potList		index
potList.py

A 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.
  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.
 
  append(pot)          - add a new term to the list.
 
  byName(instanceName) - return the potential term specified.
 
  keys()               - return a list of instanceNames of all potential
                         terms in the list.
 
 
 
 
# This file was created automatically by SWIG.
# Don't modify this file, modify the SWIG interface instead.
# This file is compatible with both classic and new-style classes.

 
Classes
       
__builtin__.object
CDSList_rc_Pot
CDSList_rc_PotPtr
Modified
ModifiedPtr
ModifiedBase
ModifiedBasePtr
PotList_LetterClass
PotList_LetterClassPtr
rc_Pot
PotList
PotListPtr
rc_PotPtr

 
class CDSList_rc_Pot(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_CDSList_rc_Pot>)

 
__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 0x27615c8>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_rc_Pot' objects>

 
list of weak references to the object (if defined)

 
class CDSList_rc_PotPtr(CDSList_rc_Pot)
   
 

 
 
Method resolution order:
CDSList_rc_PotPtr
CDSList_rc_Pot
__builtin__.object
Methods defined here:
__init__(self, this)

 
Methods inherited from CDSList_rc_Pot:
__del__(self, destroy=<built-in function delete_CDSList_rc_Pot>)

 
__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_rc_Pot:
__dict__ = <dictproxy object at 0x27614b0>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_rc_Pot' 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 0x2761670>

 
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 0x2761670>

 
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 0x27615c8>

 
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 0x27612b8>

 
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 PotList(rc_Pot)
   
 

 
 
Method resolution order:
PotList
rc_Pot
__builtin__.object
Methods defined here:
__del__(self, destroy=<built-in function delete_PotList>)

 
__deref__(*args)

 
__getattr__ lambda self, name

 
__getitem__(self, cnt)

 
__getslice__(*args)

 
__init__(self, *args)

 
__len__(*args)

 
__mul__(*args)

 
__oldinit__ = __init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
add(self, pot)

 
addEnergyReport(*args)

 
append(self, pot)

 
byName(*args)

 
clearEnergyReports(*args)

 
copy(self, potList)

 
decrRefCount(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
energyMaybeDerivs3(*args)

 
energyMaybeDerivs4(*args)

 
energyReports(*args)

 
ensWeight(*args)

 
getitem_int(*args)

 
getitem_string(*args)

 
help(*args)

 
incrRefCount(*args)

 
instanceData(*args)

 
keys(self)

 
list(*args)

 
numRestraints(*args)

 
pointer(*args)

 
registerInstanceData(*args)

 
registerTo(*args)

 
remove(self, name)

 
removeAll(*args)

 
renamed_add(*args)

 
renamed_remove(*args)

 
resetPotName(*args)

 
rms(*args)

 
setEnsWeights(*args)

 
setThreshold(*args)

 
setUseSimEnsWeights(*args)

 
showReport(*args)

 
simulation(*args)

 
size(*args)

 
threshold(*args)

 
unRegister(*args)

 
updateDelta(*args)

 
updateValues(*args)

 
useSimEnsWeights(*args)

 
violations(*args)

 
Properties defined here:
instanceData_

 
get = PotList_instanceData__get(...)

 
set = PotList_instanceData__set(...)

 
modified

 
get = PotList_modified_get(...)

 
set = PotList_modified_set(...)

 
registeredSimulations

 
get = PotList_registeredSimulations_get(...)

 
set = PotList_registeredSimulations_set(...)

 
Data and other attributes defined here:
__swig_getmethods__ = {'instanceData_': <built-in function PotList_instanceData__get>, 'modified': <built-in function PotList_modified_get>, 'registeredSimulations': <built-in function PotList_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function PotList_instanceData__set>, 'modified': <built-in function PotList_modified_set>, 'registeredSimulations': <built-in function PotList_registeredSimulations_set>}
Methods inherited from rc_Pot:
calcEnergy(*args)

 
calcEnergyAndDerivs(*args)

 
instanceName(*args)

 
potName(*args)

 
scale(*args)

 
setScale(*args)

 
Data and other attributes inherited from rc_Pot:
__dict__ = <dictproxy object at 0x27618a0>

 
dictionary for instance variables (if defined)
__weakref__ = <attribute '__weakref__' of 'rc_Pot' objects>

 
list of weak references to the object (if defined)

 
class PotListPtr(PotList)
   
 

 
 
Method resolution order:
PotListPtr
PotList
rc_Pot
__builtin__.object
Methods defined here:
__init__(self, this)

 
Methods inherited from PotList:
__del__(self, destroy=<built-in function delete_PotList>)

 
__deref__(*args)

 
__getattr__ lambda self, name

 
__getitem__(self, cnt)

 
__getslice__(*args)

 
__len__(*args)

 
__mul__(*args)

 
__oldinit__ = __init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
add(self, pot)

 
addEnergyReport(*args)

 
append(self, pot)

 
byName(*args)

 
clearEnergyReports(*args)

 
copy(self, potList)

 
decrRefCount(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
energyMaybeDerivs3(*args)

 
energyMaybeDerivs4(*args)

 
energyReports(*args)

 
ensWeight(*args)

 
getitem_int(*args)

 
getitem_string(*args)

 
help(*args)

 
incrRefCount(*args)

 
instanceData(*args)

 
keys(self)

 
list(*args)

 
numRestraints(*args)

 
pointer(*args)

 
registerInstanceData(*args)

 
registerTo(*args)

 
remove(self, name)

 
removeAll(*args)

 
renamed_add(*args)

 
renamed_remove(*args)

 
resetPotName(*args)

 
rms(*args)

 
setEnsWeights(*args)

 
setThreshold(*args)

 
setUseSimEnsWeights(*args)

 
showReport(*args)

 
simulation(*args)

 
size(*args)

 
threshold(*args)

 
unRegister(*args)

 
updateDelta(*args)

 
updateValues(*args)

 
useSimEnsWeights(*args)

 
violations(*args)

 
Properties inherited from PotList:
instanceData_

 
get = PotList_instanceData__get(...)

 
set = PotList_instanceData__set(...)

 
modified

 
get = PotList_modified_get(...)

 
set = PotList_modified_set(...)

 
registeredSimulations

 
get = PotList_registeredSimulations_get(...)

 
set = PotList_registeredSimulations_set(...)

 
Data and other attributes inherited from PotList:
__swig_getmethods__ = {'instanceData_': <built-in function PotList_instanceData__get>, 'modified': <built-in function PotList_modified_get>, 'registeredSimulations': <built-in function PotList_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function PotList_instanceData__set>, 'modified': <built-in function PotList_modified_set>, 'registeredSimulations': <built-in function PotList_registeredSimulations_set>}
Methods inherited from rc_Pot:
calcEnergy(*args)

 
calcEnergyAndDerivs(*args)

 
instanceName(*args)

 
potName(*args)

 
scale(*args)

 
setScale(*args)

 
Data and other attributes inherited from rc_Pot:
__dict__ = <dictproxy object at 0x2761328>

 
dictionary for instance variables (if defined)
__weakref__ = <attribute '__weakref__' of 'rc_Pot' objects>

 
list of weak references to the object (if defined)

 
class PotList_LetterClass(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_PotList_LetterClass>)

 
__getattr__ lambda self, name

 
__getitem__(self, cnt)

 
__getslice__(*args)

 
__init__(self, *args)

 
__len__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
add(self, pot)

 
addEnergyReport(*args)

 
append(self, pot)

 
byName(*args)

 
calcEnergy(*args)

 
calcEnergyAndDerivs(*args)

 
clearEnergyReports(*args)

 
copy(self, potList)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
energyMaybeDerivs3(*args)

 
energyMaybeDerivs4(*args)

 
energyReports(*args)

 
getitem_int(*args)

 
getitem_string(*args)

 
help(*args)

 
keys(self)

 
list(*args)

 
numRestraints(*args)

 
remove(self, name)

 
removeAll(*args)

 
renamed_add(*args)

 
renamed_remove(*args)

 
rms(*args)

 
showReport(*args)

 
size(*args)

 
updateDelta(*args)

 
violations(*args)

 
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x2761718>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'PotList_LetterClass' objects>

 
list of weak references to the object (if defined)

 
class PotList_LetterClassPtr(PotList_LetterClass)
   
 

 
 
Method resolution order:
PotList_LetterClassPtr
PotList_LetterClass
__builtin__.object
Methods defined here:
__init__(self, this)

 
Methods inherited from PotList_LetterClass:
__del__(self, destroy=<built-in function delete_PotList_LetterClass>)

 
__getattr__ lambda self, name

 
__getitem__(self, cnt)

 
__getslice__(*args)

 
__len__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
add(self, pot)

 
addEnergyReport(*args)

 
append(self, pot)

 
byName(*args)

 
calcEnergy(*args)

 
calcEnergyAndDerivs(*args)

 
clearEnergyReports(*args)

 
copy(self, potList)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
energyMaybeDerivs3(*args)

 
energyMaybeDerivs4(*args)

 
energyReports(*args)

 
getitem_int(*args)

 
getitem_string(*args)

 
help(*args)

 
keys(self)

 
list(*args)

 
numRestraints(*args)

 
remove(self, name)

 
removeAll(*args)

 
renamed_add(*args)

 
renamed_remove(*args)

 
rms(*args)

 
showReport(*args)

 
size(*args)

 
updateDelta(*args)

 
violations(*args)

 
Data and other attributes inherited from PotList_LetterClass:
__dict__ = <dictproxy object at 0x2761600>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'PotList_LetterClass' objects>

 
list of weak references to the object (if defined)

 
class rc_Pot(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_rc_Pot>)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
calcEnergy(*args)

 
calcEnergyAndDerivs(*args)

 
instanceData(*args)

 
instanceName(*args)

 
potName(*args)

 
scale(*args)

 
setScale(*args)

 
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x27617c0>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'rc_Pot' objects>

 
list of weak references to the object (if defined)

 
class rc_PotPtr(rc_Pot)
   
 

 
 
Method resolution order:
rc_PotPtr
rc_Pot
__builtin__.object
Methods defined here:
__init__(self, this)

 
Methods inherited from rc_Pot:
__del__(self, destroy=<built-in function delete_rc_Pot>)

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
calcEnergy(*args)

 
calcEnergyAndDerivs(*args)

 
instanceData(*args)

 
instanceName(*args)

 
potName(*args)

 
scale(*args)

 
setScale(*args)

 
Data and other attributes inherited from rc_Pot:
__dict__ = <dictproxy object at 0x2761600>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'rc_Pot' objects>

 
list of weak references to the object (if defined)

 
Functions
       
help(...)

 

 
Data
        __package__ = None
pyXplorHelp = Type help() for interactive help, or help(object) for help about object.