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

An ordered collection of Pot objects - which is itself a Pot object. 
 
An instantiated object will act like a Python Sequence- it is iterable,
indexable (by position number, and by instance name), and the len()
builtin works as expected.
 
Constructor:
  PotList(NAME) 
   NAME is a name given to this instance of the PotList class.
 
Methods:
 
  only the standard potential terms exist:
 
  potName()      - returns 'PotList'
  instanceName() - returns NAME given in the constructor
 
  scale()/ setScale(scaleFac) 
                 - get/set a scale factor for this term
                   NOTE: this is independent of scalings set within
                        the XPLOR interface.
 
  calcEnergy()                   - calc energy without and with gradient
  calcEnergyAndDerivs(DerivList) -   evaluation. Return the value of energy
                                 - these calculate and sum energy of each term
                                 - in the list.
 
  energyReports()      - return a list of energyReport.EnergyReports for 
                         each term. This list is sorted by the instanceNames
                         of each term.
 
  clearEnergyReports() - clear the EnergyReport list.
 
  violations()         - report the sum of all violations
  rms()                - report the average rmsd. If the PotList consists of 
                         term which are all the same type, and which contain
                         restraints, the returned value R is computed as
                         
                             R^2 = sum_i N_i * w_i * R_i^2 / (sum_i N_i * w_i)
 
                         where for term i, R_i is rms(), w_i is scale(), N_i is
                         numRestraints(). If the terms are of the same type, 
                         but don't have a meaningful concept of restraint 
                         (numRestraints()==-1), then N_i is set to 1 in the 
                         above equation. If all terms return rms=-1, then 
                         return rms, else skip those terms which have 
                         negative rms
  numRestraints()      - return the sum of the values of numRestraints() for
                         all included potential terms, for positive values of
                         numRestraints.
 
  append(pot)          - add a new term to the end of the list.
 
  byName(instanceName) - return the potential term specified.
 
  keys()               - return a list of instanceNames of all potential
                         terms in the list.
 
  ensWeights()    - ensemble weights. Not directly used in any computations.
  setEnsWeights() - set ensemble weights for all contain potential terms. 
 
 
 
 
# 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_rc_Pot
Modified
ModifiedBase
PotList_LetterClass
rc_Pot
PotList
rc_ptr_Pot

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

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< rc_Pot >'
__getslice__(self, *args, **kwargs) -> 'CDSList< rc_Pot >'
__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_rc_Pot(...)

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 PotList_LetterClass(builtins.object)
    PotList_LetterClass(*args, **kwargs)
 

 
  Methods defined here:
__getitem__(self, cnt)
__getslice__(self, *args, **kwargs) -> 'PotList'
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__len__(self, *args, **kwargs) -> 'int'
__repr__ = _swig_repr(self)
add(self, pot)
addEnergyReport(self, *args, **kwargs) -> 'void'
append(self, pot)
byName(self, *args, **kwargs) -> 'rc_Pot'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
clearEnergyReports(self, *args, **kwargs) -> 'void'
copy(self, potList)
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'
energyReports(self, *args, **kwargs) -> 'CDSList< EnergyReport >'
getitem_int(self, *args, **kwargs) -> 'rc_Pot'
getitem_string(self, *args, **kwargs) -> 'rc_Pot'
keys(self)
list(self, *args, **kwargs) -> 'CDSList< rc_Pot >'
numRestraints(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
remove(self, name)
removeAll(self, *args, **kwargs) -> 'void'
renamed_add(self, *args, **kwargs) -> 'void'
renamed_remove(self, *args, **kwargs) -> 'void'
rms(self, *args, **kwargs) -> 'float_type'
setEnsWeights(self, *args, **kwargs) -> 'void'
showReport(self, *args, **kwargs) -> 'String'
size(self, *args, **kwargs) -> 'int'
updateDelta(self, *args, **kwargs) -> 'void'
violations(self, *args, **kwargs) -> 'float_type'

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

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:
noViolationStats = True

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

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'String'
potName(self, *args, **kwargs) -> 'String'
scale(self, *args, **kwargs) -> 'float_type'
setScale(self, *args, **kwargs) -> 'void'

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

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_Pot(builtins.object)
    rc_ptr_Pot(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'Pot *'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__ref__(self, *args, **kwargs) -> 'Pot &'
__repr__ = _swig_repr(self)
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
count(self, *args, **kwargs) -> 'int'
decr(self, *args, **kwargs) -> 'void'
forceDelete(self, *args, **kwargs) -> 'void'
incr(self, *args, **kwargs) -> 'void'
instanceName(self, *args, **kwargs) -> 'char const *'
numRestraints(self, *args, **kwargs) -> 'int'
potName(self, *args, **kwargs) -> 'char const *'
ptr(self, *args, **kwargs) -> 'Pot *'
registerTo(self, *args, **kwargs) -> 'void'
release(self, *args, **kwargs) -> 'Pot *'
reset(self, *args, **kwargs) -> 'void'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
setScale(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
violations(self, *args, **kwargs) -> 'float_type'

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

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

 
registeredSimulations

 
thisown

 
The membership flag

 
realPotList = class PotList(rc_Pot)
    realPotList(*args)
 

 
 
Method resolution order:
PotList
rc_Pot
builtins.object

Methods defined here:
__deref__(self, *args, **kwargs) -> 'PotList *'
__getitem__(self, cnt)
__getslice__(self, *args, **kwargs) -> 'PotList'
__init__(self, *args)
__len__(self, *args, **kwargs) -> 'int'
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'PotList &'
__repr__ = _swig_repr(self)
add(self, pot)
addEnergyReport(self, *args, **kwargs) -> 'void'
addEnsWeights(self, *args, **kwargs) -> 'void'
append(self, pot)
byName(self, *args, **kwargs) -> 'rc_Pot'
calcWDerivs(self, *args, **kwargs) -> 'bool const'
clearEnergyReports(self, *args, **kwargs) -> 'void'
clearEnsWeights(self, *args, **kwargs) -> 'void'
copy(self, potList)
decrRefCnt(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'
energyReports(self, *args, **kwargs) -> 'CDSList< EnergyReport >'
ensWeight(self, *args, **kwargs) -> 'float_type'
ensWeights(self, *args, **kwargs) -> 'CDSList< float_type >'
ensWeightsInfo(self, *args, **kwargs) -> 'String'
getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &'
getitem_int(self, *args, **kwargs) -> 'rc_Pot'
getitem_string(self, *args, **kwargs) -> 'rc_Pot'
incrRefCnt(self, *args, **kwargs) -> 'void'
instanceData(self, *args, **kwargs) -> 'PyObject *'
keys(self)
list(self, *args, **kwargs) -> 'CDSList< rc_Pot >'
numRestraints(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
remove(self, name)
removeAll(self, *args, **kwargs) -> 'void'
renamed_add(self, *args, **kwargs) -> 'void'
renamed_remove(self, *args, **kwargs) -> 'void'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
rms(self, *args, **kwargs) -> 'float_type'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
showReport(self, *args, **kwargs) -> 'String'
simulation(self, *args) -> 'EnsembleSimulation const *'
size(self, *args, **kwargs) -> 'int'
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'
violations(self, *args, **kwargs) -> 'float_type'

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

Data descriptors defined here:
instanceDataCleanup

 
instanceDataCreate

 
instanceData_

 
modified

 
registeredSimulations

 
thisown

 
The membership flag

Data and other attributes defined here:
noViolationStats = True

Methods inherited from rc_Pot:
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
instanceName(self, *args, **kwargs) -> 'String'
potName(self, *args, **kwargs) -> 'String'
scale(self, *args, **kwargs) -> 'float_type'
setScale(self, *args, **kwargs) -> 'void'

Data descriptors inherited from rc_Pot:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

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