density_alg module

Code author: Niklaus Johner <niklaus.johner@a3.epfl.ch>

This module is used to generate densities from trajectories and extract surfaces from these densities in the form of sets of points. Some algebra can be done on these surfaces, found in the surface_alg module

CreateDensityMapFromEntityView(view, sampling=1, resolution=5, margin=0, ucell_center=None, ucell_vecs=None, cut_back=True)

CreateDensityMapFromTrajectory(traj, sele_view, sampling=0.5, stride=1, resolution=2.0, update_sele=False, update_sele_chain='', margin=10)

This function creates a density map for the position of the atoms of an EntityView during a trajectory It returns a map If update_sele is set to true, then for each frame the density is calculated from sele_view.Select(update_sele_chain) Sampling was changed to 1/sampling, careful!

CreateDensityMapFromTrajectoryWithPBC(traj, sele_view, sampling=2, stride=1, resolution=2.0, cell_centers=None, cell_vectors=None, margin=10)

This function creates a density map for the position of the atoms of an EntityView during a trajectory It returns a map and uses periodic boundary conditions while generating the map

CalculateVolumeFromDensityMap(den_map, cutoff=0.1)

This function calculates the volume of a density map with a certain cutoff It simply sums up all the volume where the density is higher than the cutoff

GetBoundaryBetweenDensities(den_map1, den_map2, cutoff=0.05, PBC=False, cell_center=None, cell_size=None, sampling=None, density_ratio=1.0)

This function returns a set of points at the the boundary between Two density maps. The boundary is determined as the set of points where the ratio between the densities from the two maps changes from >1 to <1.

GetMaxDensitySurface(den_map, cutoff=0.1, PBC=False, cell_center=None, cell_size=None, sampling=None)

This function calculates a set of points that have local maximal density