Reference#

Python Module#

To use MD DaVis as Python module:

import md_davis

CLI Reference#

md-davis#

MD DaVis: A python package for comparative analysis of molecular dynamics trajectories

md-davis [OPTIONS] COMMAND [ARGS]...

Options

--version#: Show the version and exit.

collate#

Input TOML files.

md-davis collate [OPTIONS] INPUT_FILES...

Arguments

INPUT_FILES#: Required argument(s)

electrodynamics#

Click wrapper for get_electrodynamics. Otherwise GUI was giving an error

md-davis electrodynamics [OPTIONS] DIRECTORY

Options

-n, --name <name>#: Required Name for the PyMOL obeject to be created for the molecule. (No spaces!)

--surface#: Show molecular surface

--ss_color#: Color the structure based on secondary structure

--spacing <spacing>#: Spacing of field lines

-t, --time_step <time_step>#: time step for frames to show

-l, --length <length>#: length of field lines

-w, --width <width>#: length of field lines

--light, --dark#: Enable dark or light mode

-o, --output <output>#: Name for saving the PyMOL session

--hide#: Hide PyMOL window

Arguments

DIRECTORY#: Required argument

electrostatics#

Get the electrostatic potential on the surface points generated by MSMS

md-davis electrostatics [OPTIONS] [PDB_FILES]...

Options

-m, --msms <PATH>#: Required full path to MSMS executable

-d, --delphi <PATH>#: Required full path to Delphi executable

-r, --radius <PATH>#: path to radius file

-c, --charge <PATH>#: path to charge file

-g, --grid_size <odd_int>#: Grid size to use for Delphi calculation

--surface#: Calculate electrostatic potential on the surface

--center#: Center the grid for Delphi at the origin

-o, --output <PATH>#: Directory to place the output files.

Arguments

PDB_FILES#: Optional argument(s)

hbond#

Parse contacts evaluated by gmx hbonds

md-davis hbond [OPTIONS]

Options

-x, --xpm_file <.xpm>#: Required Contact/H-bond file obtained from GROMACS

-i, --index_file <.ndx>#: Required Index file

-s, --structure <.pdb/.gro>#: Required Structure file

-g, --group <string>#: Required Group to match from index file to get the list of Contacts/H-bonds

-o, --output <.p>#: Output Pickle file

--contacts, --hbonds#: Select the type of input: contacts or H-bonds

--silent, --verbose#: Choose silent to suppress the displaying to result to standard output

--save_pickle <save_pickle>#: Save the output to a pickle file

--save_hdf <save_hdf>#: Save the output to a HDF file

--save_csv <save_csv>#: Save the output to a CSV file

--save_matrix <save_matrix>#: Save a file containing the contact matrix

--save_pdb <save_pdb>#: Save a pdb file with percentage of frames in the B-factor column

landscape#

Plot free energy landscapes from .xvg files generated by GROMACS or HDF files created by md_davis collate

md-davis landscape [OPTIONS] [HDF_FILES]...

Options

-x <x>#: Data to plot on x-axis

-y <y>#: Data to plot on y-axis

-n, --name <name>#: Names of each landscape object

-l, --label <label>#: Label to show in plots

-c, --common#: Use common ranges for all the landscapes

-T, --temperature <temperature>#: Temperature of the system. If this option is provided the energy landscape is calculated using Boltzmann inversion, else only the histogram is evaluated

--shape <'X-bins', 'Y-bins'>#: Number of bins in the X and Y direction

-o, --output <output>#: Name for the output HTML file containing the plots

-s, --save <FILENAME>#: Name for HDF5 file to save the landscapes

-b, --begin <int>#: Starting index for the data to include

-e, --end <int>#: Last index for the data to include

--limits <limits>#: A dictionary containing the limits for x, y, and x axes

--width <int>#: Width of the plot

--height <int>#: Height of the plot

--layout <layout>#: Layout of subplots

--title <str>#: Title for the figure

--axis_labels <axis_labels>#: A dictionary of strings specifying the labels for the x, y and z-axis. For example: dict(x=’RMSD (in nm)’, y=’Rg (in nm)’, z=’Free Energy (kJ mol-1) ‘)

--orthographic, --perspective#: Orthographic projection for 3D plots

--font <str>#: Font style

--font_size <int>#: Size of text and labels in the plot

--dtick <dtick>#: Tick interval on each axes

-p, --plot#: Plot the precomputed energy landscape

-d, --dict <dict>#: Dictionary containing input data

--order <order>#: Array specifying the order in which to plot the landscapes

--columns <columns>#: Columns to use (start from second column = 1)

Arguments

HDF_FILES#: Optional argument(s)

landscape_animate#

md-davis landscape_animate [OPTIONS] HDF_FILE

Options

--static, --animate#: Chose if the trajectory should be plotted or animated on the surface

-o, --output <output>#: Name for the output HTML file containing the plots

--select <str>#: Select which landscape to plot in a file containing multiple landscapes

--begin <int>#: Starting index for the data to include

--end <int>#: Last index for the data to include

--step <int>#: step size to iterate over the data

--title <str>#: Title for the figure

--orthographic, --perspective#: Orthographic projection for 3D plots

--axis_labels <axis_labels>#: A dictionary of strings specifying the labels for the x, y and z-axis

--width <int>#: Width of the plot

--height <int>#: Height of the plot

--font <str>#: Font style

--font_size <int>#: Size of text and labels in the plot

--marker_size <int>#: Size of markers in the plot

--dtick <dtick>#: Tick interval on each axes

--hide_surface <hide_surface>#: Hide the energy landscape surface

--camera <dict(eye=dict(>#: Dictionary to specify the camera for plotly

Arguments

HDF_FILE#: Required argument

landscape_xvg#

Wrapper function for Click

md-davis landscape_xvg [OPTIONS]

Options

-x <x>#: Required Data to plot on x-axis

-y <y>#: Required Data to plot on y-axis

-n, --name <name>#: Required Names of each landscape object

-l, --label <label>#: Required Label to show in plots

-c, --common#: Use common ranges for all the landscapes

-T, --temperature <temperature>#: Temperature of the system. If this option is provided the energy landscape is calculated using Boltzmann inversion, else only the histogram is evaluated

-o, --output <output>#: Name for the output HTML file containing the plots

--shape <'X-bins', 'Y-bins'>#: Number of bins in the X and Y direction

-b, --begin <int>#: Starting index for the data to include

-e, --end <int>#: Last index for the data to include

--limits <limits>#: A dictionary containing the limits for x, y, and x axes

-s, --save <FILENAME>#: Name for HDF5 file to save the landscapes

--title <str>#: Title for the figure

--orthographic, --perspective#: Orthographic projection for 3D plots

--width <int>#: Width of the plot

--height <int>#: Height of the plot

--font <str>#: Font style

--font_size <int>#: Size of text and labels in the plot

--dtick <dtick>#: Tick interval on each axes

--axis_labels <axis_labels>#: A dictionary of strings specifying the labels for the x, y and z-axis. For example: dict(x=’RMSD (in nm)’, y=’Rg (in nm)’, z=’Free Energy (kJ mol-1) ‘)

--layout <layout>#: Layout of subplots

--columns <columns>#: Columns to use (start from second column = 1)

plot_hbond#

H-bond or contact dataframe obtained from md_davis hbond

md-davis plot_hbond [OPTIONS] HBOND_FILE

Options

-t, --total_frames <total_frames>#: Required Total number of frames in the trajectory used for H-bond/Contact evaluation.

-c, --cutoff <cutoff>#: Cutoff for percentage or number of Hbonds above which to include in the plot.

-o, --output <output>#: Output filename

--percent#: Plot the percentages

--title <title>#: Title for the plot

Arguments

HBOND_FILE#: Required argument

plot_residue#

main function

md-davis plot_residue [OPTIONS] PICKLE_FILE

Options

--start <start>#: Starting index of the plot

--end <end>#: Last index of the plot

-o, --output <output>#: output HTML file

--width <width>#: Width of the plot in pixels

--height <height>#: Height of the plot in pixels

-t, --title <title>#: title for the plot

-l, --line_color <line_color>#: Array of colors for lines

-f, --fill_color <fill_color>#: Array of colors for shaded error bars

--show_markers, --hide_markers#: Show the markers on the line plots

--show_error_bars, --hide_error_bars#: show error bars for electrostatic potential and SASA

Arguments

PICKLE_FILE#: Required argument

potential_into_pdb#

md-davis potential_into_pdb [OPTIONS] POTENTIAL_FILE PDB_FILE OUTPUT_FILENAME

Options

--atomic_potentials, --residue_potential#: Write electrostatic potential per atom into the mean

--save_mean_potentials, --save_total_potentials#: Save total or mean electrostatic potential per residue or atom

--rescale#: Rescale and limit the electrostatic potential to -9.99 to 9.99 so that the b-factor columns strictly conforms to the PDB format.

--fillna#: Fill nan values in the b-factor column with 0.00

Arguments

POTENTIAL_FILE#: Required argument

PDB_FILE#: Required argument

OUTPUT_FILENAME#: Required argument

residue#

md-davis residue [OPTIONS] INPUT_FILES...

Options

-o, --output <output>#

-a, --annotations <annotations>#: Annotations

--alignment <alignment>#: Alignment file to align the residue data

Arguments

INPUT_FILES#: Required argument(s)

sequence#

Get the sequence of amino acid residues from a PDB file

Determines the sequence from the order of amino acid residues in the Protein Data Bank (PDB) file. The SEQRES records in the PDB file are not used, because it is sometimes different from the actual list of amino acids in the PDB file.

It is assumed that a PDB file used for dynamics will not contain any missing residues. The sequence gets truncated at the first missing residue

md-davis sequence [OPTIONS] STRUCTURE

Options

-l, --label <label>#

-r, --return-type <return_type>#

dict returns a dictionary containing chain labels as keys and each chain’s sequence as values. fasta returns each chain’s sequence separately in FASTA format.

Options: dict | fasta | modeller | toml

Arguments

STRUCTURE#: Required argument

xvg#

Plot xmgrace (.xvg) files generated by GROMACS.

Arguments:

xvg_files (Files): Input xmgrace (.xvg) files’

md-davis xvg [OPTIONS] XVG_FILES...

Options

-o, --output <output>#: Output filename

--matplotlib, --plotly#: Use plotly for plotting

Arguments

XVG_FILES#: Required argument(s)

Table of Contents

Reference#

Python Module#

CLI Reference#

md-davis#

collate#

electrodynamics#

electrostatics#

hbond#

landscape#

landscape_animate#

landscape_xvg#

plot_hbond#

plot_residue#

potential_into_pdb#

residue#

sequence#

xvg#