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]
                    [-CGN CGN_UNIPROT] [-KLIFS KLIFS_STRING] [--save_nomenclature] [-od OUTPUT_DIR]
                    [-o OUTPUT_DESC] [--stride STRIDE] [--n_smooth_hw N_SMOOTH_HW] [-nf]
                    [--ctc_cutoff_Ang CTC_CUTOFF_ANG] [--no-pbc] [--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 GPCR consensus nomenclature, e.g Ballesteros-Weinstein, using this UniProt name, e.g. adrb2_human. First, try locally with ‘adrb2_human.xlsx’ (or a full path to the file), then do a web-lookup on the fly on the GPCRdb. See https://gpcrdb.org/services/ for more details.Default is None.

Default: “None”

-CGN, --CGN_UniProt

Look for Common-G-protein-Nomenclature, CGN, using this UniProt name, e.g. gnas2_human. First, try locally with ‘gnas2_human.xlsx’ (or a full path to the file), then do a web-lookup on the fly on the GPCRdb. See https://gpcrdb.org/services/ for more details.Default is None.

Default: “None”

-KLIFS, --KLIFS_string

Look for Kinase consensus nomenclature, KLIFS, using this string. e.g. P31751. First, try locally with ‘KLIFS_P31751.xlsx’ (or a full path to the file), then do a web-lookup on the fly on KLIFS. For web-lookups, the string has to be formatted as key:value, eg. ‘UniProtAC:P31751’. See the online documentation on mdciao’s LabelerKLIFS object and also https://klifs.net/ for more details.

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

-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 4.5 Angstrom.

Default: 4.5

--no-pbc

Do not consider periodic boundary conditions when computing distances. Default is to consider them

Default: True

--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