posSymmPot		index
posSymmPot.py


 
Potential term restraining atomic positions relative to those in a
similar structure. This term is similar to the (nonstrict) NCS XPLOR
energy term, but there is no need that the equivalent pairs of atoms
have the same atom name, have the same residue name, or even be of the
same number.
 
 
Constructor:
 
  It is suggested that this potential term be created using the helper 
  function posSymmPotTools.create_PosSymmPot().
 
 
  PosSymmPot(instanceName)  - creates a potential term with the given name. 
  
Methods:
 
  calcEnergy()                    - calcs energy
  calcEnergyAndDerivs(DerivList)  - calcs energy and derivative info
  
  
  addEquivAtomSelPair(atomSel1,
                      atomSel2)    - specify a pair of atomSel.AtomSels, 
                                     the centroids of which will be restrained
                                     to have the same relative position.
  equivAtomSelPairs()              - return a list containing the current
                                     set of AtomSel pairs.
  removeEquivAtomSelPair(atomSel1,
                         atomSel2) - remove the specified pair.
 
  addEquivAtomPair(atomSel1,
                   atomSel2)       - specify a pair of atom.Atoms,
                                     whose positions will be restrained
                                     to have the same relative position.
  equivAtomPairs()                 - return a list containing the current
                                     set of Atom pairs.
  removeEquivAtomPair(atomSel1,
                      atomSel2)   - remove the specified pair.
 
  rms()                           - returns the best-fit RMSD between the two
                                    selection sets.
  violations()                    - returns 0 if upperBound > rms > lowerBound,
                                    1 otherwise.
  
  individualRMSDs()               - returns a list containg the distances
                                    between each equivalent pair after 
                                    best-fitting
 
  rotMat()                        - returns the rotation matrix which best-
                                    fits the two selection sets translated
                                    to the origin.
 
  centroid(whichOne)              - returns the centroid position of each
                                    selection set, specified by whichOne
                                    (either 0 or 1).
 
  translatedCoords(whichOne)      - returns a sequence of vec3.Vec3s
                                    which represent the positions of the 
                                    specified selection set (by whichOne - 
                                    either 0 or 1).
 
 
 
 Read-Write accessors:
  scale           - scale factor for the potential term.
  lowerBound      - see below. If lowerBound>0, equivalent pairs
                    will be forced apart [default: 0].
  upperBound      - see below. This specifies the rmsd amount the equivalent 
                    pairs are allowed to differ [default: 0].
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
The potential term is defined as
 
  E = scale() * dRMSD^2
 
with
 
          / rmsd - upperBound, if rmsd > upperBound
  dRMSD = | rmsd - lowerBound, if rmsd < lowerBound
          \ 0                , if rmsd < upperBound and rmsd > lowerBound
 
and
 
  rmsd^2 =  1/Ni sum_i |(q_1i-q_1c) - R(q_2i-q_2c)|^2
 
where q_1i and q_2i are the average position of the ith respective
equivalent pair, and the sum is over all pairs, and Ni is the number of
equivalent pairs. R is the rotation matrix which minimizes rmsd2.
 
q_1c and q_2c are the average positions of the equivalent pair
positions, e.g.
 
  q_1c = 1/N1 * sum_i q_1i.
 
 
 

 
Classes
       
__builtin__.object
CDSList_Pair_Atom
CDSList_Pair_AtomPtr
CDSList_Pair_AtomSel
CDSList_Pair_AtomSelPtr
Modified
ModifiedPtr
ModifiedBase
ModifiedBasePtr
PosSymmPot
PosSymmPotPtr
PosSymmPot_LetterClass
PosSymmPot_LetterClassPtr

 
class CDSList_Pair_Atom(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_CDSList_Pair_Atom>)
__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 0x14b49b8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_Pair_Atom' objects>
list of weak references to the object (if defined)

 
class CDSList_Pair_AtomPtr(CDSList_Pair_Atom)
    
Method resolution order:
CDSList_Pair_AtomPtr
CDSList_Pair_Atom
__builtin__.object
Methods defined here:
__init__(self, this)
Methods inherited from CDSList_Pair_Atom:
__del__(self, destroy=<built-in function delete_CDSList_Pair_Atom>)
__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_Pair_Atom:
__dict__ = <dictproxy object at 0x14b4980>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_Pair_Atom' objects>
list of weak references to the object (if defined)

 
class CDSList_Pair_AtomSel(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_CDSList_Pair_AtomSel>)
__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 0x14b4a98>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_Pair_AtomSel' objects>
list of weak references to the object (if defined)

 
class CDSList_Pair_AtomSelPtr(CDSList_Pair_AtomSel)
    
Method resolution order:
CDSList_Pair_AtomSelPtr
CDSList_Pair_AtomSel
__builtin__.object
Methods defined here:
__init__(self, this)
Methods inherited from CDSList_Pair_AtomSel:
__del__(self, destroy=<built-in function delete_CDSList_Pair_AtomSel>)
__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_Pair_AtomSel:
__dict__ = <dictproxy object at 0x14b4a60>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_Pair_AtomSel' 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 0x14b4b40>
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 0x14b4980>
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 0x14b4788>
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 0x14b4788>
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 PosSymmPot(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_PosSymmPot>)
__deref__(*args)
__getattr__ lambda self, name
__init__(self, *args)
__mul__(*args)
__oldinit__ = __init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
addEquivAtomPair(*args)
addEquivAtomSelPair(*args)
calcEnergy(*args)
calcEnergyAndDerivs(*args)
centroid(*args)
equivAtomPairs(*args)
equivAtomSelPairs(*args)
help(*args)
incrRefCount(*args)
individualRMSDs(*args)
instanceData(*args)
instanceName(*args)
lowerBound(*args)
numEquivAtomPairs(*args)
numEquivAtomSelPairs(*args)
numEquivPairs(*args)
numRestraints(*args)
pointer(*args)
potName(*args)
registerInstanceData(*args)
registerTo(*args)
removeEquivAtomPair(*args)
removeEquivAtomSelPair(*args)
resetPotName(*args)
rms(*args)
rotMat(*args)
scale(*args)
setLowerBound(*args)
setScale(*args)
setThreshold(*args)
setUpperBound(*args)
threshold(*args)
translatedCoords(*args)
unRegister(*args)
updateValues(*args)
upperBound(*args)
violations(*args)
Properties defined here:
instanceData_
get = PosSymmPot_instanceData__get(...)
set = PosSymmPot_instanceData__set(...)
modified
get = PosSymmPot_modified_get(...)
set = PosSymmPot_modified_set(...)
registeredSimulations
get = PosSymmPot_registeredSimulations_get(...)
set = PosSymmPot_registeredSimulations_set(...)
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x14b4a28>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'instanceData_': <built-in function PosSymmPot_instanceData__get>, 'modified': <built-in function PosSymmPot_modified_get>, 'registeredSimulations': <built-in function PosSymmPot_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function PosSymmPot_instanceData__set>, 'modified': <built-in function PosSymmPot_modified_set>, 'registeredSimulations': <built-in function PosSymmPot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'PosSymmPot' objects>
list of weak references to the object (if defined)

 
class PosSymmPotPtr(PosSymmPot)
    
Method resolution order:
PosSymmPotPtr
PosSymmPot
__builtin__.object
Methods defined here:
__init__(self, this)
Methods inherited from PosSymmPot:
__del__(self, destroy=<built-in function delete_PosSymmPot>)
__deref__(*args)
__getattr__ lambda self, name
__mul__(*args)
__oldinit__ = __init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
addEquivAtomPair(*args)
addEquivAtomSelPair(*args)
calcEnergy(*args)
calcEnergyAndDerivs(*args)
centroid(*args)
equivAtomPairs(*args)
equivAtomSelPairs(*args)
help(*args)
incrRefCount(*args)
individualRMSDs(*args)
instanceData(*args)
instanceName(*args)
lowerBound(*args)
numEquivAtomPairs(*args)
numEquivAtomSelPairs(*args)
numEquivPairs(*args)
numRestraints(*args)
pointer(*args)
potName(*args)
registerInstanceData(*args)
registerTo(*args)
removeEquivAtomPair(*args)
removeEquivAtomSelPair(*args)
resetPotName(*args)
rms(*args)
rotMat(*args)
scale(*args)
setLowerBound(*args)
setScale(*args)
setThreshold(*args)
setUpperBound(*args)
threshold(*args)
translatedCoords(*args)
unRegister(*args)
updateValues(*args)
upperBound(*args)
violations(*args)
Properties inherited from PosSymmPot:
instanceData_
get = PosSymmPot_instanceData__get(...)
set = PosSymmPot_instanceData__set(...)
modified
get = PosSymmPot_modified_get(...)
set = PosSymmPot_modified_set(...)
registeredSimulations
get = PosSymmPot_registeredSimulations_get(...)
set = PosSymmPot_registeredSimulations_set(...)
Data and other attributes inherited from PosSymmPot:
__dict__ = <dictproxy object at 0x14b49b8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'instanceData_': <built-in function PosSymmPot_instanceData__get>, 'modified': <built-in function PosSymmPot_modified_get>, 'registeredSimulations': <built-in function PosSymmPot_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function PosSymmPot_instanceData__set>, 'modified': <built-in function PosSymmPot_modified_set>, 'registeredSimulations': <built-in function PosSymmPot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'PosSymmPot' objects>
list of weak references to the object (if defined)

 
class PosSymmPot_LetterClass(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_PosSymmPot_LetterClass>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
addEquivAtomPair(*args)
addEquivAtomSelPair(*args)
calcEnergy(*args)
calcEnergyAndDerivs(*args)
centroid(*args)
equivAtomPairs(*args)
equivAtomSelPairs(*args)
help(*args)
individualRMSDs(*args)
lowerBound(*args)
numEquivAtomPairs(*args)
numEquivAtomSelPairs(*args)
numEquivPairs(*args)
numRestraints(*args)
removeEquivAtomPair(*args)
removeEquivAtomSelPair(*args)
rms(*args)
rotMat(*args)
setLowerBound(*args)
setUpperBound(*args)
translatedCoords(*args)
upperBound(*args)
violations(*args)
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x14b4a60>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'PosSymmPot_LetterClass' objects>
list of weak references to the object (if defined)

 
class PosSymmPot_LetterClassPtr(PosSymmPot_LetterClass)
    
Method resolution order:
PosSymmPot_LetterClassPtr
PosSymmPot_LetterClass
__builtin__.object
Methods defined here:
__init__(self, this)
Methods inherited from PosSymmPot_LetterClass:
__del__(self, destroy=<built-in function delete_PosSymmPot_LetterClass>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
addEquivAtomPair(*args)
addEquivAtomSelPair(*args)
calcEnergy(*args)
calcEnergyAndDerivs(*args)
centroid(*args)
equivAtomPairs(*args)
equivAtomSelPairs(*args)
help(*args)
individualRMSDs(*args)
lowerBound(*args)
numEquivAtomPairs(*args)
numEquivAtomSelPairs(*args)
numEquivPairs(*args)
numRestraints(*args)
removeEquivAtomPair(*args)
removeEquivAtomSelPair(*args)
rms(*args)
rotMat(*args)
setLowerBound(*args)
setUpperBound(*args)
translatedCoords(*args)
upperBound(*args)
violations(*args)
Data and other attributes inherited from PosSymmPot_LetterClass:
__dict__ = <dictproxy object at 0x14b4788>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'PosSymmPot_LetterClass' objects>
list of weak references to the object (if defined)

 
Functions
       
help(...)