Trees | Indices | Help |
|
---|
|
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|
Diffusion tensor parameter default values ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________________________________________________ | | | | | Data type | Object name | Value | |________________________|____________________|________________________| | | | | | tm | 'tm' | 10 * 1e-9 | | | | | | Diso | 'Diso' | 1.666 * 1e7 | | | | | | Da | 'Da' | 0.0 | | | | | | Dr | 'Dr' | 0.0 | | | | | | Dx | 'Dx' | 1.666 * 1e7 | | | | | | Dy | 'Dy' | 1.666 * 1e7 | | | | | | Dz | 'Dz' | 1.666 * 1e7 | | | | | | Dpar | 'Dpar' | 1.666 * 1e7 | | | | | | Dper | 'Dper' | 1.666 * 1e7 | | | | | | Dratio | 'Dratio' | 1.0 | | | | | | alpha | 'alpha' | 0.0 | | | | | | beta | 'beta' | 0.0 | | | | | | gamma | 'gamma' | 0.0 | | | | | | theta | 'theta' | 0.0 | | | | | | phi | 'phi' | 0.0 | |________________________|____________________|________________________| |
Wrap the Euler or spherical angles and remove the glide reflection and translational symmetries. Wrap the angles such that 0 <= theta <= pi, 0 <= phi <= 2pi, and 0 <= alpha <= 2pi, 0 <= beta <= pi, 0 <= gamma <= 2pi. For the simulated values, the angles are wrapped as theta - pi/2 <= theta_sim <= theta + pi/2 phi - pi <= phi_sim <= phi + pi and alpha - pi <= alpha_sim <= alpha + pi beta - pi/2 <= beta_sim <= beta + pi/2 gamma - pi <= gamma_sim <= gamma + pi |
Function for returning the factor of conversion between different parameter units. For example, the internal representation of tm is in seconds, whereas the external representation is in nanoseconds, therefore this function will return 1e-9 for tm. |
Diffusion tensor parameter string matching patterns ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ____________________________________________________________________________________________ | | | | | Data type | Object name | Patterns | |________________________________________________________|______________|__________________| | | | | | Global correlation time - tm | 'tm' | '^tm$' | | | | | | Isotropic component of the diffusion tensor - Diso | 'Diso' | '[Dd]iso' | | | | | | Anisotropic component of the diffusion tensor - Da | 'Da' | '[Dd]a' | | | | | | Rhombic component of the diffusion tensor - Dr | 'Dr' | '[Dd]r$' | | | | | | Eigenvalue associated with the x-axis of the diffusion | 'Dx' | '[Dd]x' | | diffusion tensor - Dx | | | | | | | | Eigenvalue associated with the y-axis of the diffusion | 'Dy' | '[Dd]y' | | diffusion tensor - Dy | | | | | | | | Eigenvalue associated with the z-axis of the diffusion | 'Dz' | '[Dd]z' | | diffusion tensor - Dz | | | | | | | | Diffusion coefficient parallel to the major axis of | 'Dpar' | '[Dd]par' | | the spheroid diffusion tensor - Dpar | | | | | | | | Diffusion coefficient perpendicular to the major axis | 'Dper' | '[Dd]per' | | of the spheroid diffusion tensor - Dper | | | | | | | | Ratio of the parallel and perpendicular components of | 'Dratio' | '[Dd]ratio' | | the spheroid diffusion tensor - Dratio | | | | | | | | The first Euler angle of the ellipsoid diffusion | 'alpha' | '^a$' or 'alpha' | | tensor - alpha | | | | | | | | The second Euler angle of the ellipsoid diffusion | 'beta' | '^b$' or 'beta' | | tensor - beta | | | | | | | | The third Euler angle of the ellipsoid diffusion | 'gamma' | '^g$' or 'gamma' | | tensor - gamma | | | | | | | | The polar angle defining the major axis of the | 'theta' | 'theta' | | spheroid diffusion tensor - theta | | | | | | | | The azimuthal angle defining the major axis of the | 'phi' | 'phi' | | spheroid diffusion tensor - phi | | | |________________________________________________________|______________|__________________| |
Function for returning a string representing the parameters units. For example, the internal representation of tm is in seconds, whereas the external representation is in nanoseconds, therefore this function will return the string 'nanoseconds' for tm. |
Diffusion tensor set details ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ If the diffusion tensor has not been setup, use the more powerful function 'diffusion_tensor.init' to initialise the tensor parameters. The diffusion tensor parameters can only be set when the run corresponds to model-free analysis. The units of the parameters are: Inverse seconds for tm. Seconds for Diso, Da, Dx, Dy, Dz, Dpar, Dper. Unitless for Dratio and Dr. Radians for all angles (alpha, beta, gamma, theta, phi). When setting a diffusion tensor parameter, the residue number has no effect. As the internal parameters of spherical diffusion are {tm}, spheroidal diffusion are {tm, Da, theta, phi}, and ellipsoidal diffusion are {tm, Da, Dr, alpha, beta, gamma}, supplying geometric parameters must be done in the following way. If a single geometric parameter is supplied, it must be one of tm, Diso, Da, Dr, or Dratio. For the parameters Dpar, Dper, Dx, Dy, and Dx, it is not possible to determine how to use the currently set values together with the supplied value to calculate the new internal parameters. For spheroidal diffusion, when supplying multiple geometric parameters, the set must belong to one of {tm, Da}, {Diso, Da}, {tm, Dratio}, {Dpar, Dper}, {Diso, Dratio}, where either theta, phi, or both orientational parameters can be additionally supplied. For ellipsoidal diffusion, again when supplying multiple geometric parameters, the set must belong to one of {tm, Da, Dr}, {Diso, Da, Dr}, {Dx, Dy, Dz}, where any number of the orientational parameters, alpha, beta, or gamma can be additionally supplied. |
Function for calculating the unit axes of the diffusion tensor. Spheroid ~~~~~~~~ The unit Dpar vector is | sin(theta) * cos(phi) | Dpar = | sin(theta) * sin(phi) | | cos(theta) | Ellipsoid ~~~~~~~~~ The unit Dx vector is | -sin(alpha) * sin(gamma) + cos(alpha) * cos(beta) * cos(gamma) | Dx = | -sin(alpha) * cos(gamma) - cos(alpha) * cos(beta) * sin(gamma) | | cos(alpha) * sin(beta) | The unit Dy vector is | cos(alpha) * sin(gamma) + sin(alpha) * cos(beta) * cos(gamma) | Dy = | cos(alpha) * cos(gamma) - sin(alpha) * cos(beta) * sin(gamma) | | sin(alpha) * sin(beta) | The unit Dz vector is | -sin(beta) * cos(gamma) | Dz = | sin(beta) * sin(gamma) | | cos(beta) | |
Trees | Indices | Help |
|
---|
Generated by Epydoc 3.0.1 on Wed Apr 10 14:04:15 2013 | http://epydoc.sourceforge.net |