mdc_interface.py
Analyse interfaces between any two groups of residues using a distance cutoff. To help in the identification of these two groups of residues, the peptide-chain in the input topology can be automatically broken down into fragments and use them as input. The number of shown contacts depends on the parameters “ctc_control” and “min_freq”.
usage: mdc_interface.py [-h] [-fr FRAGMENTS [FRAGMENTS ...]] [-isel1 INTERFACE_SELECTION_1]
[-isel2 INTERFACE_SELECTION_2] [--ctc_cutoff_Ang CTC_CUTOFF_ANG] [-cc CTC_CONTROL]
[-mf MIN_FREQ] [--cmap CMAP] [--n_nearest N_NEAREST] [--stride STRIDE]
[--n_smooth_hw N_SMOOTH_HW] [-nt] [-st] [--n_jobs N_JOBS] [--fragment_names FRAGMENT_NAMES]
[-nf] [--no-pbc] [-GPCR GPCR_UNIPROT] [-CGN CGN_UNIPROT] [-KLIFS KLIFS_STRING]
[--save_nomenclature] [--chunksize_in_frames CHUNKSIZE_IN_FRAMES] [-o OUTPUT_DESC]
[-od OUTPUT_DIR] [-gx GRAPHIC_EXT] [--graphic_dpi GRAPHIC_DPI] [--curve_color CURVE_COLOR]
[--t_unit T_UNIT] [--background BACKGROUND] [-sa] [--no-sort_by_av_ctcs] [--scheme SCHEME]
[--no-flare] [--no-matrix] [--pop_N_ctcs] [-ni] [-t TITLE] [--n_repframes N_REPFRAMES]
topology trajectories [trajectories ...]
Positional Arguments
- topology
Topology file
- trajectories
trajectory file(s)
Named Arguments
- -fr, --fragments
R|How to sub-divide the topology into fragments. Several options possible. Taking the example sequence: …-A27,Lig28,K29-…-W40,D45-…-W50,CYSP51,GDP52
- ‘resSeq’
breaks at jumps in resSeq entry: […A27,Lig28,K29,…,W40],[D45,…,W50,CYSP51,GDP52]
- ‘resSeq+’
breaks only at negative jumps in resSeq: […A27,Lig28,K29,…,W40,D45,…,W50,CYSP51,GDP52]
- ‘bonds’
breaks when AAs are not connected by bonds, ignores resSeq: […A27][Lig28],[K29,…,W40],[D45,…,W50],[CYSP51],[GDP52] notice that because phosphorylated CYSP51 didn’t get a bond in the topology, it’s considered a ligand
- ‘resSeq_bonds’
breaks both at resSeq jumps or missing bond
- ‘lig_resSeq+’
Like resSeq+ but put’s any non-AA residue into it’s own fragment: […A27][Lig28],[K29,…,W40],[D45,…,W50,CYSP51],[GDP52]
- ‘chains’
breaks into chains of the PDB file/entry
None or ‘None’ all residues are in one fragment, fragment 0
- ‘consensus’
If any consensus nomenclature is provided, ask the user for definitions using consensus labels
- 0-10,15,14 20,21,30-50 51 (example, advanced users only)
Input arbitrary fragments via their residue serial indices (zero-indexed) using space as separator. Not recommended.
- ‘None’
All residues are in one fragment (fragment 0). Can be harmless or potentially dangerous if residue labels are repeated.
If you are unsure of any of these options, use the command line tool mdc_fragments.py on your topology file.
Default: “lig_resSeq+”
- -isel1, --interface_selection_1
Indices of the fragments that belong to the one side of the interface, as CSVs or range, e.g. ‘1,3-4’. Defaults to None which will prompt the user of information, except when only two fragments are present. Then it defaults to [0]
- -isel2, --interface_selection_2
Indices of the fragments that belong to the other side of the interface, as CSVs or range, e.g. ‘1,3-4’. Defaults to None which will prompt the user of information, except when only two fragments are present. Then it defaults to [1]
- --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
- -cc, --ctc_control
Control the number of reported contacts. Can be an integer (keep the first n contacts) or a float representing a fraction [0,1] of the totalnumber of contacts.Default is 50.
Default: 50
- -mf, --min_freq
Do not show frequencies smaller than this. Default is 0.05. If you notice the output being truncated at values much larger than this, but suspect that some contacts are not being reported, increase the ‘ctc_control’ parameter
Default: 0.05
- --cmap
The colormap for the contact matrix. Default is ‘binary’ which is black and white, but you can choose anthing from here: https://matplotlib.org/3.1.0/tutorials/colors/colormaps.html
Default: “binary”
- --n_nearest, -nn
Ignore this many nearest neighbors when computing neighbor lists. ‘Near’ means ‘connected by this many bonds’. Default is 0.
Default: 0
- --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
- -nt, --no-time-trace
Don’t plot the time-traces of the contacts. Default is to plot them.
Default: True
- -st, --save-trajs
Save trajectory data, default is not to save it.
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
- --fragment_names
Name of the fragments. Default is to name them automatically. Otherwise, give a quoted list of strings separated by commas, e.g. ‘TM1, TM2, TM3,’Use ‘None’ to avoid naming them altogether.
Default: “auto”
- -nf, --no-fragments
Do not use fragments. Default is to use them
Default: True
- --no-pbc
Do not consider periodic boundary conditions when computing distances. Default is to consider them
Default: True
- -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
- --chunksize_in_frames
Trajectories are read in chunks of this size. Helps with big files and/or large number of contacts when you run into memory problems. Default is 2000
Default: 2000
- -o, --output_desc
Descriptor for output files. Default is interface
Default: “interface”
- -od, --output_dir
directory to which the results are written. Default is ‘.’
Default: “.”
- -gx, --graphic_ext
Extension of the output graphics, default is .pdf
Default: “.pdf”
- --graphic_dpi
Dots per Inch (DPI) of the graphic output. Only has an effect for bitmap outputs. Default is 150.
Default: 150
- --curve_color
Type of color used for the curves. Default is auto. Alternatives are ‘P’ or ‘H’
Default: “auto”
- --t_unit
Unit used for the temporal axis, default is ns.
Default: “ns”
- --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
- -sa, --short_AAs
Use one-letter aminoacid names when possible, e.g. K145 insted of Lys145. Default is False
Default: False
- --no-sort_by_av_ctcs
When presenting the results summarized by residue, don’t sort by sum of frequencies (~average number of contacts), but by ascending order whithin each interface member. Default is to sort them by frequencies.
Default: True
- --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”
- --no-flare
Do not produce a flare plot of the interface contact matrix. If produced, regardless of the ‘–graphic_ext’, the flareplot will always be in .pdf-format, unless ‘–graphic_ext’ is ‘svg’.
Default: True
- --no-matrix
Do not produce a plot of the interface contact matrix
Default: True
- --pop_N_ctcs
Separate the plot with the total number contacts from the time-trace plot. 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
- -t, --title
Name of the system. Used for figure titles (not filenames)Defaults to –output_desc if None is given
- --n_repframes
Number of representative frames to use when writing theinterface strength into a .pdb-file
Default: 1