msmhelper¶

msmhelper v1.1.1

Unlock the power of protein dynamics time series with Markov state modeling, by simplifying scientific analysis.

Usage:

msmhelper [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

ck-test: Estimation and visualization of the Chapman-Kolmogorov test.
compare-discretization: Similarity measure of two different state discretizations.
contact-rep: Contact representation of states.
dynamical-coring: Applying dynamical coring on state trajectory.
gaussian-filtering: Applying gaussian filter on time series.
implied-timescales: Estimation and visualization of the implied timescales.
waiting-time-dist: Estimation and visualization of the waiting time distributions.
waiting-times: Estimation and visualization of the waiting times.

msmhelper ck-test¶

Estimation and visualization of the Chapman-Kolmogorov test.

Usage:

msmhelper ck-test [OPTIONS]

Options:

  -f, --filename PATH          Path to state trajectory file (single column
                               ascii file).  [required]
  --microfilename PATH         Path to microstate trajectory file (single
                               column ascii file) to use Hummer-Szabo
                               projection.
  -c, --concat-limits PATH     Path to concatination limit file given the
                               length of all trajectories, e.g. "3\n3\n5"
  -o, --output PATH            Output basename of figure. Needs to have a
                               valid extension (".pdf", ".svg", ".png").
                               Default format is pdf.
  --lagtimes INTEGER RANGE...  5 (!) Lag times given in frames to estimate
                               Markov state model.  [x>=1; required]
  --frames-per-unit FLOAT      Number of frames per unit.  [required]
  --unit [fs|ps|ns|us|frames]  Unit of data.  [required]
  --grid INTEGER RANGE...      Number of rows and cols.  [x>=1]
  --max-time INTEGER RANGE     Largest time value to evaluate and plot the
                               test.  [x>=1]
  --help                       Show this message and exit.

msmhelper compare-discretization¶

Similarity measure of two different state discretizations.

Usage:

msmhelper compare-discretization [OPTIONS]

Options:

  --traj1 PATH                   Path to first state trajectory file (single
                                 column ascii file).  [required]
  --traj2 PATH                   Path to second state trajectory file (single
                                 column ascii file).  [required]
  --method [symmetric|directed]  Method of calculating similarity.
  --help                         Show this message and exit.

msmhelper contact-rep¶

Contact representation of states.

This script creates a contact representation of states. Were the states are obtained by MoSAIC and the contact representation was introduced in Nagel et al.¹.

Usage:

msmhelper contact-rep [OPTIONS]

Options:

  --contacts PATH          Path to file holding all contacts (features) of
                           shape `(n_frames, n_contacts)`.  [required]
  --clusters PATH          Path to contacts cluster file, where every row is a
                           cluster and in each row the indices corresponding
                           to the columns of the clusters are stated.
                           [required]
  --state PATH             Path to state trajectory.  [required]
  -o, --output PATH        Output basename of figure. Needs to have a valid
                           extension (".pdf", ".svg", ".png"). Default format
                           is pdf.
  --grid INTEGER RANGE...  Number of rows and cols per figure.  [x>=1]
  --help                   Show this message and exit.

msmhelper dynamical-coring¶

Applying dynamical coring on state trajectory.

Usage:

msmhelper dynamical-coring [OPTIONS]

Options:

  -i, --input PATH          Path to input file. Needs to be of shape
                            (n_samples, n_features). All comment lines need to
                            start with "#"  [required]
  -c, --concat-limits PATH  Path to concatination limit file given the length
                            of all trajectories, e.g. "3\n3\n5"
  -t, --tcor INTEGER RANGE  Coring window given in [frames] used for dynamical
                            coring.  [x>=1; required]
  -o, --output PATH         Path to output file.
  --help                    Show this message and exit.

msmhelper gaussian-filtering¶

Applying gaussian filter on time series.

Usage:

msmhelper gaussian-filtering [OPTIONS]

Options:

  -i, --input PATH          Path to input file. Needs to be of shape
                            (n_samples, n_features). All comment lines need to
                            start with "#"  [required]
  -c, --concat-limits PATH  Path to concatination limit file given the length
                            of all trajectories, e.g. "3\n3\n5"
  -s, --sigma FLOAT RANGE   Standard deviation given in [frames] used for
                            Gaussian kernel  [x>=1; required]
  -o, --output PATH         Path to output file, will be of same shape as
                            input
  --help                    Show this message and exit.

msmhelper implied-timescales¶

Estimation and visualization of the implied timescales.

Usage:

msmhelper implied-timescales [OPTIONS]

Options:

  -f, --filename PATH          Path to state trajectory file (single column
                               ascii file).  [required]
  --microfilename PATH         Path to microstate trajectory file (single
                               column ascii file) to use Hummer-Szabo
                               projection.
  -c, --concat-limits PATH     Path to concatination limit file given the
                               length of all trajectories, e.g. "3\n3\n5"
  -o, --output PATH            Output name of figure. Needs to have a valid
                               suffix (".pdf", ".svg", ".png"). Default format
                               is pdf.
  --max-lagtime INTEGER RANGE  Maximal lag time to estimate Markov state model
                               in frames.  [x>=0; required]
  --frames-per-unit FLOAT      Number of frames per unit.  [required]
  --unit [fs|ps|ns|us|frames]  Unit of data.  [required]
  --n-lagtimes INTEGER RANGE   Number of lagtimes to plot.  [x>=1]
  --ylog                       Use logarithmic y-axis.
  --help                       Show this message and exit.

msmhelper waiting-time-dist¶

Estimation and visualization of the waiting time distributions.

Usage:

msmhelper waiting-time-dist [OPTIONS]

Options:

  -f, --filename PATH          Path to state trajectory file (single column
                               ascii file).  [required]
  --microfilename PATH         Path to microstate trajectory file (single
                               column ascii file) to use Hummer-Szabo
                               projection.
  -c, --concat-limits PATH     Path to concatination limit file given the
                               length of all trajectories, e.g. "3\n3\n5"
  -o, --output PATH            Output name of figure. Needs to have a valid
                               suffix (".pdf", ".svg", ".png"). Default format
                               is pdf.
  --max-lagtime INTEGER RANGE  Maximal lag time given in frames to estimate
                               Markov state model.  [x>=1; required]
  --start INTEGER RANGE        State to start from.  [x>=1; required]
  --final INTEGER RANGE        State to end in.  [x>=1; required]
  --nsteps INTEGER RANGE       State to end in.  [x>=1; required]
  --frames-per-unit FLOAT      Number of frames per unit.  [required]
  --unit [fs|ps|ns|us|frames]  Unit of data.  [required]
  --help                       Show this message and exit.

msmhelper waiting-times¶

Estimation and visualization of the waiting times.

Usage:

msmhelper waiting-times [OPTIONS]

Options:

  -f, --filename PATH          Path to state trajectory file (single column
                               ascii file).  [required]
  --microfilename PATH         Path to microstate trajectory file (single
                               column ascii file) to use Hummer-Szabo
                               projection.
  -c, --concat-limits PATH     Path to concatination limit file given the
                               length of all trajectories, e.g. "3\n3\n5"
  -o, --output PATH            Output name of figure. Needs to have a valid
                               suffix (".pdf", ".svg", ".png"). Default format
                               is pdf.
  --lagtimes INTEGER RANGE...  3 (!) Lag times given in frames to estimate
                               Markov state model.  [x>=1; required]
  --start INTEGER RANGE        State to start from.  [x>=1; required]
  --final INTEGER RANGE        State to end in.  [x>=1; required]
  --nsteps INTEGER RANGE       State to end in.  [x>=1; required]
  --frames-per-unit FLOAT      Number of frames per unit.  [required]
  --unit [fs|ps|ns|us|frames]  Unit of data.  [required]
  --help                       Show this message and exit.

Nagel et al., Selecting Features for Markov Modeling: A Case Study on HP35., J. Chem. Theory Comput., submitted, ↩