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

potential term for restraining the distance between atoms and a plane.
Please use the helper function create_PlaneDistPot in the module 
planeDistTools to simplify creation of this term.
 
This term was first described in 
 Chenqi Xu, Etienne Gagnon, Matthew E. Call, Jason
 R. Schnell, Charles D. Schwieters, Christopher V. Carman,
 James J. Chou, and Kai W. Wucherpfennig, ``Regulation of T
 cell Receptor Activation by Dynamic Membrane Binding of the
 CD3epsilon Cytoplasmic Tyrosine-Based Motif,'' Cell 135,
 702-713 (2008).
 
 
constructor: PlaneDistPot(instanceName,
                          oAtom, xAtom, yAtom,
                          restraintList,
                          sim                )
 
  instanceName is a user-specified identifier
  oAtom, xAtom, yAtom are atoms defining the plane.
  restraintList is an optional XPLOR-style restraint table (string).
  sim, is an optional simulation.Simulation specification
  [they default to the current Simulation.]
 
methods
  planeNorm()                  - the current value of the plane normal.
  addRestraints(restraintList) - add the specified XPLOR-style restraints
 
  calcEnergy()                 - calc energy, returns the energy value.
  calcEnergyAndDerivs(derivs)  - calc energy, derivs, returns the energy value.
 
  rms()            - return the restraint rms violation
  numRestraints()  - return the number of restraints defined for this term.
  violations()     - return number of violations
  
  info()                    - current info about the state of this instance
  showRestraints(violated)  - return info on restraints. Argument violated is
                              boolean specifying whether to return only 
                              violated restraints.
  showViolations()          - return string containing pretty-printed info
                              on all violated restraints.
 
 The following parameters can be set [defaults in square brackets]
 
  oAtom      - the plane-defining atoms
  xAtom  
  yAtom      
  useSign    - whether to consider the sign of the plane-atom distance.
               If True, one can specify on which side of the plane the
               atoms lay. [False]
  nMono      - number of monomers [1]
  verbose    - if true, sporadically spit out info [False]
  scale      - scale factor [1]
  aveExp     - exponential to use in sum averaging [6]
  dOffset    - potential offset [0]
  hardExp    - exponential in hard region of potential [2]
  rSwitch    - distance at which to switch from hard form [0.5]
  softExp    - exponential in soft region of potential [1]
  asympSlope - slope in linear asymptotic region of pot [1]
  threshold  - threshold in violation calculation [0.5]
  potType    - type of potential: "soft", "hard", "gaussian", or
               "sigmoid" [hard]
  freedom    - topology specification for the plane atoms or pseudo-atoms.
               This is described in more detail in 
               planeDistTools.topologySetup.
               The default, "group" is allows the restraining plane to
               rotation and translate. "ignore" is appropriate if the 
               restraining plane is defined using actual atoms, "translate" 
               will allow the plane to translate only, "rotate" allows only 
               plane rotation, "fix" will fix the plane in space, and "free"
               should normally not be used.
  aveType    - type of restraint averaging: "average", "center" or "sum" [sum]
  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. [False]
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
 
 The energy function is defined as
 
        if potType=gaussian:
             scale * weight * exp( -1/2 * r^2/ hardExp^2 )
 
        if potType=sigmoid:
             scale * weight / ( 1 + ( dist / cdist )^hardExp )
 
        if potType=HARD or  r<rSwitch: 
                scale * weight * r^hardExp
        potType=SOFT and r>rSwitch: 
                scale * weight *(a + b / r^softExp + asympSlope * r)
 
        where
        b =  rSwitch^(softExp+1) * 
            (asympSlope - hardExp * rSwitch^(hardExp-1)) / softExp
        a = rSwitch^hardExp - b * rSwitch^(-softExp) - 
            asympSlope * rSwitch;
        
 The distance r is related to the calculated restraint distance d by:
        if d < cdist - cMinus:      r = cdist - d - cMinus
        if d > cdist+cPlus-dOffset: r = d - (cdist + cPlus - dOffset )
        otherwise, r = 0
 
 The restraint distance d is calculated as
   for aveTypes=average,sum:
         d = sig(sumPow) [ |sumPow| ] ^(-1/aveExp)
 
      where for aveType=average:
       sumPow = sum_i sig(dot(q_i-p1, n)) * | dot(q_i-p1, n) |^(-aveExp) / Ni ]
      for aveType=sum:
       sumPow = sum_i sig(dot(q_i-p1, n))* | dot(q_i-p1, n) |^(-aveExp) / nMono
        
      q_i is the position of the i-th atom, and Ni is the number
      of atoms in the sum. p1 is the position of oAtom, while n is the unit
      vector in the direction 
          (p2-p1) X (p3-p1),
      where p2 is xAtom.pos() and p3 is yAtom.pos(). The function sig is
 
          sig(x) = sign(x)  if useSign==True
                   1        if useSign==False
 
   for aveType=center:
        d = | dot(sum_i q_i/Ni - p1, n) | * sig(dot(sum_i q_i/Ni - p1, n))
      
PlaneDist restraint table format:
 
  ASSIgn <selection>  <cDist> <cMinus> <cPlus> ! optional comment
 
the statement can be split across muliple lines, but the comment, if
specified, should be on the same line at cPlus.
 
  WEIGHT <value>
 
set the per-restraint weight value for restraints subsequently added.
 
 
 
# 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_PlaneDistRestraint
Modified
ModifiedBase
PlaneDistPot
PlaneDistPot_LetterClass
Restraint_PlaneDistPot
PlaneDistRestraint
rc_ptr_PlaneDistRestraint

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

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< CDS::rc_ptr< PlaneDistRestraint > >'
__getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< PlaneDistRestraint > >'
__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_PlaneDistRestraint(...)

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 PlaneDistPot_LetterClass(builtins.object)
    PlaneDistPot_LetterClass(*args, **kwargs)
 

 
  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'
asympSlope(self, *args, **kwargs) -> 'float_type const'
aveExp(self, *args, **kwargs) -> 'float_type const'
aveType(self, *args, **kwargs) -> 'PlaneDistPot::PlaneDistAveType'
calcDerivs(self, *args, **kwargs) -> 'void'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
dOffset(self, *args, **kwargs) -> 'float_type const'
freedom(self, *args, **kwargs) -> 'String const'
hardExp(self, *args, **kwargs) -> 'float_type const'
info(self, *args, **kwargs) -> 'String'
nMono(self, *args, **kwargs) -> 'int const'
numRestraints(self, *args, **kwargs) -> 'int'
oAtom(self, *args, **kwargs) -> 'Atom const'
planeNorm(self, *args, **kwargs) -> 'Vec3'
potType(self, *args, **kwargs) -> 'PlaneDistPot::PlaneDistPotType'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rSwitch(self, *args, **kwargs) -> 'float_type const'
restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< PlaneDistRestraint > >'
rms(self, *args, **kwargs) -> 'double'
setAsympSlope(self, *args, **kwargs) -> 'void'
setAveExp(self, *args, **kwargs) -> 'void'
setAveType(self, *args, **kwargs) -> 'void'
setDOffset(self, *args, **kwargs) -> 'void'
setFreedom(self, *args, **kwargs) -> 'void'
setHardExp(self, *args, **kwargs) -> 'void'
setNMono(self, *args, **kwargs) -> 'void'
setOAtom(self, *args, **kwargs) -> 'void'
setPotType(self, *args, **kwargs) -> 'void'
setRSwitch(self, *args, **kwargs) -> 'void'
setShowAllRestraints(self, *args, **kwargs) -> 'void'
setSoftExp(self, *args, **kwargs) -> 'void'
setUseSign(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
setXAtom(self, *args, **kwargs) -> 'void'
setYAtom(self, *args, **kwargs) -> 'void'
showAllRestraints(self, *args, **kwargs) -> 'bool const'
showRestraints(self, *args, **kwargs) -> 'String'
showViolations(self, *args, **kwargs) -> 'String'
simulation(self, *args, **kwargs) -> 'Simulation *'
softExp(self, *args, **kwargs) -> 'float_type const'
updateValues(self, *args, **kwargs) -> 'void'
useSign(self, *args, **kwargs) -> 'bool const'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'
xAtom(self, *args, **kwargs) -> 'Atom const'
yAtom(self, *args, **kwargs) -> 'Atom const'

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

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:
AVERAGE = 0
CENTER = 1
GAUSSIAN = 3
HARD = 1
LOGNORMAL = 2
SIGMOID = 4
SOFT = 0
SUM = 2

 
class PlaneDistRestraint(Restraint_PlaneDistPot)
    PlaneDistRestraint(*args, **kwargs)
 

 
 
Method resolution order:
PlaneDistRestraint
Restraint_PlaneDistPot
builtins.object

Methods defined here:
__eq__(self, *args, **kwargs) -> 'void'
Return self==value.
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
asString(self, *args, **kwargs) -> 'String'
calcDistanceDiff(self, *args, **kwargs) -> 'double'
comment(self, *args, **kwargs) -> 'String'
d(self, *args, **kwargs) -> 'double'
dMinus(self, *args, **kwargs) -> 'double'
dPlus(self, *args, **kwargs) -> 'double'
deriv(self, *args, **kwargs) -> 'void'
dist(self, *args, **kwargs) -> 'double'
energy(self, *args, **kwargs) -> 'double'
logDiff(self, *args, **kwargs) -> 'double'
name(self, *args, **kwargs) -> 'String'
ok(self, *args, **kwargs) -> 'int'
setWeight(self, *args, **kwargs) -> 'void'
status(self, *args, **kwargs) -> 'PlaneDistRestraint::Status'
weight(self, *args, **kwargs) -> 'float_type'

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

Data descriptors defined here:
sel

 
thisown

 
The membership flag
variance

 
verbose

 

Data and other attributes defined here:
GREATER = 1
INSIDE = 2
LESS = 0
__hash__ = None

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

Data descriptors inherited from Restraint_PlaneDistPot:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

 
class Restraint_PlaneDistPot(builtins.object)
    Restraint_PlaneDistPot(*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_PlaneDistPot(...)

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_PlaneDistRestraint(builtins.object)
    rc_ptr_PlaneDistRestraint(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'PlaneDistRestraint *'
__eq__(self, *args, **kwargs) -> 'void'
Return self==value.
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__ref__(self, *args, **kwargs) -> 'PlaneDistRestraint &'
__repr__ = _swig_repr(self)
asString(self, *args, **kwargs) -> 'String'
calcDistanceDiff(self, *args, **kwargs) -> 'double'
comment(self, *args, **kwargs) -> 'String'
count(self, *args, **kwargs) -> 'int'
d(self, *args, **kwargs) -> 'double'
dMinus(self, *args, **kwargs) -> 'double'
dPlus(self, *args, **kwargs) -> 'double'
decr(self, *args, **kwargs) -> 'void'
deriv(self, *args, **kwargs) -> 'void'
diff(self, *args, **kwargs) -> 'float_type'
dist(self, *args, **kwargs) -> 'double'
energy(self, *args, **kwargs) -> 'double'
forceDelete(self, *args, **kwargs) -> 'void'
incr(self, *args, **kwargs) -> 'void'
logDiff(self, *args, **kwargs) -> 'double'
name(self, *args, **kwargs) -> 'String'
ok(self, *args, **kwargs) -> 'int'
ptr(self, *args, **kwargs) -> 'PlaneDistRestraint *'
release(self, *args, **kwargs) -> 'PlaneDistRestraint *'
reset(self, *args, **kwargs) -> 'void'
setName(self, *args, **kwargs) -> 'void'
setWeight(self, *args, **kwargs) -> 'void'
status(self, *args, **kwargs) -> 'PlaneDistRestraint::Status'
violated(self, *args, **kwargs) -> 'bool'
weight(self, *args, **kwargs) -> 'float_type'

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
thisown

 
The membership flag
variance

 
verbose

 

Data and other attributes defined here:
__hash__ = None

 
realPlaneDistPot = class PlaneDistPot(builtins.object)
    realPlaneDistPot(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'PlaneDistPot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'PlaneDistPot &'
__repr__ = _swig_repr(self)
addRestraints(self, *args, **kwargs) -> 'void'
asympSlope(self, *args, **kwargs) -> 'float_type const'
aveExp(self, *args, **kwargs) -> 'float_type const'
aveType(self, *args, **kwargs) -> 'PlaneDistPot::PlaneDistAveType'
calcDerivs(self, *args, **kwargs) -> 'void'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
dOffset(self, *args, **kwargs) -> 'float_type const'
decrRefCnt(self, *args, **kwargs) -> 'void'
freedom(self, *args, **kwargs) -> 'String const'
hardExp(self, *args, **kwargs) -> 'float_type const'
incrRefCnt(self, *args, **kwargs) -> 'void'
info(self, *args, **kwargs) -> 'String'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
nMono(self, *args, **kwargs) -> 'int const'
numRestraints(self, *args, **kwargs) -> 'int'
oAtom(self, *args, **kwargs) -> 'Atom const'
planeNorm(self, *args, **kwargs) -> 'Vec3'
potName(self, *args, **kwargs) -> 'char const *'
potType(self, *args, **kwargs) -> 'PlaneDistPot::PlaneDistPotType'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rSwitch(self, *args, **kwargs) -> 'float_type const'
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< PlaneDistRestraint > >'
rms(self, *args, **kwargs) -> 'double'
scale(self, *args, **kwargs) -> 'float_type const'
setAsympSlope(self, *args, **kwargs) -> 'void'
setAveExp(self, *args, **kwargs) -> 'void'
setAveType(self, *args, **kwargs) -> 'void'
setDOffset(self, *args, **kwargs) -> 'void'
setFreedom(self, *args, **kwargs) -> 'void'
setHardExp(self, *args, **kwargs) -> 'void'
setNMono(self, *args, **kwargs) -> 'void'
setOAtom(self, *args, **kwargs) -> 'void'
setPotType(self, *args, **kwargs) -> 'void'
setRSwitch(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setShowAllRestraints(self, *args, **kwargs) -> 'void'
setSoftExp(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setUseSign(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
setXAtom(self, *args, **kwargs) -> 'void'
setYAtom(self, *args, **kwargs) -> 'void'
showAllRestraints(self, *args, **kwargs) -> 'bool const'
showRestraints(self, *args, **kwargs) -> 'String'
showViolations(self, *args, **kwargs) -> 'String'
simulation(self, *args, **kwargs) -> 'Simulation *'
softExp(self, *args, **kwargs) -> 'float_type const'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
useSign(self, *args, **kwargs) -> 'bool const'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'
xAtom(self, *args, **kwargs) -> 'Atom const'
yAtom(self, *args, **kwargs) -> 'Atom const'

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

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
       
PlaneDistPot(*args)
pyXplorHelp(*args) -> 'String'