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Pydoc: module vecPairOrientPot
 
vecPairOrientPot		 index


Energy term to restrain angles between vectors defined by two pair of atom
selections.
 
 
Constructor:   
 
  VecPairOrientPot(instanceName,
                   restraintString="",
                   simulation=None)
 
  instanceName is a user-specified identifier. The restraintString argument
  is an optional XPLOR-style restraint table. simulation is an optional 
  simulation.Simulation specification. If not specified, the
  simulation.currentSimulation() is used.
 
 
  calcEnergy()                 - calc energy, returns the energy value.
  calcEnergyAndDerivs(derivs)  - calc energy, derivs, returns the energy value.
 
 
 
  rms()           - return the rms of the restriants' diff() values.
  numRestraints() - return the number of restraints defined for this term.
  violations()    - return number of violations
 
 
  restraints() - return the list of restraints. See the description of the
                 Restraint class below. Restraint properties can thus be
                 queried and modified.
 
  readRestraints(restraintString,
                 verbose=False) - add restraints specified in restraintString.
 
  addRestraint(abbrevString,
               ensIndex1=-1,
               ensIndex2=-1,
               verbose=False) -add the specified XPLOR-style restraint.
                               The abbrevString format is the same as the
                               format below, but with the leading ASSIgn
                               keyword omitted. This method can be used to
                               add restraints between different ensemble
                               members in an ensembleSimulation
                               calculation, where ensIndex1 and
                               ensIndex2 specify indices of the
                               respective EnsembleMemberSimulations.
 
 
VecPairOrient_Restraint Class
 
  These are created by the VecPairOrientPot's readRestraints orr
  addRestraint methods.
 
methods:
 
  name()    - the restraint name
  comment() - the restraint comment (entered after the ! in the PRE table)
 
  calcd()   - calculated value of vector pair angle (in degrees) -
              θ  in the equations below.
  target()  - target angle value (in degrees) - θ0  in the equations below.
  err()     - allowed deviation of the angle (in degrees) -  Δθ  in the equations below.
 
  setTarget(val) - set the target value (θ0 ).
  setErr(val)    - set the err value (Δθ ).
 
  energy() - energy associated with this restraint (see below).
 
  
  sel11() - atomSel.AtomSel object defining  q11
  sel12()  - atomSel.AtomSel object defining  q12
  sel21()  - atomSel.AtomSel object defining  q21
  sel22()  - atomSel.AtomSel object defining  q22
 
  
  v1() - The vector v1  below. 
  v2() - The vector v2  below.
 
 
 
<string>

The energy of each restraint is

EVPO = ⎛⎜⎜⎜⎜⎜⎝ (θ − θ0 − Δθ)2  for θ > θ0 + Δθ     0  for |θ − θ0| < Δθ     (θ − θ0 + Δθ)2  for θ < θ0 − Δθ    

where cos(θ) = v̂1⋅ v̂2 and v̂ denotes unit vector in the direction of v.

The vectors v1 and v2 are defined as vi = qi2 −  qi1, i = 1, 2, where qi1 and qi2 are the average positions in the selections seli1 and seli2.


 
 
 
# 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_VecPairOrient_Restraint
EnsemblePot
VecPairOrientPot_LetterClass
Modified
ModifiedBase
Restraint_VecPairOrient
VecPairOrient_Restraint
VarEnsWeights
VecPairOrientPot
rc_EnsemblePot
rc_ptr_VecPairOrient_Restraint

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

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< CDS::rc_ptr< VecPairOrient_Restraint > >'
__getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< VecPairOrient_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_VecPairOrient_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) -> 'EnsembleSimulationBase 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)
asString(self, *args, **kwargs) -> 'String'
assertClear(self, *args, **kwargs) -> 'void'
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 Restraint_VecPairOrient(builtins.object)
    Restraint_VecPairOrient(*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_VecPairOrient(...)
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 VecPairOrientPot_LetterClass(EnsemblePot)
    VecPairOrientPot_LetterClass(*args, **kwargs)
 

 
 
Method resolution order:
VecPairOrientPot_LetterClass
EnsemblePot
builtins.object
Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
addRestraint(self, *args, **kwargs) -> 'void'
energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type'
numRestraints(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
readRestraints(self, *args, **kwargs) -> 'void'
restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< VecPairOrient_Restraint > > &'
rms(self, *args, **kwargs) -> 'float_type'
violations(self, *args, **kwargs) -> 'float_type'
Static methods defined here:
__swig_destroy__ = delete_VecPairOrientPot_LetterClass(...)
Data descriptors defined here:
thisown

 
The membership flag
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'
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) -> 'EnsembleSimulationBase 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 VecPairOrient_Restraint(Restraint_VecPairOrient)
    VecPairOrient_Restraint(*args, **kwargs)
 

 
 
Method resolution order:
VecPairOrient_Restraint
Restraint_VecPairOrient
builtins.object
Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
calcd(self, *args, **kwargs) -> 'float_type const &'
comment(self, *args, **kwargs) -> 'String const &'
deriv(self, *args, **kwargs) -> 'void'
energy(self, *args, **kwargs) -> 'float_type'
err(self, *args, **kwargs) -> 'float_type const &'
name(self, *args, **kwargs) -> 'String'
ok(self, *args, **kwargs) -> 'bool'
sel11(self, *args, **kwargs) -> 'AtomSel const &'
sel12(self, *args, **kwargs) -> 'AtomSel const &'
sel21(self, *args, **kwargs) -> 'AtomSel const &'
sel22(self, *args, **kwargs) -> 'AtomSel const &'
setErr(self, *args, **kwargs) -> 'void'
setTarget(self, *args, **kwargs) -> 'void'
target(self, *args, **kwargs) -> 'float_type const &'
v1(self, *args, **kwargs) -> 'Vec3 const &'
v2(self, *args, **kwargs) -> 'Vec3 const &'
Static methods defined here:
__swig_destroy__ = delete_VecPairOrient_Restraint(...)
Data descriptors defined here:
thisown

 
The membership flag
Methods inherited from Restraint_VecPairOrient:
diff(self, *args, **kwargs) -> 'float_type'
setName(self, *args, **kwargs) -> 'void'
violated(self, *args, **kwargs) -> 'bool'
Data descriptors inherited from Restraint_VecPairOrient:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

 
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_VecPairOrient_Restraint(builtins.object)
    rc_ptr_VecPairOrient_Restraint(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'VecPairOrient_Restraint *'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__ref__(self, *args, **kwargs) -> 'VecPairOrient_Restraint &'
__repr__ = _swig_repr(self)
calcd(self, *args, **kwargs) -> 'float_type const &'
comment(self, *args, **kwargs) -> 'String const &'
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) -> 'float_type'
err(self, *args, **kwargs) -> 'float_type const &'
forceDelete(self, *args, **kwargs) -> 'void'
incr(self, *args, **kwargs) -> 'void'
name(self, *args, **kwargs) -> 'String'
ok(self, *args, **kwargs) -> 'bool'
ptr(self, *args, **kwargs) -> 'VecPairOrient_Restraint *'
release(self, *args, **kwargs) -> 'VecPairOrient_Restraint *'
reset(self, *args, **kwargs) -> 'void'
sel11(self, *args, **kwargs) -> 'AtomSel const &'
sel12(self, *args, **kwargs) -> 'AtomSel const &'
sel21(self, *args, **kwargs) -> 'AtomSel const &'
sel22(self, *args, **kwargs) -> 'AtomSel const &'
setErr(self, *args, **kwargs) -> 'void'
setName(self, *args, **kwargs) -> 'void'
setTarget(self, *args, **kwargs) -> 'void'
target(self, *args, **kwargs) -> 'float_type const &'
v1(self, *args, **kwargs) -> 'Vec3 const &'
v2(self, *args, **kwargs) -> 'Vec3 const &'
violated(self, *args, **kwargs) -> 'bool'
Static methods defined here:
__swig_destroy__ = delete_rc_ptr_VecPairOrient_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

 
realVecPairOrientPot = class VecPairOrientPot(builtins.object)
    realVecPairOrientPot(*args, **kwargs)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'VecPairOrientPot *'
__init__(self, *args, **kwargs)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'VecPairOrientPot &'
__repr__ = _swig_repr(self)
addEnsWeights(self, *args, **kwargs) -> 'void'
addRestraint(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'
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'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
numRestraints(self, *args, **kwargs) -> 'int'
potName(self, *args, **kwargs) -> 'char const *'
pyXplorHelp(self, *args, **kwargs) -> 'String'
readRestraints(self, *args, **kwargs) -> 'void'
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< VecPairOrient_Restraint > > &'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
setCalcWDerivs(self, *args, **kwargs) -> 'void'
setEnsWeights(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
simulation(self, *args) -> 'EnsembleSimulationBase 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'
violations(self, *args, **kwargs) -> 'float_type'
Static methods defined here:
__swig_destroy__ = delete_VecPairOrientPot(...)
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
       
VecPairOrientPot(*args, **kwargs)
pyXplorHelp(*args) -> 'String'