
setExpTemp(*args)
setForce(*args)
setFreqI(*args)
setFunType(*args)
setGammaI(*args)
setGfac(*args)
setHardExp(*args)
setIaAtom(*args)
setIbAtom(*args)
setIoAtom(*args)
setKaAtom(*args)
setKbAtom(*args)
setKoAtom(*args)
setMScale(*args)
setNpc(*args)
setOmegaRatio(*args)
setPotType(*args)
setRSwitch(*args)
setRlxType(*args)
setSbmfType(*args)
setScale(*args)
setSclType(*args)
setSoftExp(*args)
setSqn(*args)
setTaAtom(*args)
setTauC(*args)
setTauI(*args)
setTauR(*args)
setTauT(*args)
setTaucAtoms(*args)
setTauiAtoms(*args)
setTautAtoms(*args)
setTbAtom(*args)
setTcMax(*args)
setTcMin(*args)
setTcType(*args)
setThreshold(*args)
setTiMax(*args)
setTiMin(*args)
setTiType(*args)
setToAtom(*args)
setTtType(*args)
setVerbose(*args)
setWeightMax(*args)
showCurrentTauc(*args)
showCurrentTaui(*args)
showCurrentTaut(*args)
showRestraints(*args)
showViolations(*args)
softExp(*args)
sqn(*args)
taAtom(*args)
tauc(*args)
taui(*args)
taur(*args)
taut(*args)
tbAtom(*args)
tc(*args)
tcType(*args)
tcmax(*args)
tcmin(*args)
threshold(*args)
ti(*args)
tiType(*args)
timax(*args)
timin(*args)
toAtom(*args)
tt(*args)
ttType(*args)
unRegister(*args)
updateValues(*args)
verbose(*args)
violations(*args)
weightMax(*args)
weightedAveSqObs(*args)
weightedQFactor(*args)

Properties inherited from PREPot:
instanceData_
get = PREPot_instanceData__get(...)
set = PREPot_instanceData__set(...)
modified
get = PREPot_modified_get(...)
set = PREPot_modified_set(...)
registeredSimulations
get = PREPot_registeredSimulations_get(...)
set = PREPot_registeredSimulations_set(...)

Data and other attributes inherited from PREPot:
__dict__ = <dictproxy object at 0x13c7478>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'instanceData_': <built-in function PREPot_instanceData__get>, 'modified': <built-in function PREPot_modified_get>, 'registeredSimulations': <built-in function PREPot_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function PREPot_instanceData__set>, 'modified': <built-in function PREPot_modified_set>, 'registeredSimulations': <built-in function PREPot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'PREPot' objects>
list of weak references to the object (if defined)

 
class PREPot_LetterClass(__builtin__.object)
     Methods defined here:
AveSqObs(*args)
Qfactor(*args)
Rfactor(*args)
__del__(self, destroy=<built-in function delete_PREPot_LetterClass>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
addRestraints(*args)
assignType(*args)
asympSlope(*args)
aveS2(*args)
aveType(*args)
calcDerivs(*args)
calcEnergy(*args)
calcEnergyAndDerivs(*args)
checkClockAtoms(*args)
coeff(*args)
coeff2(*args)
equType(*args)
expTemp(*args)
force(*args)
freqI(*args)
funType(*args)
gammaI(*args)
gfac(*args)
hardExp(*args)
help(*args)
iaAtom(*args)
ibAtom(*args)
info(*args)
ioAtom(*args)
kForOpt(*args)
kaAtom(*args)
kbAtom(*args)
koAtom(*args)
mScale(*args)
minS2(*args)
npc(*args)
numRestraints(*args)
omegaRatio(*args)
potType(*args)
qFactor(*args)
rFactor(*args)
rSwitch(*args)
restraints(*args)
restraintsSize(*args)
rlxType(*args)
rms(*args)
sbmfType(*args)
sclType(*args)
setAsympSlope(*args)
setAveType(*args)
setCoeff(*args)
setEquType(*args)
setExpTemp(*args)
setForce(*args)
setFreqI(*args)
setFunType(*args)
setGammaI(*args)
setGfac(*args)
setHardExp(*args)
setIaAtom(*args)
setIbAtom(*args)
setIoAtom(*args)
setKaAtom(*args)
setKbAtom(*args)
setKoAtom(*args)
setMScale(*args)
setNpc(*args)
setOmegaRatio(*args)
setPotType(*args)
setRSwitch(*args)
setRlxType(*args)
setSbmfType(*args)
setSclType(*args)
setSoftExp(*args)
setSqn(*args)
setTaAtom(*args)
setTauC(*args)
setTauI(*args)
setTauR(*args)
setTauT(*args)
setTaucAtoms(*args)
setTauiAtoms(*args)
setTautAtoms(*args)
setTbAtom(*args)
setTcMax(*args)
setTcMin(*args)
setTcType(*args)
setThreshold(*args)
setTiMax(*args)
setTiMin(*args)
setTiType(*args)
setToAtom(*args)
setTtType(*args)
setVerbose(*args)
setWeightMax(*args)
showCurrentTauc(*args)
showCurrentTaui(*args)
showCurrentTaut(*args)
showRestraints(*args)
showViolations(*args)
softExp(*args)
sqn(*args)
taAtom(*args)
tauc(*args)
taui(*args)
taur(*args)
taut(*args)
tbAtom(*args)
tc(*args)
tcType(*args)
tcmax(*args)
tcmin(*args)
threshold(*args)
ti(*args)
tiType(*args)
timax(*args)
timin(*args)
toAtom(*args)
tt(*args)
ttType(*args)
verbose(*args)
violations(*args)
weightMax(*args)
weightedAveSqObs(*args)
weightedQFactor(*args)

Data and other attributes defined here:
CENTER = 0
CONST = 0
FIX = 0
FIXTI = 0
FIXTT = 0
HARD = 1
HARMONIC = 1
NONSTEREO = 1
NORMAL = 0
OBSIG = 2
ONESIXTH = 2
OPT = 1
OPTTI = 1
OPTTT = 1
R1CURIE = 4
R1DD = 3
R1MIX = 5
R2CURIE = 1
R2DD = 0
R2MIX = 2
R_3 = 2
R_6 = 1
SB = 0
SBMF = 1
SIGMA = 1
SOFT = 0
SQUARE = 0
TIMODE = 1
TTMODE = 0
__dict__ = <dictproxy object at 0x13a8f68>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'PREPot_LetterClass' objects>
list of weak references to the object (if defined)

 
class PREPot_LetterClassPtr(PREPot_LetterClass)
    
Method resolution order:
PREPot_LetterClassPtr
PREPot_LetterClass
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from PREPot_LetterClass:
AveSqObs(*args)
Qfactor(*args)
Rfactor(*args)
__del__(self, destroy=<built-in function delete_PREPot_LetterClass>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
addRestraints(*args)
assignType(*args)
asympSlope(*args)
aveS2(*args)
aveType(*args)
calcDerivs(*args)
calcEnergy(*args)
calcEnergyAndDerivs(*args)
checkClockAtoms(*args)
coeff(*args)
coeff2(*args)
equType(*args)
expTemp(*args)
force(*args)
freqI(*args)
funType(*args)
gammaI(*args)
gfac(*args)
hardExp(*args)
help(*args)
iaAtom(*args)
ibAtom(*args)
info(*args)
ioAtom(*args)
kForOpt(*args)
kaAtom(*args)
kbAtom(*args)
koAtom(*args)
mScale(*args)
minS2(*args)
npc(*args)
numRestraints(*args)
omegaRatio(*args)
potType(*args)
qFactor(*args)
rFactor(*args)
rSwitch(*args)
restraints(*args)
restraintsSize(*args)
rlxType(*args)
rms(*args)
sbmfType(*args)
sclType(*args)
setAsympSlope(*args)
setAveType(*args)
setCoeff(*args)
setEquType(*args)
setExpTemp(*args)
setForce(*args)
setFreqI(*args)
setFunType(*args)
setGammaI(*args)
setGfac(*args)
setHardExp(*args)
setIaAtom(*args)
setIbAtom(*args)
setIoAtom(*args)
setKaAtom(*args)
setKbAtom(*args)
setKoAtom(*args)
setMScale(*args)
setNpc(*args)
setOmegaRatio(*args)
setPotType(*args)
setRSwitch(*args)
setRlxType(*args)
setSbmfType(*args)
setSclType(*args)
setSoftExp(*args)
setSqn(*args)
setTaAtom(*args)
setTauC(*args)
setTauI(*args)
setTauR(*args)
setTauT(*args)
setTaucAtoms(*args)
setTauiAtoms(*args)
setTautAtoms(*args)
setTbAtom(*args)
setTcMax(*args)
setTcMin(*args)
setTcType(*args)
setThreshold(*args)
setTiMax(*args)
setTiMin(*args)
setTiType(*args)
setToAtom(*args)
setTtType(*args)
setVerbose(*args)
setWeightMax(*args)
showCurrentTauc(*args)
showCurrentTaui(*args)
showCurrentTaut(*args)
showRestraints(*args)
showViolations(*args)
softExp(*args)
sqn(*args)
taAtom(*args)
tauc(*args)
taui(*args)
taur(*args)
taut(*args)
tbAtom(*args)
tc(*args)
tcType(*args)
tcmax(*args)
tcmin(*args)
threshold(*args)
ti(*args)
tiType(*args)
timax(*args)
timin(*args)
toAtom(*args)
tt(*args)
ttType(*args)
verbose(*args)
violations(*args)
weightMax(*args)
weightedAveSqObs(*args)
weightedQFactor(*args)

Data and other attributes inherited from PREPot_LetterClass:
CENTER = 0
CONST = 0
FIX = 0
FIXTI = 0
FIXTT = 0
HARD = 1
HARMONIC = 1
NONSTEREO = 1
NORMAL = 0
OBSIG = 2
ONESIXTH = 2
OPT = 1
OPTTI = 1
OPTTT = 1
R1CURIE = 4
R1DD = 3
R1MIX = 5
R2CURIE = 1
R2DD = 0
R2MIX = 2
R_3 = 2
R_6 = 1
SB = 0
SBMF = 1
SIGMA = 1
SOFT = 0
SQUARE = 0
TIMODE = 1
TTMODE = 0
__dict__ = <dictproxy object at 0x13a8fd8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'PREPot_LetterClass' objects>
list of weak references to the object (if defined)

 
class PRERestraint(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_PRERestraint>)
__eq__(*args)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
asString(*args)
calcGvalueNonStereo(*args)
calcGvalueNormal(*args)
comment(*args)
contrib(*args)
contribB(*args)
deriv(*args)
difAB(*args)
difCalc(*args)
difObs(*args)
diff(*args)
dtdp(*args)
emstatus(*args)
energy(*args)
energyNonStereo(*args)
g(*args)
gB(*args)
gBSigma(*args)
gSigma(*args)
gamma(*args)
gammaB(*args)
kdfsb(*args)
largeCalc(*args)
largeObs(*args)
ok(*args)
reff(*args)
reffB(*args)
s2(*args)
s2B(*args)
s2angular(*args)
s2angularB(*args)
s2radial(*args)
s2radialB(*args)
setClockDeriv(*args)
setEmStatus(*args)
setMF(*args)
setWF(*args)
smallCalc(*args)
smallObs(*args)
status(*args)
sumAB(*args)
sumCalc(*args)
sumObs(*args)
sumTerms(*args)
sumWeight(*args)
weight(*args)

Properties defined here:
sel1
get = PRERestraint_sel1_get(...)
set = PRERestraint_sel1_set(...)
sel2
get = PRERestraint_sel2_get(...)
set = PRERestraint_sel2_set(...)
sel3
get = PRERestraint_sel3_get(...)
set = PRERestraint_sel3_set(...)
sumList
get = PRERestraint_sumList_get(...)
set = PRERestraint_sumList_set(...)
verbose
get = PRERestraint_verbose_get(...)
set = PRERestraint_verbose_set(...)

Data and other attributes defined here:
AB = 0
BA = 1
EM1 = 0
EM2 = 1
EM3 = 2
FOR_TC = 0
FOR_TI = 2
FOR_TT = 1
GREATER = 1
INSIDE = 2
LESS = 0
__dict__ = <dictproxy object at 0x13c60f8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'sel1': <built-in function PRERestraint_sel1_get>, 'sel2': <built-in function PRERestraint_sel2_get>, 'sel3': <built-in function PRERestraint_sel3_get>, 'sumList': <built-in function PRERestraint_sumList_get>, 'verbose': <built-in function PRERestraint_verbose_get>}
__swig_setmethods__ = {'sel1': <built-in function PRERestraint_sel1_set>, 'sel2': <built-in function PRERestraint_sel2_set>, 'sel3': <built-in function PRERestraint_sel3_set>, 'sumList': <built-in function PRERestraint_sumList_set>, 'verbose': <built-in function PRERestraint_verbose_set>}
__weakref__ = <attribute '__weakref__' of 'PRERestraint' objects>
list of weak references to the object (if defined)

 
class PRERestraintPtr(PRERestraint)
    
Method resolution order:
PRERestraintPtr
PRERestraint
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from PRERestraint:
__del__(self, destroy=<built-in function delete_PRERestraint>)
__eq__(*args)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
asString(*args)
calcGvalueNonStereo(*args)
calcGvalueNormal(*args)
comment(*args)
contrib(*args)
contribB(*args)
deriv(*args)
difAB(*args)
difCalc(*args)
difObs(*args)
diff(*args)
dtdp(*args)
emstatus(*args)
energy(*args)
energyNonStereo(*args)
g(*args)
gB(*args)
gBSigma(*args)
gSigma(*args)
gamma(*args)
gammaB(*args)
kdfsb(*args)
largeCalc(*args)
largeObs(*args)
ok(*args)
reff(*args)
reffB(*args)
s2(*args)
s2B(*args)
s2angular(*args)
s2angularB(*args)
s2radial(*args)
s2radialB(*args)
setClockDeriv(*args)
setEmStatus(*args)
setMF(*args)
setWF(*args)
smallCalc(*args)
smallObs(*args)
status(*args)
sumAB(*args)
sumCalc(*args)
sumObs(*args)
sumTerms(*args)
sumWeight(*args)
weight(*args)

Properties inherited from PRERestraint:
sel1
get = PRERestraint_sel1_get(...)
set = PRERestraint_sel1_set(...)
sel2
get = PRERestraint_sel2_get(...)
set = PRERestraint_sel2_set(...)
sel3
get = PRERestraint_sel3_get(...)
set = PRERestraint_sel3_set(...)
sumList
get = PRERestraint_sumList_get(...)
set = PRERestraint_sumList_set(...)
verbose
get = PRERestraint_verbose_get(...)
set = PRERestraint_verbose_set(...)

Data and other attributes inherited from PRERestraint:
AB = 0
BA = 1
EM1 = 0
EM2 = 1
EM3 = 2
FOR_TC = 0
FOR_TI = 2
FOR_TT = 1
GREATER = 1
INSIDE = 2
LESS = 0
__dict__ = <dictproxy object at 0x13a8cc8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'sel1': <built-in function PRERestraint_sel1_get>, 'sel2': <built-in function PRERestraint_sel2_get>, 'sel3': <built-in function PRERestraint_sel3_get>, 'sumList': <built-in function PRERestraint_sumList_get>, 'verbose': <built-in function PRERestraint_verbose_get>}
__swig_setmethods__ = {'sel1': <built-in function PRERestraint_sel1_set>, 'sel2': <built-in function PRERestraint_sel2_set>, 'sel3': <built-in function PRERestraint_sel3_set>, 'sumList': <built-in function PRERestraint_sumList_set>, 'verbose': <built-in function PRERestraint_verbose_set>}
__weakref__ = <attribute '__weakref__' of 'PRERestraint' objects>
list of weak references to the object (if defined)

 
Functions
       
help(...)