twodanalysis.BioPolymer2D
- class twodanalysis.BioPolymer2D(obj)[source]
- __init__(obj)[source]
Class Initialization.
- Parameters:
obj (AtomGroup or Universe) – Selection to initialize the class. If initialized with a Universe it will take the whole Universe as AtomGroup. The MDAnalysis Universe and AtomGroup will be accesible to with the self.universe and self.atom_group class attributes.
- Raises:
TypeError – Error raised if class is not initialized with a Universe or AtomGroup
Methods
FilterMinFrames(pos, zlim, Nframes[, ...])Selects a set of Nframes in which the AtomGroup is closer to the surface and bellow a zlim threshold distance to the surface.
HbondsPerResidues([sorted])Computes the number of H-bonds of each residue during the simulation.
INFO()Prints general information of the Universe and/or Atomgroup
KDEAnalysisSelection(select_res[, Nframes, ...])KDE Contours for a set of selected residues.
ListPathsInLevel(kde_plot, contour_level[, ...])Lists vertices of a path in a contour level of the KDE plot.
PolarAnalysis(select_res, Nframes[, ...])Makes a Polar Histogram of the positions of the center of mass of select_res residues considering Nframes closest to the surface within the < zlim threshold.
RgPerpvsRgsPar(rgs, color[, marker, plot, show])Generates \(R_{g\perp}\) vs.
__init__(obj)Class Initialization.
computeRG2D(masses[, total_mass])Computes parallel, perpendicular and 3D radius of gyration in 1 frame.
getAreas(paths, contour_lvl[, getTotal])Computes the area of each path a given contour level.
getCOMs([inplace, select])Computes positions of selection from self.startT to self.endT with self.stepT steps of frames.
getHbonds(selection1, selection2[, ...])Computes H-bonds between to selection1 and selection2 of the trajectory using MDAnalysis.analysis.hydrogenbonds.HydrogenBondAnalysis.
getKDEAnalysis(zlim, Nframes[, inplace, ...])Computes KDE Contours using seaborn.kde_plot() function and extracts the paths of each contour level.
getPositions([pos_type, inplace, select, ...])Computes positions of selection from self.startT to self.endT with self.stepT steps of frames.
getRgs2D([plot])Computes the radii of gyration over the trajectory using computeRG2D method.
makeCmapColor(def_color)plotHbondsPerResidues(paths_for_contour[, ...])Makes a figure showing the center of mass of the residues with H-bonds.
plotPathsInLevel(paths, contour_lvl[, ...])Plots the paths of a given contour level.
Attributes