From 93a20f437f54fb8dbd05a78570a2cde539855b47 Mon Sep 17 00:00:00 2001 From: clami66 Date: Thu, 16 May 2024 13:58:12 +0200 Subject: [PATCH] update flags in README --- README.md | 22 ++++++++++++++-------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 7bb6f7f..e916c45 100644 --- a/README.md +++ b/README.md @@ -158,9 +158,9 @@ Interfaces involving nucleic acids are seamlessly scored along with protein inte Run DockQ with `-h/--help` to see a list of the available flags: ``` -bash$ DockQ -h - -usage: DockQ [-h] [--capri_peptide] [--short] [--verbose] [--no_align] [--n_cpu n_cpu] [--optDockQF1] [--allowed_mismatches ALLOWED_MISMATCHES] [--mapping MODELCHAINS:NATIVECHAINS] +usage: DockQ [-h] [--capri_peptide] [--small_molecule] [--short] [--verbose] [--no_align] [--n_cpu CPU] + [--max_chunk CHUNK] [--optDockQF1] [--allowed_mismatches ALLOWED_MISMATCHES] + [--mapping MODELCHAINS:NATIVECHAINS] DockQ - Quality measure for protein-protein docking models @@ -172,17 +172,23 @@ positional arguments: optional arguments: -h, --help show this help message and exit --capri_peptide use version for capri_peptide (DockQ cannot not be trusted for this setting) + --small_molecule If the docking pose of a small molecule should be evaluated --short Short output --verbose, -v Verbose output - --no_align Do not align native and model using sequence alignments, but use the numbering of residues instead - --n_cpu n_cpu Number of cores to use + --no_align Do not align native and model using sequence alignments, but use the numbering of residues + instead + --n_cpu CPU Number of cores to use + --max_chunk CHUNK Maximum size of chunks given to the cores, actual chunksize is min(max_chunk,combos/cpus) --optDockQF1 Optimize on DockQ_F1 instead of DockQ --allowed_mismatches ALLOWED_MISMATCHES Number of allowed mismatches when mapping model sequence to native sequence. --mapping MODELCHAINS:NATIVECHAINS - Specify a chain mapping between model and native structure. If the native contains two chains "H" and "L" while the model contains two chains "A" and "B", - and chain A is a model of native chain H and chain B is a model of native chain L, the flag can be set as: '--mapping AB:HL'. This can also help limit the - search to specific native interfaces. For example, if the native is a tetramer (ABCD) but the user is only interested in the interface between chains B and + Specify a chain mapping between model and native structure. If the native contains two chains + "H" and "L" while the model contains two chains "A" and "B", and chain A is a model of native + chain H and chain B is a model of native chain L, the flag can be set as: '--mapping AB:HL'. + This can also help limit the search to specific native interfaces. For example, if the native + is a tetramer (ABCD) but the user is only interested in the interface between chains B and C, + the flag can be set as: '--mapping :BC' or the equivalent '--mapping *:BC'. C, the flag can be set as: '--mapping :BC' or the equivalent '--mapping *:BC'. ```