gyrPot		index
gyrPot.py


Potential term to restrain the volume associated with the gyration
tensor. This is used as an alternative to a radius of gyration
resrtaint- to allow elongated structures.  The target value is set in
gyrPotTools.create_GyrPot based on values observed in the PDB.
 
 
constructor: GyrPot(instanceName,
                    selection   )
 
  instanceName is a user-specified identifier
  selection is a atomSel.AtomSel object specifying the atoms to include
  when calculating the gyration tensor.
 
methods
  calcEnergy()                 - calc energy, returns the energy value.
  calcEnergyAndDerivs(derivs)  - calc energy, derivs, returns the energy value.
 
  rms()                        - return the magnitude of violation of this
                                 term -- abs(diff).
  scale()                      - scale factor for this energy term.
 
  selection()                  - return the atom selection specified in
                                 the constructor.
 
  info()                    - current info about the state of this instance
 
  qc()             - The calculated centroid of selection().
  gyrTensor()      - The calculated gyration tensor.
  Rg()             - The calculated radius of gyration ( Tr G )
  volume()         - The calculated gyration volume.
  eigenPairs()     - The three principal moments and directions of the 
                     gyration tensor.
 
 The following parameters can be set [defaults in square brackets]
 
  volTarget      -   The target gyration volume.
  volRange       -   The +/- range about the target volume about which to
                     evaluate zero energy (see below).
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
 
The gyration tensor is defined as 
 
              
     G = 1/N sum_i  (q_i - qc ) X (q_i - qc)
 
where N is the number of selected atoms, q_i is atom i's position and qc is 
the centroid of the selected atoms. The ``X'' denotes outer product.
 
The gyration volume is
 
     Vg =  4/3 pi sqrt(det G)
              
The energy function is defined as 
 
      V = scale * diff^2
 
  where 
 
             Vg - targetVol - rangeVol       if Vg>targetVol+rangeVol
     diff =  targetVol - rangeVol - Vg       if Vg<targetVol-rangeVol
             0                               otherwise
 
 

 
Classes
       
__builtin__.object
CDSList_EigenPair
CDSList_EigenPairPtr
GyrPot
GyrPotPtr
GyrPot_EigenPair
GyrPot_EigenPairPtr
GyrPot_LetterClass
GyrPot_LetterClassPtr
Modified
ModifiedPtr
ModifiedBase
ModifiedBasePtr

 
class CDSList_EigenPair(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_CDSList_EigenPair>)
__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 0x1518c58>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_EigenPair' objects>
list of weak references to the object (if defined)

 
class CDSList_EigenPairPtr(CDSList_EigenPair)
    
Method resolution order:
CDSList_EigenPairPtr
CDSList_EigenPair
__builtin__.object
Methods defined here:
__init__(self, this)
Methods inherited from CDSList_EigenPair:
__del__(self, destroy=<built-in function delete_CDSList_EigenPair>)
__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_EigenPair:
__dict__ = <dictproxy object at 0x1518b40>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_EigenPair' objects>
list of weak references to the object (if defined)

 
class GyrPot(__builtin__.object)
     Methods defined here:
Rg(*args)
__del__(self, destroy=<built-in function delete_GyrPot>)
__deref__(*args)
__getattr__ lambda self, name
__init__(self, *args)
__mul__(*args)
__oldinit__ = __init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
calcEnergy(*args)
calcEnergyAndDerivs(*args)
eigenPairs(*args)
gyrTensor(*args)
help(*args)
incrRefCount(*args)
info(*args)
instanceData(*args)
instanceName(*args)
numRestraints(*args)
pointer(*args)
potName(*args)
qc(*args)
rRange(*args)
rTarget(*args)
registerInstanceData(*args)
registerTo(*args)
resetPotName(*args)
rms(*args)
scale(*args)
selection(*args)
setRRange(*args)
setRTarget(*args)
setScale(*args)
setTargetType(*args)
setThreshold(*args)
setVerbose(*args)
setVolRange(*args)
setVolTarget(*args)
targetType(*args)
threshold(*args)
unRegister(*args)
updateValues(*args)
valuesVectors(*args)
verbose(*args)
violations(*args)
volRange(*args)
volTarget(*args)
volume(*args)
Properties defined here:
eigenPairs_
get = GyrPot_eigenPairs__get(...)
set = GyrPot_eigenPairs__set(...)
instanceData_
get = GyrPot_instanceData__get(...)
set = GyrPot_instanceData__set(...)
modified
get = GyrPot_modified_get(...)
set = GyrPot_modified_set(...)
registeredSimulations
get = GyrPot_registeredSimulations_get(...)
set = GyrPot_registeredSimulations_set(...)
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x15291a0>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'eigenPairs_': <built-in function GyrPot_eigenPairs__get>, 'instanceData_': <built-in function GyrPot_instanceData__get>, 'modified': <built-in function GyrPot_modified_get>, 'registeredSimulations': <built-in function GyrPot_registeredSimulations_get>}
__swig_setmethods__ = {'eigenPairs_': <built-in function GyrPot_eigenPairs__set>, 'instanceData_': <built-in function GyrPot_instanceData__set>, 'modified': <built-in function GyrPot_modified_set>, 'registeredSimulations': <built-in function GyrPot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'GyrPot' objects>
list of weak references to the object (if defined)

 
class GyrPotPtr(GyrPot)
    
Method resolution order:
GyrPotPtr
GyrPot
__builtin__.object
Methods defined here:
__init__(self, this)
Methods inherited from GyrPot:
Rg(*args)
__del__(self, destroy=<built-in function delete_GyrPot>)
__deref__(*args)
__getattr__ lambda self, name
__mul__(*args)
__oldinit__ = __init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
calcEnergy(*args)
calcEnergyAndDerivs(*args)
eigenPairs(*args)
gyrTensor(*args)
help(*args)
incrRefCount(*args)
info(*args)
instanceData(*args)
instanceName(*args)
numRestraints(*args)
pointer(*args)
potName(*args)
qc(*args)
rRange(*args)
rTarget(*args)
registerInstanceData(*args)
registerTo(*args)
resetPotName(*args)
rms(*args)
scale(*args)
selection(*args)
setRRange(*args)
setRTarget(*args)
setScale(*args)
setTargetType(*args)
setThreshold(*args)
setVerbose(*args)
setVolRange(*args)
setVolTarget(*args)
targetType(*args)
threshold(*args)
unRegister(*args)
updateValues(*args)
valuesVectors(*args)
verbose(*args)
violations(*args)
volRange(*args)
volTarget(*args)
volume(*args)
Properties inherited from GyrPot:
eigenPairs_
get = GyrPot_eigenPairs__get(...)
set = GyrPot_eigenPairs__set(...)
instanceData_
get = GyrPot_instanceData__get(...)
set = GyrPot_instanceData__set(...)
modified
get = GyrPot_modified_get(...)
set = GyrPot_modified_set(...)
registeredSimulations
get = GyrPot_registeredSimulations_get(...)
set = GyrPot_registeredSimulations_set(...)
Data and other attributes inherited from GyrPot:
__dict__ = <dictproxy object at 0x1518fa0>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'eigenPairs_': <built-in function GyrPot_eigenPairs__get>, 'instanceData_': <built-in function GyrPot_instanceData__get>, 'modified': <built-in function GyrPot_modified_get>, 'registeredSimulations': <built-in function GyrPot_registeredSimulations_get>}
__swig_setmethods__ = {'eigenPairs_': <built-in function GyrPot_eigenPairs__set>, 'instanceData_': <built-in function GyrPot_instanceData__set>, 'modified': <built-in function GyrPot_modified_set>, 'registeredSimulations': <built-in function GyrPot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'GyrPot' objects>
list of weak references to the object (if defined)

 
class GyrPot_EigenPair(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_GyrPot_EigenPair>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
Properties defined here:
value
get = GyrPot_EigenPair_value_get(...)
set = GyrPot_EigenPair_value_set(...)
vector
get = GyrPot_EigenPair_vector_get(...)
set = GyrPot_EigenPair_vector_set(...)
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x1518da8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'value': <built-in function GyrPot_EigenPair_value_get>, 'vector': <built-in function GyrPot_EigenPair_vector_get>}
__swig_setmethods__ = {'value': <built-in function GyrPot_EigenPair_value_set>, 'vector': <built-in function GyrPot_EigenPair_vector_set>}
__weakref__ = <attribute '__weakref__' of 'GyrPot_EigenPair' objects>
list of weak references to the object (if defined)

 
class GyrPot_EigenPairPtr(GyrPot_EigenPair)
    
Method resolution order:
GyrPot_EigenPairPtr
GyrPot_EigenPair
__builtin__.object
Methods defined here:
__init__(self, this)
Methods inherited from GyrPot_EigenPair:
__del__(self, destroy=<built-in function delete_GyrPot_EigenPair>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
Properties inherited from GyrPot_EigenPair:
value
get = GyrPot_EigenPair_value_get(...)
set = GyrPot_EigenPair_value_set(...)
vector
get = GyrPot_EigenPair_vector_get(...)
set = GyrPot_EigenPair_vector_set(...)
Data and other attributes inherited from GyrPot_EigenPair:
__dict__ = <dictproxy object at 0x1518d70>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'value': <built-in function GyrPot_EigenPair_value_get>, 'vector': <built-in function GyrPot_EigenPair_vector_get>}
__swig_setmethods__ = {'value': <built-in function GyrPot_EigenPair_value_set>, 'vector': <built-in function GyrPot_EigenPair_vector_set>}
__weakref__ = <attribute '__weakref__' of 'GyrPot_EigenPair' objects>
list of weak references to the object (if defined)

 
class GyrPot_LetterClass(__builtin__.object)
     Methods defined here:
Rg(*args)
__del__(self, destroy=<built-in function delete_GyrPot_LetterClass>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
calcEnergy(*args)
calcEnergyAndDerivs(*args)
eigenPairs(*args)
gyrTensor(*args)
help(*args)
info(*args)
numRestraints(*args)
qc(*args)
rRange(*args)
rTarget(*args)
rms(*args)
selection(*args)
setRRange(*args)
setRTarget(*args)
setTargetType(*args)
setVerbose(*args)
setVolRange(*args)
setVolTarget(*args)
targetType(*args)
updateValues(*args)
verbose(*args)
violations(*args)
volRange(*args)
volTarget(*args)
volume(*args)
Properties defined here:
eigenPairs_
get = GyrPot_LetterClass_eigenPairs__get(...)
set = GyrPot_LetterClass_eigenPairs__set(...)
Data and other attributes defined here:
RADIUS = 0
VOLUME = 1
__dict__ = <dictproxy object at 0x1518a28>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'eigenPairs_': <built-in function GyrPot_LetterClass_eigenPairs__get>}
__swig_setmethods__ = {'eigenPairs_': <built-in function GyrPot_LetterClass_eigenPairs__set>}
__weakref__ = <attribute '__weakref__' of 'GyrPot_LetterClass' objects>
list of weak references to the object (if defined)

 
class GyrPot_LetterClassPtr(GyrPot_LetterClass)
    
Method resolution order:
GyrPot_LetterClassPtr
GyrPot_LetterClass
__builtin__.object
Methods defined here:
__init__(self, this)
Methods inherited from GyrPot_LetterClass:
Rg(*args)
__del__(self, destroy=<built-in function delete_GyrPot_LetterClass>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
calcEnergy(*args)
calcEnergyAndDerivs(*args)
eigenPairs(*args)
gyrTensor(*args)
help(*args)
info(*args)
numRestraints(*args)
qc(*args)
rRange(*args)
rTarget(*args)
rms(*args)
selection(*args)
setRRange(*args)
setRTarget(*args)
setTargetType(*args)
setVerbose(*args)
setVolRange(*args)
setVolTarget(*args)
targetType(*args)
updateValues(*args)
verbose(*args)
violations(*args)
volRange(*args)
volTarget(*args)
volume(*args)
Properties inherited from GyrPot_LetterClass:
eigenPairs_
get = GyrPot_LetterClass_eigenPairs__get(...)
set = GyrPot_LetterClass_eigenPairs__set(...)
Data and other attributes inherited from GyrPot_LetterClass:
RADIUS = 0
VOLUME = 1
__dict__ = <dictproxy object at 0x1518c90>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'eigenPairs_': <built-in function GyrPot_LetterClass_eigenPairs__get>}
__swig_setmethods__ = {'eigenPairs_': <built-in function GyrPot_LetterClass_eigenPairs__set>}
__weakref__ = <attribute '__weakref__' of 'GyrPot_LetterClass' 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 0x1518d00>
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 0x1518d70>
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 0x1518de0>
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 0x1518de0>
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)

 
Functions
       
help(...)

 
Data
        cvar = <Global variables>