| diffPot |
index |
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 | ||||||||||||||||||||||||||||||||||
|
| ||||||||||||||||||||||||||||||||||
| Functions | ||
| ||