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


J-Coupling Potential term
 
Constructor:
  JCoupPot(instanceName ,
           restraints   ,
           simulation   )  - creates a potential term with the given name.
                             restraints is a string which contains a restraint
                             table (defaults to an empty string).
                             simulation defaults to 
                             simulation.currentSimulation.
 
Methods:
  calcEnergy()                    - calcs energy
  calcEnergyAndDerivs(DerivList)  - calcs energy and derivative info
    note that these routines also update all other potential-specific data.
 
  addRestraints(restraints)- add entries to the restraint table.
 
  ensWeigth(index) - return the ensemble weight associated with the
                     specified member.
  setEnsWeights(vals) - use the specified ensemble weights instead of those
                        in the underlying EnsembleSimulation.
Read-Write Accessors:
  A         - coefficient of cos^2 term (see formula below).
  B         - coefficient of cos term (see formula below).
  C         - constant term (see formula below).
  phase     - phase in j-coupling formula (see formula below).
  potType   - potential type: 'harmonic' or 'square' [harmonic].
  verbose   - if true, sporadically spit out info [False]
  threshold - threshold in violation calculation ( defaults to 0).
  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.
 
Read-only accessors:
 
  violations()    - return number of violations. Defined in terms of jDiff_i.
  rms()           - return rms of jDiff_i
  numRestraints() - the number of restraints defined for this term.
  deviation()     - ensemble deviation of jCalc-jObs averaged over all 
                    restraints
 
  simulation()    - simulation used by this shape term. Is an EnsembleSimulation.
 
  info()                   - return string synopsis of potential info.
  showRestraints(violated) - return pretty-printed restraint info.
  showViolations()         - return pretty-printed violation info.
 
 
The potential term is defined as
 
  E = scale() * sum_i jDiff_i^2
 
where
   jDiff = jCalc - jDiff  if potType=='harmonic'
 
   if potType=='square, jDiff is
       jCalc-jObs-jPlus    if jCalc-jObs>jPlus
       jCalc-jObs+jMinus   if jCalc-jObs<-jMinus
             0             otherwise
 
  jObs is the observed j-coupling value.
  jCalc is the ensemble-average calulated j-coupling value:
 
      jCalc = A*cos(phi+phase)^2 + B*cos(phi+phase) + C
 
    where the constants A,B,C, and phase are inputs, and phi is the dihedral
    angle as specified in the assignment table.
 
 
The j-coupling assignment table consists of entries of the following form
 
ASSIgn  (sel1) (sel2) (sel3) (sel4) jObs jMinus [jPlus]
 
where the four single atom selections specify the dihedral angle. jMinus
and jPlus specify the range of the square potential, with jPlus defaulting
to jMinus if it is omitted.
 
 
Note that the degenerate assignments of the XPLOR COUP term are not
implemented here yet.
 
 
 
# 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_JCoup_Restraint
EnsemblePot
JCoupPot_LetterClass
JCoupPot
Modified
ModifiedBase
Restraint_JCoupPot
JCoup_Restraint
VarEnsWeights
rc_EnsemblePot
rc_ptr_JCoup_Restraint

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

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< CDS::rc_ptr< JCoup_Restraint > >'
__getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< JCoup_Restraint > >'
__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_JCoup_Restraint(...)

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 JCoupPot_LetterClass(EnsemblePot)
    JCoupPot_LetterClass(*args, **kwargs)
 

 
 
Method resolution order:
JCoupPot_LetterClass
EnsemblePot
builtins.object

Methods defined here:
A(self, *args, **kwargs) -> 'float_type const'
B(self, *args, **kwargs) -> 'float_type const'
C(self, *args, **kwargs) -> 'float_type const'
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
addRestraints(self, *args, **kwargs) -> 'void'
deviation(self, *args, **kwargs) -> 'double'
energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type'
energyMaybeDerivs2(self, *args, **kwargs) -> 'float_type'
info(self, *args, **kwargs) -> 'String'
numRestraints(self, *args, **kwargs) -> 'int'
phase(self, *args, **kwargs) -> 'float_type'
potType(self, *args, **kwargs) -> 'JCoupPot::JCoupPotType'
pyXplorHelp(self, *args, **kwargs) -> 'String'
restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< JCoup_Restraint > >'
rms(self, *args, **kwargs) -> 'double'
setA(self, *args, **kwargs) -> 'void'
setB(self, *args, **kwargs) -> 'void'
setC(self, *args, **kwargs) -> 'void'
setPhase(self, *args, **kwargs) -> 'void'
setPotType(self, *args, **kwargs) -> 'void'
setShowAllRestraints(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
showAllRestraints(self, *args, **kwargs) -> 'bool const'
showRestraints(self, *args, **kwargs) -> 'String'
showViolations(self, *args, **kwargs) -> 'String'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'

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

Data descriptors defined here:
phaseInRadians

 
thisown

 
The membership flag

Data and other attributes defined here:
HARMONIC = 0
SQUARE = 1

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 JCoup_Restraint(Restraint_JCoupPot)
    JCoup_Restraint(*args, **kwargs)
 

 
 
Method resolution order:
JCoup_Restraint
Restraint_JCoupPot
builtins.object

Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
calcContrib(self, *args, **kwargs) -> 'void'
deriv(self, *args, **kwargs) -> 'void'
energy(self, *args, **kwargs) -> 'double'
name(self, *args, **kwargs) -> 'String'
ok(self, *args, **kwargs) -> 'int'

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

Data descriptors defined here:
contrib

 
thisown

 
The membership flag
verbose

 

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

Data descriptors inherited from Restraint_JCoupPot:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

 
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 Restraint_JCoupPot(builtins.object)
    Restraint_JCoupPot(*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_JCoupPot(...)

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_JCoup_Restraint(builtins.object)
    rc_ptr_JCoup_Restraint(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'JCoup_Restraint *'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__ref__(self, *args, **kwargs) -> 'JCoup_Restraint &'
__repr__ = _swig_repr(self)
calcContrib(self, *args, **kwargs) -> 'void'
count(self, *args, **kwargs) -> 'int'
decr(self, *args, **kwargs) -> 'void'
deriv(self, *args, **kwargs) -> 'void'
diff(self, *args, **kwargs) -> 'float_type'
energy(self, *args, **kwargs) -> 'double'
forceDelete(self, *args, **kwargs) -> 'void'
incr(self, *args, **kwargs) -> 'void'
name(self, *args, **kwargs) -> 'String'
ok(self, *args, **kwargs) -> 'int'
ptr(self, *args, **kwargs) -> 'JCoup_Restraint *'
release(self, *args, **kwargs) -> 'JCoup_Restraint *'
reset(self, *args, **kwargs) -> 'void'
setName(self, *args, **kwargs) -> 'void'
violated(self, *args, **kwargs) -> 'bool'

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
thisown

 
The membership flag
verbose

 

 
realJCoupPot = class JCoupPot(builtins.object)
    realJCoupPot(*args)
 

 
  Methods defined here:
A(self, *args, **kwargs) -> 'float_type const'
B(self, *args, **kwargs) -> 'float_type const'
C(self, *args, **kwargs) -> 'float_type const'
__deref__(self, *args, **kwargs) -> 'JCoupPot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'JCoupPot &'
__repr__ = _swig_repr(self)
addEnsWeights(self, *args, **kwargs) -> 'void'
addRestraints(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'
decrRefCnt(self, *args, **kwargs) -> 'void'
deviation(self, *args, **kwargs) -> 'double'
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 > &'
incrRefCnt(self, *args, **kwargs) -> 'void'
info(self, *args, **kwargs) -> 'String'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
numRestraints(self, *args, **kwargs) -> 'int'
phase(self, *args, **kwargs) -> 'float_type'
potName(self, *args, **kwargs) -> 'char const *'
potType(self, *args, **kwargs) -> 'JCoupPot::JCoupPotType'
pyXplorHelp(self, *args, **kwargs) -> 'String'
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< JCoup_Restraint > >'
rms(self, *args, **kwargs) -> 'double'
scale(self, *args, **kwargs) -> 'float_type const'
setA(self, *args, **kwargs) -> 'void'
setB(self, *args, **kwargs) -> 'void'
setC(self, *args, **kwargs) -> 'void'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setPhase(self, *args, **kwargs) -> 'void'
setPotType(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setShowAllRestraints(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
showAllRestraints(self, *args, **kwargs) -> 'bool const'
showRestraints(self, *args, **kwargs) -> 'String'
showViolations(self, *args, **kwargs) -> 'String'
simulation(self, *args) -> 'EnsembleSimulation const *'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateEnsWeights(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
useSimEnsWeights(self, *args, **kwargs) -> 'bool const'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
instanceDataCreate

 
instanceData_

 
modified

 
phaseInRadians

 
registeredSimulations

 
thisown

 
The membership flag

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