Python: module distSplinePot

distSplinePot

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)

asString(self, *args, **kwargs) -> 'String'

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