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

A splined energy term depending on the distance between two atoms. A switching
function forces the energy to zero at large distances.
 
Constructor
 
  DistSplinePot(instanceName,
                rValues,
                eValues,
                rSwitch=1,
                Simulation=None )
 
  rValues and eValues are arrays containing r values and the associented
  energy values; they must have the same length.
  Initially, rOn is set to the final value of rValues, and rOff is set to
  rOn+rSwitch.
 
Methods
 
  simulation() - return the associated simulation.Simulation.
 
  energy(r)    - return the energy associated with the specified
                 internuclear distance r.
  dE_dr(r)     - the derivative of the energy with respect to r.
 
  sw(r)        - switching function at distance r.
  dsw(r)       - derivative of the switching function with respect to r.
 
  calcEnergy() - calculate and return associated energy.
 
  addRestraint(sel0,
               sel1,
               comment="")  - add a restraint with the specified two
                              atomSel.AtomSels, and an optional comment.
 
  numRestraints()   - return the number of restaints.
  clearRestraints() - delete all restraints.
  showViolations()  - return a string with info on all violated restraints.
                      If showAllRestraints==True, all restraints are reported
                      on.
 
  restraints()      - return a list of DistSpline_Restraints, described below.
 
  info()       - return an informational string.
 
  violations() - return the number of violations.
 
Member:
 
  spline  - the raw spline.Spline object which give the unswitched
            function of r.
  
 The following parameters can be set [defaults in square brackets]
 
   rOn  - the inter-nuclear distance below which the switching function
          takes value 1.
   rOff - the inter-nuclear distance above which the switching function
          takes value 0.
   
   aveType - used to define the distance between sel0 and sel1 when one or
             both specify more than one atom. Valid values are "center", for
             using the distance between the average position of each selection,
             or "shortest" where the distance is computed from those
             two atoms which are closest together. ["center"]
 
   violEnergy - Energy above which a restraint is considered to be
                violated. [0]
 
   showAllRestraints - Controls printing of restraints during analysis. If
                       False, only violated restraints are printed. [True]
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
 
 
                      DistSpline_Restraint Class
 
Methods
  energy()   - associated energy
  violated() - the restraint is considered to be violated if
               energy()-pot.violEnergy() > pot.threshold().
 
Members:
 
  comment - string given with addRestraint
  sel0    - these are the atomSel.AtomSel objects created from the 
  sel1    - associated call to addRestraint.
 
  dist - the distance between atom selections.
 
  dv   - a unit vector in the direction q0-q1, where q0 and q1 are computed
         from sel0 and sel1, respectively.
 
  atom0 - for "shortest" aveType, these are the two atoms corresponding to the
  atom1 - shortest distance.
 
 
 
 
# 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_DistSpline_Restraint
DistSplinePot
DistSplinePot_LetterClass
Modified
ModifiedBase
Restraint_DistSplinePot
DistSpline_Restraint
rc_ptr_DistSpline_Restraint

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

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< CDS::rc_ptr< DistSpline_Restraint > >'
__getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< DistSpline_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_DistSpline_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 DistSplinePot_LetterClass(builtins.object)
    DistSplinePot_LetterClass(*args, **kwargs)
 

 
  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'
addRestraints(self, *args, **kwargs) -> 'void'
aveType(self, *args, **kwargs) -> 'DistSplinePot::DistSplineAveType const'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
clearRestraints(self, *args, **kwargs) -> 'void'
dE_dr(self, *args, **kwargs) -> 'float_type'
dsw(self, *args, **kwargs) -> 'float_type'
eValues(self, *args, **kwargs) -> 'CDSVector< float_type >'
energy(self, *args, **kwargs) -> 'float_type'
info(self, *args, **kwargs) -> 'String'
numRestraints(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rOff(self, *args, **kwargs) -> 'float_type const'
rOn(self, *args, **kwargs) -> 'float_type const'
rValues(self, *args, **kwargs) -> 'CDSVector< float_type >'
restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< DistSpline_Restraint > >'
rms(self, *args, **kwargs) -> 'float_type'
setAveType(self, *args, **kwargs) -> 'void'
setROff(self, *args, **kwargs) -> 'void'
setROn(self, *args, **kwargs) -> 'void'
setShowAllRestraints(self, *args, **kwargs) -> 'void'
setViolEnergy(self, *args, **kwargs) -> 'void'
showAllRestraints(self, *args, **kwargs) -> 'bool const'
showViolations(self, *args, **kwargs) -> 'String'
simulation(self, *args, **kwargs) -> 'Simulation *'
sw(self, *args, **kwargs) -> 'float_type'
violEnergy(self, *args, **kwargs) -> 'float_type const'
violations(self, *args, **kwargs) -> 'float_type'

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
thisown

 
The membership flag

Data and other attributes defined here:
CENTER = 0
SHORTEST = 1

 
class DistSpline_Restraint(Restraint_DistSplinePot)
    DistSpline_Restraint(*args, **kwargs)
 

 
 
Method resolution order:
DistSpline_Restraint
Restraint_DistSplinePot
builtins.object

Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
deriv(self, *args, **kwargs) -> 'void'
energy(self, *args, **kwargs) -> 'float_type'
violated(self, *args, **kwargs) -> 'bool'

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

Data descriptors defined here:
atom0

 
atom1

 
comment

 
dist

 
dv

 
sel0

 
sel1

 
thisown

 
The membership flag

Methods inherited from Restraint_DistSplinePot:
diff(self, *args, **kwargs) -> 'float_type'
name(self, *args, **kwargs) -> 'String const'
setName(self, *args, **kwargs) -> 'void'

Data descriptors inherited from Restraint_DistSplinePot:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

 
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 Restraint_DistSplinePot(builtins.object)
    Restraint_DistSplinePot(*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_DistSplinePot(...)

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_DistSpline_Restraint(builtins.object)
    rc_ptr_DistSpline_Restraint(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'DistSpline_Restraint *'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__ref__(self, *args, **kwargs) -> 'DistSpline_Restraint &'
__repr__ = _swig_repr(self)
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'
forceDelete(self, *args, **kwargs) -> 'void'
incr(self, *args, **kwargs) -> 'void'
name(self, *args, **kwargs) -> 'String const'
ptr(self, *args, **kwargs) -> 'DistSpline_Restraint *'
release(self, *args, **kwargs) -> 'DistSpline_Restraint *'
reset(self, *args, **kwargs) -> 'void'
setName(self, *args, **kwargs) -> 'void'
violated(self, *args, **kwargs) -> 'bool'

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
atom0

 
atom1

 
comment

 
dist

 
dv

 
sel0

 
sel1

 
thisown

 
The membership flag

 
realDistSplinePot = class DistSplinePot(builtins.object)
    realDistSplinePot(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'DistSplinePot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'DistSplinePot &'
__repr__ = _swig_repr(self)
addRestraint(self, *args, **kwargs) -> 'void'
addRestraints(self, *args, **kwargs) -> 'void'
aveType(self, *args, **kwargs) -> 'DistSplinePot::DistSplineAveType const'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
clearRestraints(self, *args, **kwargs) -> 'void'
dE_dr(self, *args, **kwargs) -> 'float_type'
decrRefCnt(self, *args, **kwargs) -> 'void'
dsw(self, *args, **kwargs) -> 'float_type'
eValues(self, *args, **kwargs) -> 'CDSVector< float_type >'
energy(self, *args, **kwargs) -> 'float_type'
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 *'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rOff(self, *args, **kwargs) -> 'float_type const'
rOn(self, *args, **kwargs) -> 'float_type const'
rValues(self, *args, **kwargs) -> 'CDSVector< float_type >'
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< DistSpline_Restraint > >'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
setAveType(self, *args, **kwargs) -> 'void'
setROff(self, *args, **kwargs) -> 'void'
setROn(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setShowAllRestraints(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setViolEnergy(self, *args, **kwargs) -> 'void'
showAllRestraints(self, *args, **kwargs) -> 'bool const'
showViolations(self, *args, **kwargs) -> 'String'
simulation(self, *args, **kwargs) -> 'Simulation *'
sw(self, *args, **kwargs) -> 'float_type'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
violEnergy(self, *args, **kwargs) -> 'float_type const'
violations(self, *args, **kwargs) -> 'float_type'

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

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

 
spline

 
thisown

 
The membership flag

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

 
Data
        PERIODIC_NOT = 0
PERIODIC_X = 1
PERIODIC_Y = 2