| diffPot | index diffPot.py |
DiffPot:
Potential term to restrain components of observed protein rotation diffusion tensor.
Creating a DiffPot using Python user interface: create_DiffPot(name, sel = "known", temperature = 293 )
returns a pointer to DiffPot object.
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.
Could be left blank when calling this method.
Default value "known" 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.
C++ constructor: DiffPot( instanceName, selection )
instanceName - is a user-specified identifier.
selection - is a atomSel.AtomSel object specifying the atoms to include when
calculating the diffusion tensor.
methods
calcEnergy() - calc energy, returns the energy value.
calcEnergy_eigen() - calc energy, 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 exposed to user factor 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.
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.
selection() - return the atom selection specified in
the constructor.
NOTE! Selection should NOT be reevaluated after
initial setting the potential term. This would lead to
mismatching the arrays and total disaster.
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.
info() - current info about the state of this instance.
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.
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 created automatically by SWIG.
# Don't modify this file, modify the SWIG interface instead.
# This file is compatible with both classic and new-style classes.
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| __package__ = None pyXplorHelp = Type help() for interactive help, or help(object) for help about object. | ||