Help

Basic help

BitClust help is displayed in the console when typing bitclust -h

$ bitclust -h

usage: bitclust [-h] [-top TOPOLOGY] [-traj TRAJECTORY] [-first FIRST]
                [-last LAST] [-stride STRIDE] [-sel SELECTION]
                [-cutoff CUTOFF] [-minsize MINSIZE] [-max_clust MAX_CLUST]
                [-ref REFERENCE] [-numouts NUM_OUTS] [-odir OUTDIR]

BitClust: Fast & memory efficient clustering of long MD trajectories

optional arguments:
  -h, --help            show this help message and exit
  -top TOPOLOGY         path to topology file (psf/pdb)
  -traj TRAJECTORY      path to trajectory file
  -first FIRST          first frame to analyze (starting from 0)
  -last LAST            last frame to analyze (starting from 0)
  -stride STRIDE        stride of frames to analyze
  -sel SELECTION        atom selection (MDTraj syntax)
  -cutoff CUTOFF        RMSD cutoff for pairwise comparisons in A
  -minsize MINSIZE      minimum number of frames inside returned clusters
  -max_clust MAX_CLUST  maximum number of returned clusters
  -ref REFERENCE        reference frame to align trajectory
  -numouts NUM_OUTS     number of clusters and leaders to print as pdb
  -odir OUTDIR          output directory to store analysis

Arguments details

-traj (str): This is the only argument that is always required. Valid extensions for trajectories are .dcd, .dtr, .hdf5, .xyz, .binpos, .netcdf, .prmtop, .lh5, .pdb, .trr, .xtc, .xml, .arc, .lammpstrj and .hoomdxml.

-top (str): If trajectory format includes topological information this argument is not required. Otherwise, user must pass a path to a topology file. Valid topology extensions are .pdb, .pdb.gz, .h5, .lh5, .prmtop, .parm7, .prm7, .psf, .mol2, .hoomdxml, .gro, .arc and .hdf5.

-first (int, default=0): First frame to analyze (starting count from 0)

-last (int, default=-1): Last frame to analyze (starting count from 0). Value -1 indicates that last frame will be used.

-stride (int, default=1): Stride of frames to analyze. Use this argument to reduce trajectory size when performing exploratory analysis of cutoff value.

-sel (str, default='all'): Atom selection. BitClust inherits MDtraj syntax selection which is very flexible. For a deeper insight please refer to the MDTraj atom selection reference original documentation. Common cases are listed at usage examples section.

-cutoff (int, default=1): RMSD cutoff for similarity measures given in Angstroms (1 A = 0.1 nm).

-minsize (int, default=2): Minimum number of frames inside returned clusters. 0 is not a meaningful value and 1 implies an unclustered frame (no other frame is similar to it). Greater values of this parameter can speed up the algorithm.

-max_clust (int, default=all): Maximum number of calculated clusters. Change the default for a better performance whenever you need only the first clusters.

-ref (int, default=0): Reference frame to align trajectory.

-numouts (int, default=5): Number of clusters and their corresponding representative frames (leaders) to print as pdb.

-odir (str, default="."): Output directory to store analysis. If not specified, files and figs will be stored in current working directory.