Index

Symbols

'Y-bins'> md-davis-landscape command line option md-davis-landscape_xvg command line option --alignment md-davis-residue command line option --animate md-davis-landscape_animate command line option --annotations md-davis-residue command line option --atomic_potentials md-davis-potential_into_pdb command line option --axis_labels md-davis-landscape command line option md-davis-landscape_animate command line option md-davis-landscape_xvg command line option --begin md-davis-landscape command line option md-davis-landscape_animate command line option md-davis-landscape_xvg command line option --camera md-davis-landscape_animate command line option --center md-davis-electrostatics command line option --charge md-davis-electrostatics command line option --columns md-davis-landscape command line option md-davis-landscape_xvg command line option --common md-davis-landscape command line option md-davis-landscape_xvg command line option --contacts md-davis-hbond command line option --cutoff md-davis-plot_hbond command line option --dark md-davis-electrodynamics command line option --delphi md-davis-electrostatics command line option --dict md-davis-landscape command line option --dtick md-davis-landscape command line option md-davis-landscape_animate command line option md-davis-landscape_xvg command line option --end md-davis-landscape command line option md-davis-landscape_animate command line option md-davis-landscape_xvg command line option md-davis-plot_residue command line option --fill_color md-davis-plot_residue command line option --fillna md-davis-potential_into_pdb command line option --font md-davis-landscape command line option md-davis-landscape_animate command line option md-davis-landscape_xvg command line option --font_size md-davis-landscape command line option md-davis-landscape_animate command line option md-davis-landscape_xvg command line option --grid_size md-davis-electrostatics command line option --group md-davis-hbond command line option --hbonds md-davis-hbond command line option --height md-davis-landscape command line option md-davis-landscape_animate command line option md-davis-landscape_xvg command line option md-davis-plot_residue command line option --hide md-davis-electrodynamics command line option --hide_error_bars md-davis-plot_residue command line option --hide_markers md-davis-plot_residue command line option --hide_surface md-davis-landscape_animate command line option --index_file md-davis-hbond command line option --label md-davis-landscape command line option md-davis-landscape_xvg command line option md-davis-sequence command line option --layout md-davis-landscape command line option md-davis-landscape_xvg command line option --length md-davis-electrodynamics command line option --light md-davis-electrodynamics command line option --limits md-davis-landscape command line option md-davis-landscape_xvg command line option --line_color md-davis-plot_residue command line option --marker_size md-davis-landscape_animate command line option --matplotlib md-davis-xvg command line option, [1] --msms md-davis-electrostatics command line option --name md-davis-electrodynamics command line option md-davis-landscape command line option md-davis-landscape_xvg command line option --order md-davis-landscape command line option --orthographic md-davis-landscape command line option md-davis-landscape_animate command line option md-davis-landscape_xvg command line option --output md-davis-electrodynamics command line option md-davis-electrostatics command line option md-davis-hbond command line option md-davis-landscape command line option md-davis-landscape_animate command line option md-davis-landscape_xvg command line option md-davis-plot_hbond command line option md-davis-plot_residue command line option md-davis-residue command line option md-davis-xvg command line option, [1] --percent md-davis-plot_hbond command line option --perspective md-davis-landscape command line option md-davis-landscape_animate command line option md-davis-landscape_xvg command line option --plot md-davis-landscape command line option --plotly md-davis-xvg command line option, [1] --radius md-davis-electrostatics command line option --rescale md-davis-potential_into_pdb command line option --residue_potential md-davis-potential_into_pdb command line option

--return-type md-davis-sequence command line option --save md-davis-landscape command line option md-davis-landscape_xvg command line option --save_csv md-davis-hbond command line option --save_hdf md-davis-hbond command line option --save_matrix md-davis-hbond command line option --save_mean_potentials md-davis-potential_into_pdb command line option --save_pdb md-davis-hbond command line option --save_pickle md-davis-hbond command line option --save_total_potentials md-davis-potential_into_pdb command line option --select md-davis-landscape_animate command line option --shape md-davis-landscape command line option md-davis-landscape_xvg command line option --show_error_bars md-davis-plot_residue command line option --show_markers md-davis-plot_residue command line option --silent md-davis-hbond command line option --spacing md-davis-electrodynamics command line option --ss_color md-davis-electrodynamics command line option --start md-davis-plot_residue command line option --static md-davis-landscape_animate command line option --step md-davis-landscape_animate command line option --structure md-davis-hbond command line option --surface md-davis-electrodynamics command line option md-davis-electrostatics command line option --temperature md-davis-landscape command line option md-davis-landscape_xvg command line option --time_step md-davis-electrodynamics command line option --title md-davis-landscape command line option md-davis-landscape_animate command line option md-davis-landscape_xvg command line option md-davis-plot_hbond command line option md-davis-plot_residue command line option --total_frames md-davis-plot_hbond command line option --verbose md-davis-hbond command line option --version md-davis command line option --width md-davis-electrodynamics command line option md-davis-landscape command line option md-davis-landscape_animate command line option md-davis-landscape_xvg command line option md-davis-plot_residue command line option --xpm_file md-davis-hbond command line option -a md-davis-residue command line option -b md-davis-landscape command line option md-davis-landscape_xvg command line option -c md-davis-electrostatics command line option md-davis-landscape command line option md-davis-landscape_xvg command line option md-davis-plot_hbond command line option -d md-davis-electrostatics command line option md-davis-landscape command line option -e md-davis-landscape command line option md-davis-landscape_xvg command line option -f md-davis-plot_residue command line option -g md-davis-electrostatics command line option md-davis-hbond command line option -i md-davis-hbond command line option -l md-davis-electrodynamics command line option md-davis-landscape command line option md-davis-landscape_xvg command line option md-davis-plot_residue command line option md-davis-sequence command line option -m md-davis-electrostatics command line option -n md-davis-electrodynamics command line option md-davis-landscape command line option md-davis-landscape_xvg command line option -o md-davis-electrodynamics command line option md-davis-electrostatics command line option md-davis-hbond command line option md-davis-landscape command line option md-davis-landscape_animate command line option md-davis-landscape_xvg command line option md-davis-plot_hbond command line option md-davis-plot_residue command line option md-davis-residue command line option md-davis-xvg command line option, [1] -p md-davis-landscape command line option -r md-davis-electrostatics command line option md-davis-sequence command line option -s md-davis-hbond command line option md-davis-landscape command line option md-davis-landscape_xvg command line option -T md-davis-landscape command line option md-davis-landscape_xvg command line option -t md-davis-electrodynamics command line option md-davis-plot_hbond command line option md-davis-plot_residue command line option -w md-davis-electrodynamics command line option -x md-davis-hbond command line option md-davis-landscape command line option md-davis-landscape_xvg command line option -y md-davis-landscape command line option md-davis-landscape_xvg command line option

D

DIRECTORY md-davis-electrodynamics command line option

H

HBOND_FILE md-davis-plot_hbond command line option HDF_FILE md-davis-landscape_animate command line option

HDF_FILES md-davis-landscape command line option

I

INPUT_FILES md-davis-collate command line option md-davis-residue command line option

M

md-davis command line option --version md-davis-collate command line option INPUT_FILES md-davis-electrodynamics command line option --dark --hide --length --light --name --output --spacing --ss_color --surface --time_step --width -l -n -o -t -w DIRECTORY md-davis-electrostatics command line option --center --charge --delphi --grid_size --msms --output --radius --surface -c -d -g -m -o -r PDB_FILES md-davis-hbond command line option --contacts --group --hbonds --index_file --output --save_csv --save_hdf --save_matrix --save_pdb --save_pickle --silent --structure --verbose --xpm_file -g -i -o -s -x md-davis-landscape command line option 'Y-bins'> --axis_labels --begin --columns --common --dict --dtick --end --font --font_size --height --label --layout --limits --name --order --orthographic --output --perspective --plot --save --shape --temperature --title --width -b -c -d -e -l -n -o -p -s -T -x -y HDF_FILES md-davis-landscape_animate command line option --animate --axis_labels --begin --camera --dtick --end --font --font_size --height --hide_surface --marker_size --orthographic --output --perspective --select --static --step --title --width -o HDF_FILE

md-davis-landscape_xvg command line option 'Y-bins'> --axis_labels --begin --columns --common --dtick --end --font --font_size --height --label --layout --limits --name --orthographic --output --perspective --save --shape --temperature --title --width -b -c -e -l -n -o -s -T -x -y md-davis-plot_hbond command line option --cutoff --output --percent --title --total_frames -c -o -t HBOND_FILE md-davis-plot_residue command line option --end --fill_color --height --hide_error_bars --hide_markers --line_color --output --show_error_bars --show_markers --start --title --width -f -l -o -t PICKLE_FILE md-davis-potential_into_pdb command line option --atomic_potentials --fillna --rescale --residue_potential --save_mean_potentials --save_total_potentials OUTPUT_FILENAME PDB_FILE POTENTIAL_FILE md-davis-residue command line option --alignment --annotations --output -a -o INPUT_FILES md-davis-sequence command line option --label --return-type -l -r STRUCTURE md-davis-xvg command line option --matplotlib, [1] --output, [1] --plotly, [1] -o, [1] XVG_FILES, [1]

O

OUTPUT_FILENAME md-davis-potential_into_pdb command line option

P

PDB_FILE md-davis-potential_into_pdb command line option PDB_FILES md-davis-electrostatics command line option

PICKLE_FILE md-davis-plot_residue command line option POTENTIAL_FILE md-davis-potential_into_pdb command line option

S

STRUCTURE md-davis-sequence command line option

X

XVG_FILES md-davis-xvg command line option, [1]