mdc_residues.py

Find residues in an input topology using Unix filename pattern matching like in an ‘ls’ Unix operation.

usage: mdc_residues.py [-h] [-GPCR GPCR_UNIPROT] [--save_nomenclature] [-GGN CGN_PDB] [-ni] [-fr FRAGMENTS [FRAGMENTS ...]] residues topology

Positional Arguments

residues

Unix-like expressions and ranges are allowed, e.g. ‘GLU,PH*,380-394,3.50,GH.5*.’, as are consensus descriptors if consensus labels are provided

topology

Topology file

Named Arguments

-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”

-ni, -no-interactive

Try not to be interactive. This can make wrong choices for the user, advanced only.

Default: False

-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+’]