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

potential terms restraining atomic positional RMSD.
 
restrains the position of selected atoms relative to those in other
members of an ensembleSimulation.EnsembleSimulation. 
 
Constructor:
 
  It is suggested that this potential term be created using the helper 
  functions posRMSDPotTools.create_BFactorPot() or
  ncsPot.NCSPot().
 
 
  PosRMSDPot(instanceName,
             restraints="",
             simulation)  - creates a potential term with the given name. 
                         restraints is an optional string of restraints.
                         simulation should specify the appropriate 
                         EnsembleSimulation (default: 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 restraints in the given string.
 
 
  rms()                      - report rmsd value for this potential term.
  numRestraints()            - report number of restraints defined for this 
                               term.
  violations()               - report number of violations for this term.
 
  info()                     - return a string giving summary info for this
                             - term.
 
  showRestraints(violated)   - return a string listing restraints. If the 
                               boolean violated is True, only violated 
                               restraints are included, else all restraints are
                               listed.
  showViolations()           - return a string listing violated restraints.
  showPositions()            - return a string containing atom position info.
 
  restraints()               - return a list of restraints.
 
  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:
  scale         - scale factor for potential
  potType       - potential type: 'harmonic' or 'square' [default: harmonic]
  threshold     - tolerance for violation determination.
  centerSel     - selection specifying qc. If it is empty, distances are 
                  measured with respect to the origin.
  rmsdType      - string: either "bfactor" or "rap" [default: "bfactor"]
  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. [0]
  useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights
                    or to use those of the underlying EnsembleSimulation.
 
The restraint class terms have the follow members
 
  pot           - the owning potential term.
  calcd         - the most recent calculated value.
  obs           - the observed value. 
  diff          - for rmsdType='rap':
                      diff = calcd
                  for rmsdType='bfactor':
                      sqrt of V term.
                  see below.
  obsErr        - estimated error in obs 
                  (obsErrB   for rmsdType=='bfactor'
                   obsErrRAP for rmsdType=='rap'    )
  
  AtomSel sel   - atomSel.AtomSel associated with the restraint.
 
  avePos        - list of average atomic positions in each ensemble member.
  rmsd2_contrib - list of rsmd2 contributions from each ensemble member.
 
 
The potential term is defined as
 
  E = scale() * V
 
   where 
     for rmsdType='rap':
        V = calcd
     for rmsdType='bfactor':
        V = Vsq(calcd-obs,obsErrB)
     
where,
  q_{i,j} is the position of atom j in ensemble member i
  qAve_j is the ensemble-averaged position of atom j
  calcd = const sum_i w_i * rmsd2_contrib[i]
   where 
     for rmsdType='rap':
        const = 1
     for rmsdType='bfactor':
        const = 8*pi^2
  
 
  rmsd2_contrib[i] = Vsq( | (q_ij-qc) - (qAve_j-qc) | , obsErrRAP)
 
 
and
  Vsq(x,tol) = x^2             if potType=='harmonic'
               (abs(x)-tol)^2  if potType=='square'
 
 
Restraints are entered in the format:
 
  ASSIgn (atom selection) <obs> <err>
 
 
 
 
 
 
# 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_PosRMSDPot_Restraint
EnsemblePot
PosRMSDPot_LetterClass
Modified
ModifiedBase
PosRMSDPot
Restraint_PosRMSDPot
PosRMSDPot_Restraint
VarEnsWeights
rc_EnsemblePot
rc_ptr_PosRMSDPot_Restraint

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

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< CDS::rc_ptr< PosRMSDPot_Restraint > >'
__getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< PosRMSDPot_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_PosRMSDPot_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 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 PosRMSDPot_LetterClass(EnsemblePot)
    PosRMSDPot_LetterClass(*args, **kwargs)
 

 
 
Method resolution order:
PosRMSDPot_LetterClass
EnsemblePot
builtins.object

Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
addRestraints(self, *args, **kwargs) -> 'void'
centerSel(self, *args, **kwargs) -> 'AtomSel const'
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'
info(self, *args, **kwargs) -> 'String'
numRestraints(self, *args, **kwargs) -> 'int'
potType(self, *args, **kwargs) -> 'PosRMSDPot::PosRMSD_PotType'
pyXplorHelp(self, *args, **kwargs) -> 'String'
restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< PosRMSDPot_Restraint > >'
rms(self, *args, **kwargs) -> 'double'
rmsdType(self, *args, **kwargs) -> 'PosRMSDPot::PosRMSD_RMSDType'
setCenterSel(self, *args, **kwargs) -> 'void'
setPotType(self, *args, **kwargs) -> 'void'
setRMSDType(self, *args, **kwargs) -> 'void'
setShowAllRestraints(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
showAllRestraints(self, *args, **kwargs) -> 'bool const'
showPositions(self, *args, **kwargs) -> 'String'
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_PosRMSDPot_LetterClass(...)

Data descriptors defined here:
thisown

 
The membership flag

Data and other attributes defined here:
BFACTOR = 1
HARMONIC = 0
RAP = 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'
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 PosRMSDPot_Restraint(Restraint_PosRMSDPot)
    PosRMSDPot_Restraint(*args, **kwargs)
 

 
 
Method resolution order:
PosRMSDPot_Restraint
Restraint_PosRMSDPot
builtins.object

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

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

Data descriptors defined here:
calcd

 
comment_

 
obs

 
obsErr

 
ok_

 
sel

 
thisown

 
The membership flag
verbose

 

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

Data descriptors inherited from Restraint_PosRMSDPot:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

 
class Restraint_PosRMSDPot(builtins.object)
    Restraint_PosRMSDPot(*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_PosRMSDPot(...)

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_PosRMSDPot_Restraint(builtins.object)
    rc_ptr_PosRMSDPot_Restraint(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'PosRMSDPot_Restraint *'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__ref__(self, *args, **kwargs) -> 'PosRMSDPot_Restraint &'
__repr__ = _swig_repr(self)
calcAvePos(self, *args, **kwargs) -> 'void'
calcRMSDContrib(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) -> 'PosRMSDPot_Restraint *'
release(self, *args, **kwargs) -> 'PosRMSDPot_Restraint *'
reset(self, *args, **kwargs) -> 'void'
setName(self, *args, **kwargs) -> 'void'
showPositions(self, *args, **kwargs) -> 'String'
violated(self, *args, **kwargs) -> 'bool'

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
comment_

 
obs

 
obsErr

 
ok_

 
sel

 
thisown

 
The membership flag
verbose

 

 
realPosRMSDPot = class PosRMSDPot(builtins.object)
    realPosRMSDPot(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'PosRMSDPot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'PosRMSDPot &'
__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'
centerSel(self, *args, **kwargs) -> 'AtomSel const'
clearEnsWeights(self, *args, **kwargs) -> 'void'
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'
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'
potName(self, *args, **kwargs) -> 'char const *'
potType(self, *args, **kwargs) -> 'PosRMSDPot::PosRMSD_PotType'
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< PosRMSDPot_Restraint > >'
rms(self, *args, **kwargs) -> 'double'
rmsdType(self, *args, **kwargs) -> 'PosRMSDPot::PosRMSD_RMSDType'
scale(self, *args, **kwargs) -> 'float_type const'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setCenterSel(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setPotType(self, *args, **kwargs) -> 'void'
setRMSDType(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'
showPositions(self, *args, **kwargs) -> 'String'
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_PosRMSDPot(...)

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

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