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


Purely repulsive nonbonded term. This has the functional form which
depends on internuclear distance in piecewise quartic fashion.
 
   Nilges, M., Clore, G.M. and Gronenborn, A.M., ``Determination
   of three-dimensional structures of proteins from interproton
   distance data by hybrid distance geometry-dynamical simulated
   annealing calculations,'' FEBS Lett 229, 317-324 (1988).
 
 
Please use repelPotTools.create_repelPotTools to instantiate
instances of this potential term.
 
 
Constructor:
  RepelPot(instanceName,
           vdwParams,
           resExclusions,
           nbfixParams,
           selection)
 
  instanceName is a user-specified identifier, vdwParams is a map of
  atom chemical types to a list of a tuple of (eps, sigma, eps14,
  sigma14), where epsilon is a vdw well depth (unused in this term)
  and sigma is the equilibrium interatomic distance. The 14 versions
  are special values to use for atoms which are separated by three
  covalent bonds. resExclusions is a dictionary which contains pairs
  of atom names whose interactions are not to be computed. Normally,
  the interatomic distance at which the energy becomes nonzero is
  computed using the types of the two atoms involved, but exceptions
  to this rule can be specified by nbfixParams which is a dictionary
  with keys consisting of chemical types separated by the '*'
  character. The values in the dictionary is the tuple of VDW
  parameters (A,B, A14, B14). From these values sigma and sigma14 are
  computed. selection is an optional argument specifying which atoms
  in which simulation.Simulation this term should compute
  interactions for.
 
methods:
 
  calcEnergy()     - compute and return associated, scaled energy.
 
  simulation()     - return the associated Simulation.
 
  violations()     - return the number of contacts closer than threshold()
                     in all selection pairs.
 
  info()           - return an informational string.
 
  atomEnergies()   - contributions to inidivual energies - not yet supported.
 
  maxRadius()      - return the largest atomic radius
 
  typedef Pair<AtomSel,AtomSel> SelectionPair;
 
  numSelectionPairs()         - return the number of selection pairs.
 
  selectionPairs()            - return a list of selection pairs.
                         
  addSelectionPair(sel1,sel2) - add pair of atomSel.AtomSel objects
                                to compute nonbonded interactions between.
 
  setSelectionPairWeight(index
                         val) - specify a weight for the selection
                                pair identified by index.
 
  selectionPairWeight(index)  - return the associated selection pair weight.
  selectionPairEnergy(index)  - return the energy of the selection pair 
                                identified by index.
 
  nbExclusions()              - a list of lists of indices of excluded
                                interactions, indexed by atom index.
 
  deleteSelectionPair(index)  - delete the specified selection pair.
 
  resetSelectionPairs()- delete all selection pairs, and add back only
                         the default: interactions between all atoms
 
  bumps(selPairIndex)  - a list of close contacts (RepelBumps - see below),
                         closer than threshold() of the sum of the atomic
                         radii. The argument specifies a selection
                         pair index, and a negative value specifies that all 
                         selection pairs are to be reported on. [-1]
 
  neighborInfo(atom)   - return string with info about atoms in the neighbor list
                         of the specified atom. Note that if atom 1 is in atom
                         2's neighbor list, atom 2 will not be in atom 1's list.
 
  restraints()         - Return a sum of bumps() over all selection pairs.
 
 The following parameters can be set [defaults in square brackets]
 
    scale             - scale factor for energy.
    threshold         - 
    moveTol           - size of atomic displacement above which
                        recalculation of the nonbond list is
                        recalculated.
    e14Factor         - extra multiplicative factor for the 1-4
                        interaction 1.0].
    repel             - radius scale factor - see below [1.0].
    use14             - whether to disable 14 interactions
                        entirely [False].
    rMin              - smallest distance allowed for the interatomic distance
                        R [0.5]. 
 
    verbose           - a boolean describing whether or not to print
                        detailed information on the neighbor lists [False].
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
 
 
The energy is written as a sum over all atom pairs of
 
                /
  E =  scale * | ( max(rMin,R)^2 - (S R_0)^2 )^2  , for R < S R_0
               | 0                      , otherwise
                \
 
where R = | q_i - q_j |, R_0 is the sum of atomic radii specific to
the two nuclei, or specified by nxfixParams, and S is a scale factor
given by repel().
 
Each RepelBump contains the following members:
 
  atomi,
  atomj    - atoms defining the interaction
  dist     - the current intermolecular distance
  dist0    - the nominal distance (R_0) for these atoms.
  energy   - the associated, scaled energy
 
and these methods:
 
  name()     - a name for this interaction identifying the two atoms.
  diff()     - dist - dist0
  violated() - always returns True
 
 
 
# 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_Bump
CDSList_SelectionPair
Modified
ModifiedBase
PairBump
PairPot_RepelPotKernel
RepelPot_LetterClass
Pair_AtomSel_AtomSel
RepelPot
RepelPotKernel

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

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< PairBump >'
__getslice__(self, *args, **kwargs) -> 'CDSList< PairBump >'
__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_Bump(...)

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 CDSList_SelectionPair(builtins.object)
    CDSList_SelectionPair(*args)
 

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< PairPot< RepelPotKernel >::SelectionPair >'
__getslice__(self, *args, **kwargs) -> 'CDSList< PairPot< RepelPotKernel >::SelectionPair >'
__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_SelectionPair(...)

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 PairBump(builtins.object)
    PairBump(*args)
 

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

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
atomj

 
dist

 
dist0

 
energy

 
thisown

 
The membership flag

 
class PairPot_RepelPotKernel(builtins.object)
    PairPot_RepelPotKernel(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
addSelectionPair(self, *args, **kwargs) -> 'void'
atomEnergies(self, *args, **kwargs) -> 'CDSList< float_type > const &'
bumps(self, *args, **kwargs) -> 'CDSList< PairBump >'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcSelPairDerivs(self, *args, **kwargs) -> 'bool const'
defaultSelection(self, *args, **kwargs) -> 'AtomSel const'
deleteSelectionPair(self, *args, **kwargs) -> 'void'
e14Factor(self, *args, **kwargs) -> 'float_type const'
eMax(self, *args, **kwargs) -> 'float_type const'
findAtomBumps(self, *args, **kwargs) -> 'void'
info(self, *args, **kwargs) -> 'String'
moveTol(self, *args, **kwargs) -> 'float_type const'
neighborInfo(self, *args, **kwargs) -> 'String'
numRestraints(self, *args, **kwargs) -> 'int'
numSelectionPairs(self, *args, **kwargs) -> 'int'
rMin(self, *args, **kwargs) -> 'float_type const'
resetSelectionPairs(self, *args, **kwargs) -> 'void'
restraints(self, *args, **kwargs) -> 'CDSList< PairBump >'
rms(self, *args, **kwargs) -> 'float_type'
selectionPairDerivs(self, *args, **kwargs) -> 'CDSVector< Vec3 >'
selectionPairEnergy(self, *args, **kwargs) -> 'float_type'
selectionPairWeight(self, *args, **kwargs) -> 'float_type'
selectionPairs(self, *args, **kwargs) -> 'CDSList< PairPot< RepelPotKernel >::SelectionPair > const &'
setCalcSelPairDerivs(self, *args, **kwargs) -> 'void'
setE14Factor(self, *args, **kwargs) -> 'void'
setEMax(self, *args, **kwargs) -> 'void'
setMoveTol(self, *args, **kwargs) -> 'void'
setRMin(self, *args, **kwargs) -> 'void'
setSelectionPairWeight(self, *args, **kwargs) -> 'void'
setUse14(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
simulation(self, *args, **kwargs) -> 'Simulation *'
updateNeighborBin(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
use14(self, *args, **kwargs) -> 'bool const'
verbose(self, *args, **kwargs) -> 'int const'
violations(self, *args, **kwargs) -> 'float_type'

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

Readonly properties defined here:
numAtoms

 

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
selPairDerivs

 
selPairEnergies

 
selPairIncludeA

 
selPairIncludeB

 
selPairWeights

 
selPairs

 
staleGradient

 
thisown

 
The membership flag

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

 
  Methods defined here:
__eq__(self, *args, **kwargs) -> 'bool'
Return self==value.
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
b

 
thisown

 
The membership flag

Data and other attributes defined here:
__hash__ = None

 
class RepelPotKernel(builtins.object)
    RepelPotKernel(*args, **kwargs)
 

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

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
groupNames

 
maxRadius

 
pot

 
radii

 
radii14

 
repel

 
thisown

 
The membership flag
twoTo1_6

 

 
class RepelPot_LetterClass(PairPot_RepelPotKernel)
    RepelPot_LetterClass(*args, **kwargs)
 

 
 
Method resolution order:
RepelPot_LetterClass
PairPot_RepelPotKernel
builtins.object

Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
info(self, *args, **kwargs) -> 'String'
maxRadius(self, *args, **kwargs) -> 'float_type'
nbExclusions(self, *args, **kwargs) -> 'CDSList< CDSList< int > > const &'
pyXplorHelp(self, *args, **kwargs) -> 'String'
repel(self, *args, **kwargs) -> 'float_type'
setRepel(self, *args, **kwargs) -> 'void'

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

Data descriptors defined here:
thisown

 
The membership flag

Methods inherited from PairPot_RepelPotKernel:
addSelectionPair(self, *args, **kwargs) -> 'void'
atomEnergies(self, *args, **kwargs) -> 'CDSList< float_type > const &'
bumps(self, *args, **kwargs) -> 'CDSList< PairBump >'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcSelPairDerivs(self, *args, **kwargs) -> 'bool const'
defaultSelection(self, *args, **kwargs) -> 'AtomSel const'
deleteSelectionPair(self, *args, **kwargs) -> 'void'
e14Factor(self, *args, **kwargs) -> 'float_type const'
eMax(self, *args, **kwargs) -> 'float_type const'
findAtomBumps(self, *args, **kwargs) -> 'void'
moveTol(self, *args, **kwargs) -> 'float_type const'
neighborInfo(self, *args, **kwargs) -> 'String'
numRestraints(self, *args, **kwargs) -> 'int'
numSelectionPairs(self, *args, **kwargs) -> 'int'
rMin(self, *args, **kwargs) -> 'float_type const'
resetSelectionPairs(self, *args, **kwargs) -> 'void'
restraints(self, *args, **kwargs) -> 'CDSList< PairBump >'
rms(self, *args, **kwargs) -> 'float_type'
selectionPairDerivs(self, *args, **kwargs) -> 'CDSVector< Vec3 >'
selectionPairEnergy(self, *args, **kwargs) -> 'float_type'
selectionPairWeight(self, *args, **kwargs) -> 'float_type'
selectionPairs(self, *args, **kwargs) -> 'CDSList< PairPot< RepelPotKernel >::SelectionPair > const &'
setCalcSelPairDerivs(self, *args, **kwargs) -> 'void'
setE14Factor(self, *args, **kwargs) -> 'void'
setEMax(self, *args, **kwargs) -> 'void'
setMoveTol(self, *args, **kwargs) -> 'void'
setRMin(self, *args, **kwargs) -> 'void'
setSelectionPairWeight(self, *args, **kwargs) -> 'void'
setUse14(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
simulation(self, *args, **kwargs) -> 'Simulation *'
updateNeighborBin(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
use14(self, *args, **kwargs) -> 'bool const'
verbose(self, *args, **kwargs) -> 'int const'
violations(self, *args, **kwargs) -> 'float_type'

Readonly properties inherited from PairPot_RepelPotKernel:
numAtoms

 

Data descriptors inherited from PairPot_RepelPotKernel:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
selPairDerivs

 
selPairEnergies

 
selPairIncludeA

 
selPairIncludeB

 
selPairWeights

 
selPairs

 
staleGradient

 

 
realRepelPot = class RepelPot(builtins.object)
    realRepelPot(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'RepelPot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'RepelPot &'
__repr__ = _swig_repr(self)
addSelectionPair(self, *args, **kwargs) -> 'void'
atomEnergies(self, *args, **kwargs) -> 'CDSList< float_type > const &'
bumps(self, *args, **kwargs) -> 'CDSList< PairBump >'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcSelPairDerivs(self, *args, **kwargs) -> 'bool const'
decrRefCnt(self, *args, **kwargs) -> 'void'
defaultSelection(self, *args, **kwargs) -> 'AtomSel const'
deleteSelectionPair(self, *args, **kwargs) -> 'void'
e14Factor(self, *args, **kwargs) -> 'float_type const'
eMax(self, *args, **kwargs) -> 'float_type const'
findAtomBumps(self, *args, **kwargs) -> 'void'
incrRefCnt(self, *args, **kwargs) -> 'void'
info(self, *args, **kwargs) -> 'String'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
maxRadius(self, *args, **kwargs) -> 'float_type'
moveTol(self, *args, **kwargs) -> 'float_type const'
nbExclusions(self, *args, **kwargs) -> 'CDSList< CDSList< int > > const &'
neighborInfo(self, *args, **kwargs) -> 'String'
numRestraints(self, *args, **kwargs) -> 'int'
numSelectionPairs(self, *args, **kwargs) -> 'int'
potName(self, *args, **kwargs) -> 'char const *'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rMin(self, *args, **kwargs) -> 'float_type const'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
repel(self, *args, **kwargs) -> 'float_type'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
resetSelectionPairs(self, *args, **kwargs) -> 'void'
restraints(self, *args, **kwargs) -> 'CDSList< PairBump >'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
selectionPairDerivs(self, *args, **kwargs) -> 'CDSVector< Vec3 >'
selectionPairEnergy(self, *args, **kwargs) -> 'float_type'
selectionPairWeight(self, *args, **kwargs) -> 'float_type'
selectionPairs(self, *args, **kwargs) -> 'CDSList< PairPot< RepelPotKernel >::SelectionPair > const &'
setCalcSelPairDerivs(self, *args, **kwargs) -> 'void'
setE14Factor(self, *args, **kwargs) -> 'void'
setEMax(self, *args, **kwargs) -> 'void'
setMoveTol(self, *args, **kwargs) -> 'void'
setRMin(self, *args, **kwargs) -> 'void'
setRepel(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setSelectionPairWeight(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setUse14(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
simulation(self, *args, **kwargs) -> 'Simulation *'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateNeighborBin(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
use14(self, *args, **kwargs) -> 'bool const'
verbose(self, *args, **kwargs) -> 'int const'
violations(self, *args, **kwargs) -> 'float_type'

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

Readonly properties defined here:
numAtoms

 

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
instanceDataCreate

 
instanceData_

 
kernel

 
modified

 
registeredSimulations

 
selPairDerivs

 
selPairEnergies

 
selPairIncludeA

 
selPairIncludeB

 
selPairWeights

 
selPairs

 
staleGradient

 
thisown

 
The membership flag

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