mdc_sites.py¶
Analyse a specific set of residue-residue contacts using a distance cutoff. The user has to provide one or more “site” files in a .json format
usage: mdc_sites.py [-h] [--site_files SITE_FILES [SITE_FILES ...]] [--default_fragment_index DEFAULT_FRAGMENT_INDEX] [--scheme SCHEME] [-GPCR GPCR_UNIPROT] [--save_nomenclature]
[-GGN CGN_PDB] [-od OUTPUT_DIR] [-o OUTPUT_DESC] [--stride STRIDE] [--n_smooth_hw N_SMOOTH_HW] [-nf] [--ctc_cutoff_Ang CTC_CUTOFF_ANG] [--t_unit T_UNIT]
[-gx GRAPHIC_EXT] [--curve_color CURVE_COLOR] [--background BACKGROUND] [--graphic_dpi GRAPHIC_DPI] [--ylim_Ang YLIM_ANG] [-sa] [--n_jobs N_JOBS] [-tx TABLE_EXT]
[-at] [-ni] [-d] [-st]
topology trajectories [trajectories ...]
Positional Arguments¶
- topology
Topology file
- trajectories
trajectory file(s)
Named Arguments¶
- --site_files
site file(s) in json format containing site information. Check here for more info: http://proteinformatics.uni-leipzig.de/mdciao/api/generated/mdciao.sites.html
- --default_fragment_index
- In case a residue identified as, e.g, GLU30, appears more than
one time in the topology, e.g. in case of a dimer, the user can pass which fragment/monomer should be chosen by default. The default behaviour (None) will prompt the user when necessary
- --scheme
Type of scheme for computing distance between residues. Choices are {‘ca’, ‘closest’, ‘closest-heavy’, ‘sidechain’, ‘sidechain-heavy’}. See mdtraj documentation for more info
Default: “closest-heavy”
- -GPCR, --GPCR_uniprot
Look for Ballesteros-Weinstein definitions in the GPCRdb using a uniprot code, e.g. adrb2_human. See https://gpcrdb.org/services/ for more details.Default is None.
Default: “None”
- --save_nomenclature
Save available nomenclature definitions to disk so that they can be accessed locally in later uses. Default is False
Default: False
- -GGN, --CGN_PDB
PDB code for a consensus G-protein nomenclature
Default: “None”
- -od, --output_dir
directory to which the results are written. Default is ‘.’
Default: “.”
- -o, --output_desc
Descriptor for output files. Default is sites
Default: “sites”
- --stride
Stride down the input trajectoy files by this factor. Default is 1.
Default: 1
- --n_smooth_hw, -ns
Number of frames one half of the averaging window for the time-traces. Default is 0, which means no averaging.
Default: 0
- -nf, --no-fragments
Do not use fragments. Default is to use them
Default: True
- --ctc_cutoff_Ang, -co
The cutoff distance between two residues for them to be considered in contact. Default is 3.5 Angstrom.
Default: 3.5
- --t_unit
Unit used for the temporal axis, default is ns.
Default: “ns”
- -gx, --graphic_ext
Extension of the output graphics, default is .pdf
Default: “.pdf”
- --curve_color
Type of color used for the curves. Default is auto. Alternatives are ‘P’ or ‘H’
Default: “auto”
- --background, -bg
Type of background when using smoothing windows. Default (True) is to use the unsmoothed curve’s color. A color string e.g. ‘g’ or ‘red’ or ‘gray’ also works, as does an RGB string ‘0.5, 1., 0.5’. Use False for no color.
Default: True
- --graphic_dpi
Dots per Inch (DPI) of the graphic output. Only has an effect for bitmap outputs. Default is 150.
Default: 150
- --ylim_Ang
Limit in Angstrom of the y-axis of the time-traces. Default is 10. Switch to any other float or ‘auto’ for automatic scaling
Default: “10”
- -sa, --short_AAs
Use one-letter aminoacid names when possible, e.g. K145 insted of Lys145. Default is False
Default: False
- --n_jobs
Number of processors to use. The parallelization is done over trajectories and not over contacts, beyond n_jobs>n_trajs parallelization will not have any effect.
Default: 1
- -tx, --table_ext
Extension for tabled files (.dat, .txt, .xlsx, .ods). Default is ‘.dat’
Default: “dat”
- -at, --atomtypes
- Add the atom-types to the frequency bars by ‘hatching’ them.
‘–’ is sidechain-sidechain ‘|’ is backbone-backbone ‘’ is backbone-sidechain ‘/’ is sidechain-backbone
Default is false
Default: False
- -ni, -no-interactive
Try not to be interactive. This can make wrong choices for the user, advanced only.
Default: False
- -d, --distribution
Plot distance distributions instead of contact bar plots. Default is False.
Default: False
- -st, --save-trajs
Save trajectory data, default is not to save it.
Default: False