Helical parameter fitting
- analyze_foldamers.parameters.helical_fitting.calculate_p2(cgmodel)[source]
Given a coarse grained model containing positions, this function returns the ‘P2’ orientational ordering parameter value for the current pose.
Warning
By default, ‘P2’ is evaluated using the positions for only the backbone particles.
- Parameters
cgmodel (class) – CGModel() class object
- Returns
p2 ( float ) - The value for the ‘P2’ orientational ordering parameter.
- analyze_foldamers.parameters.helical_fitting.get_helical_parameters(cgmodel)[source]
Given a coarse grained model as input, this function uses the kHelios software package to analyze the helical properties of the model.
- Parameters
cgmodel (class) – CGModel() class object
- Returns
pitch ( float ) - The distance between monomers in adjacent turns of a helix
radius ( float ) - The radius of the helix
monomers_per_turn ( float ) - The number of monomrs per turn of the helix
residual ( float ) - The average distance of all backbone particles from a circle projected onto the x-y plane. Used to determine the accuracy of the helical axis, as fit to the input data. Units are in Angstroms.
Warning
This function requires a pre-installed version of kHelios . Because kHelios is formatted to accept input job scripts, this function writes and executes a job script for kHelios. In order to function properly, the user must redefine the ‘helios_path’ variable for their system.
- analyze_foldamers.parameters.helical_fitting.orient_along_z_axis(cgmodel, plot_projections=False)[source]
Given a coarse grained model as input, this function orients the model along the z-axis.
- Parameters
cgmodel (class) – CGModel() class object
plot_projections – Variable indicating whether or not to plot intermediate projections/operations during identification of a helical axis.
- Returns
cgmodel ( class ) - CGModel() class object, with positions oriented so that the helical axis is along the z-axis