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] [-CGN CGN_UNIPROT] [-KLIFS KLIFS_STRING] [--save_nomenclature] [-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 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

-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+”