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

DiffPot:
Potential term to restrain components of observed protein rotation diffusion tensor.
 
Creating a DiffPot with Python user interface: create_DiffPot(name, sel = "known", temperature = 293 )
 returns a pointer to DiffPot object. 
 
 Optional arguments: addAtoms, mass, link_to
 
 Defined in diffPotTools.py
  
  name                            - is an instance name which later transferred to C++ constructor.
 
  sel                             - string specifying selection rules which is later transferred to 
                                    C++ constructor of surfTesselation object if it is necessary to create.
                                    Could be left blank when calling this method.
                                    Default value "known and (not PSEUDO)" means selection only the atoms 
                                    with known coordinates. Must NOT be reevaluated later.
 
  temperature                     - Temperature of water where protein tumbles. 
                                    if leaved blank when calling this method assumes the default value 293 K.
                                    When this parameter is explicitly defined create_DiffPot reevaluates 
                                    the factor accounting for viscosity and temperature of solvent, diffTmpF, for 
                                    given temperature, in Kelvins, assuming tumbling in water.
                                    If solvent is different then diffTmpF cloud be set through Python interface 
                                    using setDiffTmpF( TmpF ).
                                    For definitions of diffTmpF see below.
  
  addAtoms                        - Boolean argument which specifies the pseudoatoms used for temperature 
                                    optimization created or not. If leaved blank the default value "False" is 
                                    assumed. If set "True" then the pseudoatoms will be created.
 
  mass                            - Effective mass of pseudoatoms. Default value is 1000.
 
  link_to                         - A pointer to surfTessellation object. Used to use the same surfTessellation in 
                                    several potential terms. diffPot of relaxRatioPot could be used instead
                                    of surfTessellation. In this case the pointer to surfTessellation object
                                    will be extracted from a potential automatically. If leaved blank then 
                                    new surfTessellation created using provided sel.                                      
 
C++ constructor: DiffPot( instanceName, sTess )
 
  instanceName                    - user-specified identifier.
 
  sTess                           - rc pointer to surfTesslation class object.
 
methods
 
  Tessellation()                  - returns rc pointer to the surfTessellation class object
                                    where the potential term is linked to.
 
  getAtomSel()                    - returns atom selection which is used to build the surfTessellation
                                    class object where the potential term is linked to.
 
  calcEnergy()                    - returns the energy value.
 
  calcEnergy_eigen()              - returns the energy value based on 
                                    difference of eigen values only.
 
  calcEnergyAndDerivs(derivs)     - calc energy, derivs, returns the energy value.
 
  rms()                           - return the magnitude of violation of this
                                    term -- abs(diff).
 
  rms_eigen()                     - return the magnitude of violation of this
                                    term  based on difference of eigen values only.
 
  scale()                         - scale factor exposed to user  for this energy term.
 
  sacle_Lin()                     - internal scale factor which scales derivatives and 
                                    energy with protein size: defined in diffPotTools.py. 
 
  diffShell()                     - hydration layer thickness. 
                                    Note: changes the shell thickness in surfTessellation 
                                    object where the potential is linked to. Thus, if changed for 
                                    one object then affects all the potential terms which are sharing 
                                    the same surfTessellation object.
                   
  diffTmpF()                      - factor which accounts for viscosity and temperature 
                                    of solvent.
 
  get_TmpF( double Temperature )  - returns the values of above factor calculated for water
                                    at given temperature.
 
  diffTarget()                    - target values of rotation diffusion tensor components.
 
  diffRrmsd()                     - the value of rmsd separating current structure and
                                    the one that was used for tessellation of the protein
                                    surface last time which triggers new retessellation 
                                    of the protein surface.
 
  diffRstep()                     - the number of derivatives calculations events which 
                                    triggers new retessellation of the protein surface.
 
  get_rmsd()                      - calculates rmsd separating current structure and
                                    the one that was used for tessellation of the protein
                                    surface last time.
 
  Diff_Tensor()                   - calculates components of diffusion tensor for
                                    the current structure.
 
  setMedianTmp()                  - sets value of nominal temperature when temperature optimization 
                                    is enabled.
 
  getMedianTmp()                  - returns value of nominal temperature.
 
  rangeTmpFit()                   - +/- range of temperature variations used for temperature optimization.
 
  curr_Tmp()                      - returns value of current temperature calculated form the positions
                                    of pseudoatoms when temperature optimization is enabled  
 
  info()                          - current info about the state of this potential.
 
  help()                          - this help.
 
 The following parameters can be set [defaults in square brackets]
 
  scale [1]                       - dimensionless
 
  sacle_Lin[200*(N_atoms/855)]    - dimensionless 
                                    linear scaling calibrated using protein G example 
                                    Equal 200 for a 855 residue protein. 
                                    Defined in diffPotTools.py.
 
  setMedianTmp [293]              - nominal temperature is the same as the value
                                    of temperature parameter provided in Python
                                    constructor.
 
  rangeTmpFit [0]                 - default value assumes no temperature optimization.
 
  diffShell [2.8]                 - Angstroms. Default value resembles a monolayer 
                                    of water molecules covering protein surface. 
 
  diffTmpF [80315402327.6]        - 1/s. Defult value corresponds to water at 293 K. 
                                    See definition below.
 
  diffTarget [0]                  - dummy zero input which must be reset with 
                                    meaningful values before the calculations.
 
  diffRrmsd [0.5]                 - Angstroms
 
  diffRstep [30]                  - dimensionless
                                 
 
 The diffusion tensor is calculated using ellipsoid approximation derived from covariance matrix 
 for points of hydrated protein surface obtained as a result of tessellation.
 
  The details of this method described in: Y. Ryabov, C. Geraghty, A. Varshney, and D. Fushman, 
  "An Efficient Computational Method for Predicting Rotational Diffusion Tensors of Globular Proteins
  Using an Ellipsoid Representation", J. Am. Chem. Soc. 128: 15432-15444 (2006)
 
  The subroutine for surface tessellation is build on the bases of surf program: A. Varshney, F.P. 
  Brooks Jr., W.V. Wright IEEE "Computing smooth molecular surfaces" Comput. Graphics Appl. 14: 19-25 (1994)
 
 The temperature factor, diffTmpF, absorbs dependency of rotation diffusion parameters on temperature, 
 viscosity of solvent as well as some other constants and conversion factors.
 
 diffTmpF defined as:  
 
  diffTmpF = (1.38e-23)*TmP/(16*P_I*eta_t*(1e-30))
 
  where 
 
  1.38e-23, [J/K]                 - is Boltzmann constant.
      
  PI = 3.14159265                 - is irrational pi ratio between length of a circle and its diameter.
 
  eta_t, [Pa s]                   - is viscosity of solvent.
 
  TmP, [K]                        - is absolute temperature of solvent.
 
  1e-30                           - is a conversion factor between m^3 and A^3.
 
 DiffPot provides the facility to calculate diffTmpF for water at given temperature (see get_TmpF()).
 This method uses empirical approximation for water viscosity temperature dependency from:
 Weast, R.C. Handbook of Chemistry and Physics, 59th ed. CRC press West Palm Beach, FL 1978
 
  dT=TmP-273;
 
  eta_t=(1e-3)*(1.7753-0.0565*(dT)+1.0751e-3*(dT*dT)-9.2222e-6*(dT*dT*dT));
 
  where 
 
  eta_t                           - is viscosity in Pa s
 
  273                             - is offset between Celsius and Klevin's temperature scales.
 
  viscosity of water at 293 K (20 C): 1.002*(1e-3) [Pa s]
 
 The energy function is defined as: 
 
      V = scale()* sacle_Lin() * rms()^2
 
 
 
 
 
# 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
DiffPot
DiffPot_LetterClass
Modified
ModifiedBase

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

 
  Methods defined here:
Diff_Tensor(self, *args, **kwargs) -> 'Mat3'
Tessellation(self, *args, **kwargs) -> 'rc_SurfTessellation'
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcEnergy_eigen(self, *args, **kwargs) -> 'float_type'
curr_Tmp(self, *args, **kwargs) -> 'float_type'
diffRrmsd(self, *args, **kwargs) -> 'float_type'
diffRstep(self, *args, **kwargs) -> 'int const'
diffShell(self, *args, **kwargs) -> 'float_type'
diffTarget(self, *args, **kwargs) -> 'Mat3 const'
diffTmpF(self, *args, **kwargs) -> 'float_type const'
getAtomSel(self, *args, **kwargs) -> 'AtomSel const'
getMedianTmp(self, *args, **kwargs) -> 'float_type'
get_O_TmP_atom(self, *args, **kwargs) -> 'Atom'
get_TmpF(self, *args, **kwargs) -> 'float_type'
get_X_TmP_atom(self, *args, **kwargs) -> 'Atom'
get_Y_TmP_atom(self, *args, **kwargs) -> 'Atom'
info(self, *args, **kwargs) -> 'String'
numRestraints(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rangeTmpFit(self, *args, **kwargs) -> 'float_type const'
rms(self, *args, **kwargs) -> 'float_type'
rms_eigen(self, *args, **kwargs) -> 'float_type'
scale_Lin(self, *args, **kwargs) -> 'float_type const'
setDiffRrmsd(self, *args, **kwargs) -> 'void'
setDiffRstep(self, *args, **kwargs) -> 'void'
setDiffShell(self, *args, **kwargs) -> 'void'
setDiffTarget(self, *args, **kwargs) -> 'void'
setDiffTmpF(self, *args, **kwargs) -> 'void'
setMedianTmp(self, *args, **kwargs) -> 'void'
setRangeTmpFit(self, *args, **kwargs) -> 'void'
setScale_Lin(self, *args, **kwargs) -> 'void'
setTmpAtoms(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_DiffPot_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

 
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

 
realDiffPot = class DiffPot(builtins.object)
    realDiffPot(*args)
 

 
  Methods defined here:
Diff_Tensor(self, *args, **kwargs) -> 'Mat3'
Tessellation(self, *args, **kwargs) -> 'rc_SurfTessellation'
__deref__(self, *args, **kwargs) -> 'DiffPot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'DiffPot &'
__repr__ = _swig_repr(self)
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcEnergy_eigen(self, *args, **kwargs) -> 'float_type'
curr_Tmp(self, *args, **kwargs) -> 'float_type'
decrRefCnt(self, *args, **kwargs) -> 'void'
diffRrmsd(self, *args, **kwargs) -> 'float_type'
diffRstep(self, *args, **kwargs) -> 'int const'
diffShell(self, *args, **kwargs) -> 'float_type'
diffTarget(self, *args, **kwargs) -> 'Mat3 const'
diffTmpF(self, *args, **kwargs) -> 'float_type const'
getAtomSel(self, *args, **kwargs) -> 'AtomSel const'
getMedianTmp(self, *args, **kwargs) -> 'float_type'
get_O_TmP_atom(self, *args, **kwargs) -> 'Atom'
get_TmpF(self, *args, **kwargs) -> 'float_type'
get_X_TmP_atom(self, *args, **kwargs) -> 'Atom'
get_Y_TmP_atom(self, *args, **kwargs) -> 'Atom'
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'
rangeTmpFit(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'
rms(self, *args, **kwargs) -> 'float_type'
rms_eigen(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
scale_Lin(self, *args, **kwargs) -> 'float_type const'
setDiffRrmsd(self, *args, **kwargs) -> 'void'
setDiffRstep(self, *args, **kwargs) -> 'void'
setDiffShell(self, *args, **kwargs) -> 'void'
setDiffTarget(self, *args, **kwargs) -> 'void'
setDiffTmpF(self, *args, **kwargs) -> 'void'
setMedianTmp(self, *args, **kwargs) -> 'void'
setRangeTmpFit(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setScale_Lin(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setTmpAtoms(self, *args, **kwargs) -> 'void'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
violations(self, *args, **kwargs) -> 'float_type'

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

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