molpx.generate.sample(MD_trajectories, MD_top, projected_trajectories, atom_selection=None, proj_idxs=[0, 1], n_points=100, n_geom_samples=1, keep_all_samples=False, proj_stride=1, verbose=False, return_data=False)

Returns a sample of molecular geometries and their positions in the projected space

  • MD_trajectories (list of strings) – Filenames (any extension that mdtraj can read is accepted) containing the trajectory data. There is an untested input mode where the user parses directly mdtraj.Trajectory objects
  • MD_top (str to topology filename or directly mdtraj.Topology object) –
  • projected_trajectories ((list of) strings or (list of) numpy ndarrays of shape (n_frames, n_dims)) – Time-series with the projection(s) that want to be explored. You can provide .npy-filenames or readable asciis (.dat, .txt etc). Alternatively, you can feed in your own PyEMMA-clustering object NOTE: molpx assumes that there is no time column.
  • atom_selection (string or iterable of integers, default is None) – The geometries of the original trajectory files will be filtered down to these atoms. It can be any DSL string that could understand or directly the iterable of integers. If :py:obj`MD_trajectories` is already a (list of) md.Trajectory objects, the atom-slicing can take place before calling this method.
  • proj_idxs (int, default is None) – Selection of projection idxs (zero-idxd) to visualize. The default behaviour is that proj_idxs = range(n_projs). However, if proj_idxs != None, then n_projs is ignored and proj_dim is set automatically
  • n_points (int, default is 100) – Number of points along the projection path. The higher this number, the higher the projected coordinate is resolved, at the cost of more computational effort. It’s a trade-off parameter
  • n_geom_samples (int, default is 1) – For each of the n_points along the projection path, n_geom_samples will be retrieved from the trajectory files. The higher this number, the smoother the minRMSD projection path. Also, the longer it takes for the path to be computed. This is a trade-off parameter between how smooth the transitons between geometries can be and how long it takes to generate the sample
  • keep_all_samples (boolean, default is False) – In principle, once the closest-to-ref geometry has been kept, the other geometries are discarded, and the output sample contains only n_point geometries. There are, still, special cases where the user might want to keep all sampled geometries. Typical use-case is when the n_points is low and many representatives per clustercenters will be much more informative than the other way around. This is an advanced feature that other methods of molPX use internally for generating overlays, be awere that it changes the return type of geom_smpl from the default (an mdtraj.Trajectory with n_points-frames) to a list list of length n_geom_samples, each element is an mdtraj.Trajectory object of n_points-frames
  • proj_stride (int, default is 1) – Stride value that was used in the projected_trajectories relative to the MD_trajectories If the original MD_trajectories were stored every 5 ps but the projected trajectories were stored every 50 ps, proj_stride = 10 has to be provided, otherwise an exception will be thrown informing the user that the MD_trajectories and the projected_trajectories have different number of frames.

  • pos – ndarray with the positions of the sample
  • geom_smpl – sampled geometries. Can be of two types:
    • default: mdtraj.Trajectory with n_points-frames
    • if keep_all_samples = True: list of length n_geom_samples. Each element is an mdtraj.Trajectory object of n_points-frames.