From e4cf7d5ce7fc84e8e8c8909cdb9147a47f9e1b69 Mon Sep 17 00:00:00 2001 From: VGPReys Date: Mon, 6 Apr 2026 14:08:34 +0200 Subject: [PATCH 1/3] adding link to haddock3 user manual in modules dockstrings --- .../modules/_template_cat/_template_mod/__init__.py | 4 ++++ src/haddock/modules/analysis/alascan/__init__.py | 3 +++ src/haddock/modules/analysis/caprieval/__init__.py | 3 +++ src/haddock/modules/analysis/clustfcc/__init__.py | 5 ++++- src/haddock/modules/analysis/clustrmsd/__init__.py | 10 ++++++---- src/haddock/modules/analysis/contactmap/__init__.py | 3 +++ src/haddock/modules/analysis/filter/__init__.py | 3 +++ src/haddock/modules/analysis/ilrmsdmatrix/__init__.py | 3 +++ src/haddock/modules/analysis/rmsdmatrix/__init__.py | 3 +++ src/haddock/modules/analysis/seletop/__init__.py | 3 +++ src/haddock/modules/analysis/seletopclusts/__init__.py | 3 +++ src/haddock/modules/refinement/emref/__init__.py | 3 +++ src/haddock/modules/refinement/flexref/__init__.py | 3 +++ src/haddock/modules/refinement/mdref/__init__.py | 3 +++ src/haddock/modules/refinement/openmm/__init__.py | 3 +++ src/haddock/modules/sampling/lightdock/__init__.py | 6 +++++- src/haddock/modules/sampling/rigidbody/__init__.py | 3 +++ src/haddock/modules/scoring/emscoring/__init__.py | 3 +++ src/haddock/modules/scoring/mdscoring/__init__.py | 3 +++ src/haddock/modules/scoring/prodigyligand/__init__.py | 3 +++ src/haddock/modules/scoring/prodigyprotein/__init__.py | 3 +++ src/haddock/modules/topology/topoaa/__init__.py | 3 +++ 22 files changed, 73 insertions(+), 6 deletions(-) diff --git a/src/haddock/modules/_template_cat/_template_mod/__init__.py b/src/haddock/modules/_template_cat/_template_mod/__init__.py index 8fe31b4f76..c6b4992ceb 100644 --- a/src/haddock/modules/_template_cat/_template_mod/__init__.py +++ b/src/haddock/modules/_template_cat/_template_mod/__init__.py @@ -11,6 +11,10 @@ You should use restructureText syntax: https://docutils.sourceforge.io/docs/user/rst/quickstart.html + +End this module docstring by providing a link to the haddock3-user-manual. e.g: +For more details about this module, please `refere to the haddock3 user manual +` """ # Import here what you need from pathlib import Path diff --git a/src/haddock/modules/analysis/alascan/__init__.py b/src/haddock/modules/analysis/alascan/__init__.py index 7c73aabb5f..1024cd458c 100644 --- a/src/haddock/modules/analysis/alascan/__init__.py +++ b/src/haddock/modules/analysis/alascan/__init__.py @@ -40,6 +40,9 @@ >>> resdic_A = [1,2,3,4] >>> resdic_B = [2,3,4] + +For more details about this module, please `refere to the haddock3 user manual +` """ from pathlib import Path diff --git a/src/haddock/modules/analysis/caprieval/__init__.py b/src/haddock/modules/analysis/caprieval/__init__.py index 69e4bcd297..c93d9ce0e4 100644 --- a/src/haddock/modules/analysis/caprieval/__init__.py +++ b/src/haddock/modules/analysis/caprieval/__init__.py @@ -23,6 +23,9 @@ - **capri_ss.tsv**: a table with the CAPRI metrics for each model. - **capri_clt.tsv**: a table with the CAPRI metrics for each cluster of models (if clustering information is available). + +For more details about this module, please `refere to the haddock3 user manual +` """ diff --git a/src/haddock/modules/analysis/clustfcc/__init__.py b/src/haddock/modules/analysis/clustfcc/__init__.py index fca46cb864..0c873edc08 100644 --- a/src/haddock/modules/analysis/clustfcc/__init__.py +++ b/src/haddock/modules/analysis/clustfcc/__init__.py @@ -4,10 +4,13 @@ contacts between them. Then, the module calculates the FCC matrix and clusters the models based on their contact similarities. -For more details please check +For more details about this clustering method, please check *Rodrigues, J. P. et al. Proteins: Struct. Funct. Bioinform. 80, 1810–1817 (2012)* + +For more details about this module, please `refere to the haddock3 user manual +` """ import os diff --git a/src/haddock/modules/analysis/clustrmsd/__init__.py b/src/haddock/modules/analysis/clustrmsd/__init__.py index 8ff94fe372..4e12aae2af 100644 --- a/src/haddock/modules/analysis/clustrmsd/__init__.py +++ b/src/haddock/modules/analysis/clustrmsd/__init__.py @@ -17,9 +17,8 @@ * `n_clusters`: number of desired clusters (if `criterion` is `maxclust`). * `clust_cutoff`: value of distance that separates distinct clusters (if `criterion` is ``distance``) -* `min_population` : analogously to the `clustfcc` module, it is the minimum number - of models that should be present in a cluster to consider it. If criterion is - `maxclust`, the value is ignored. +* `min_population` : set the minimum number of models that should be present + in a cluster to consider it. If criterion is `maxclust`, the value is ignored. This module passes the path to the RMSD matrix is to the next step of the workflow through the `rmsd_matrix.json` file, thus allowing to execute several @@ -27,7 +26,10 @@ matrix. .. _scipy routines: https://docs.scipy.org/doc/scipy/reference/cluster.hierarchy.html -""" # noqa: E501 + +For more details about this module, please `refere to the haddock3 user manual +` +""" from pathlib import Path from haddock import log diff --git a/src/haddock/modules/analysis/contactmap/__init__.py b/src/haddock/modules/analysis/contactmap/__init__.py index df328d0df4..fd345fc396 100644 --- a/src/haddock/modules/analysis/contactmap/__init__.py +++ b/src/haddock/modules/analysis/contactmap/__init__.py @@ -11,6 +11,9 @@ **Chordcharts** are describing only intermolecular contacts in circles, connecting with *chords* the two residues that are contacting. + +For more details about this module, please `refere to the haddock3 user manual +` """ from copy import deepcopy diff --git a/src/haddock/modules/analysis/filter/__init__.py b/src/haddock/modules/analysis/filter/__init__.py index 6dadcbfb9a..bd72855717 100644 --- a/src/haddock/modules/analysis/filter/__init__.py +++ b/src/haddock/modules/analysis/filter/__init__.py @@ -11,6 +11,9 @@ If the threshold value is too stringent, resulting in no models passed to the next module, the workflow will stop with an error message. + +For more details about this module, please `refere to the haddock3 user manual +` """ from pathlib import Path diff --git a/src/haddock/modules/analysis/ilrmsdmatrix/__init__.py b/src/haddock/modules/analysis/ilrmsdmatrix/__init__.py index ce1e645956..812fe927b9 100644 --- a/src/haddock/modules/analysis/ilrmsdmatrix/__init__.py +++ b/src/haddock/modules/analysis/ilrmsdmatrix/__init__.py @@ -14,6 +14,9 @@ IMPORTANT: the module assumes coherent numbering for all the receptor and ligand chains, as no alignment is performed. The user must ensure that the numbering is coherent. + +For more details about this module, please `refere to the haddock3 user manual +` """ import os diff --git a/src/haddock/modules/analysis/rmsdmatrix/__init__.py b/src/haddock/modules/analysis/rmsdmatrix/__init__.py index 07e4047ac2..b66e380c2e 100644 --- a/src/haddock/modules/analysis/rmsdmatrix/__init__.py +++ b/src/haddock/modules/analysis/rmsdmatrix/__init__.py @@ -24,6 +24,9 @@ thus telling the module to consider residues from 1 to 4 of chain A and from 2 to 4 of chain B for the alignment and RMSD calculation. + +For more details about this module, please `refere to the haddock3 user manual +` """ import contextlib diff --git a/src/haddock/modules/analysis/seletop/__init__.py b/src/haddock/modules/analysis/seletop/__init__.py index 43393e95b3..52bfbc9319 100644 --- a/src/haddock/modules/analysis/seletop/__init__.py +++ b/src/haddock/modules/analysis/seletop/__init__.py @@ -6,6 +6,9 @@ The number of models to be selected is defined by the parameter `select`. In the standard HADDOCK protocol, this number is 200, which can be increased if more models should be refined. + +For more details about this module, please `refere to the haddock3 user manual +` """ from pathlib import Path diff --git a/src/haddock/modules/analysis/seletopclusts/__init__.py b/src/haddock/modules/analysis/seletopclusts/__init__.py index af3f9eccc2..15b79acdec 100644 --- a/src/haddock/modules/analysis/seletopclusts/__init__.py +++ b/src/haddock/modules/analysis/seletopclusts/__init__.py @@ -7,6 +7,9 @@ are shown. In case seletopclusts is run after a sampling module, we can keep a few models from all the clusters to have more diversity at the refinement stage(s). + +For more details about this module, please `refere to the haddock3 user manual +` """ from pathlib import Path diff --git a/src/haddock/modules/refinement/emref/__init__.py b/src/haddock/modules/refinement/emref/__init__.py index acdefc5898..bb7c1cbf44 100644 --- a/src/haddock/modules/refinement/emref/__init__.py +++ b/src/haddock/modules/refinement/emref/__init__.py @@ -5,6 +5,9 @@ Coordinates of the energy minimized structures are saved, and each complex is then evaluated using the HADDOCK scoring function. + +For more details about this module, please `refere to the haddock3 user manual +` """ from pathlib import Path diff --git a/src/haddock/modules/refinement/flexref/__init__.py b/src/haddock/modules/refinement/flexref/__init__.py index bdbea226eb..9a4426656f 100644 --- a/src/haddock/modules/refinement/flexref/__init__.py +++ b/src/haddock/modules/refinement/flexref/__init__.py @@ -19,6 +19,9 @@ body molecular dynamics on. The temperature and number of steps for the various stages can be tuned. + +For more details about this module, please `refere to the haddock3 user manual +` """ from pathlib import Path diff --git a/src/haddock/modules/refinement/mdref/__init__.py b/src/haddock/modules/refinement/mdref/__init__.py index 3d651f585d..f8c6bf1c40 100644 --- a/src/haddock/modules/refinement/mdref/__init__.py +++ b/src/haddock/modules/refinement/mdref/__init__.py @@ -18,6 +18,9 @@ Number of MD steps can be modified using the ``waterheatsteps``, ``watersteps`` and ``watercoolsteps``. + +For more details about this module, please `refere to the haddock3 user manual +` """ from pathlib import Path diff --git a/src/haddock/modules/refinement/openmm/__init__.py b/src/haddock/modules/refinement/openmm/__init__.py index 2a2f85af1d..8d98be2624 100644 --- a/src/haddock/modules/refinement/openmm/__init__.py +++ b/src/haddock/modules/refinement/openmm/__init__.py @@ -26,6 +26,9 @@ such as `flexref` or `emref` after the OpenMM module, you need to recreate the topologies by simply adding a `[topoaa]` step in the workflow. See examples in `examples/thirdparty/openmm` folder. + +For more details about this module, please `refere to the haddock3 user manual +` """ import os import shutil diff --git a/src/haddock/modules/sampling/lightdock/__init__.py b/src/haddock/modules/sampling/lightdock/__init__.py index d8f58961c0..d87b352fc5 100644 --- a/src/haddock/modules/sampling/lightdock/__init__.py +++ b/src/haddock/modules/sampling/lightdock/__init__.py @@ -1,4 +1,8 @@ -"""LightDock integration sampling module.""" +"""LightDock integration sampling module. + +For more details about this module, please `refere to the haddock3 user manual +` +""" import shutil import subprocess from pathlib import Path diff --git a/src/haddock/modules/sampling/rigidbody/__init__.py b/src/haddock/modules/sampling/rigidbody/__init__.py index 739b744dba..727a0ac6f6 100644 --- a/src/haddock/modules/sampling/rigidbody/__init__.py +++ b/src/haddock/modules/sampling/rigidbody/__init__.py @@ -27,6 +27,9 @@ much better and the sampling can be limited. In *ab-initio* mode, however, very diverse solutions will be obtained and the sampling should be increased to make sure to sample enough the possible interaction space. + +For more details about this module, please `refere to the haddock3 user manual +` """ from pathlib import Path diff --git a/src/haddock/modules/scoring/emscoring/__init__.py b/src/haddock/modules/scoring/emscoring/__init__.py index 7f2b4a7bf0..d8c2339b17 100644 --- a/src/haddock/modules/scoring/emscoring/__init__.py +++ b/src/haddock/modules/scoring/emscoring/__init__.py @@ -2,6 +2,9 @@ This module performs energy minimization and scoring of the models generated in the previous step of the workflow. No restraints are applied during this step. + +For more details about this module, please `refere to the haddock3 user manual +` """ from pathlib import Path diff --git a/src/haddock/modules/scoring/mdscoring/__init__.py b/src/haddock/modules/scoring/mdscoring/__init__.py index f992c34611..2d1c2790f4 100644 --- a/src/haddock/modules/scoring/mdscoring/__init__.py +++ b/src/haddock/modules/scoring/mdscoring/__init__.py @@ -2,6 +2,9 @@ This module will perform a short MD simulation on the input models and score them. No restraints are applied during this step. + +For more details about this module, please `refere to the haddock3 user manual +` """ from pathlib import Path diff --git a/src/haddock/modules/scoring/prodigyligand/__init__.py b/src/haddock/modules/scoring/prodigyligand/__init__.py index 8c11aeadf3..32a9fa5bcf 100644 --- a/src/haddock/modules/scoring/prodigyligand/__init__.py +++ b/src/haddock/modules/scoring/prodigyligand/__init__.py @@ -3,6 +3,9 @@ This module performs the scoring of input complexes using PRODIGY-ligand. It predicts deltaG of the complex and can return predictions as either deltaG or pKd values. + +For more details about this module, please `refere to the haddock3 user manual +` """ from pathlib import Path diff --git a/src/haddock/modules/scoring/prodigyprotein/__init__.py b/src/haddock/modules/scoring/prodigyprotein/__init__.py index 65d8351cf4..56431722ac 100644 --- a/src/haddock/modules/scoring/prodigyprotein/__init__.py +++ b/src/haddock/modules/scoring/prodigyprotein/__init__.py @@ -5,6 +5,9 @@ or pKd values. Note that PRODIGY-protein is limited to natural amino-acids. + +For more details about this module, please `refere to the haddock3 user manual +` """ from pathlib import Path diff --git a/src/haddock/modules/topology/topoaa/__init__.py b/src/haddock/modules/topology/topoaa/__init__.py index 30135ff012..14ad15e374 100644 --- a/src/haddock/modules/topology/topoaa/__init__.py +++ b/src/haddock/modules/topology/topoaa/__init__.py @@ -21,6 +21,9 @@ such as small-molecules, parameters and topology must be obtained and provided by the user, as there is currently no built-in solution to generate them on the fly. + +For more details about this module, please `refere to the haddock3 user manual +` """ import operator From eefcdc3fbb4387845232cd39bc1303dd2718c157 Mon Sep 17 00:00:00 2001 From: VGPReys Date: Tue, 7 Apr 2026 09:46:10 +0200 Subject: [PATCH 2/3] improves topoaa module docstring --- src/haddock/modules/topology/topoaa/__init__.py | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/src/haddock/modules/topology/topoaa/__init__.py b/src/haddock/modules/topology/topoaa/__init__.py index 14ad15e374..376e7fa905 100644 --- a/src/haddock/modules/topology/topoaa/__init__.py +++ b/src/haddock/modules/topology/topoaa/__init__.py @@ -19,8 +19,19 @@ and carbohydrates ... see `detailed list of supported molecules `_), such as small-molecules, parameters and topology must be obtained and provided -by the user, as there is currently no built-in solution to generate -them on the fly. +by the user, using `ligand_param_fname` and `ligand_top_fname` parameters. +If you do not have them, they can be generated on-the-fly by setting +the `autotoppar` parameter to `true`. + +To define specific parameters for a given molecule (charge of terminis, +histidine protonations, peptide cyclisation, ...), you should re-define +a quasi topoaa module and specify the molecule index, right after +the ``[topoaa]`` module. e.g.: + +`` +[topoaa] +[topoaa.mol1] +`` For more details about this module, please `refere to the haddock3 user manual ` From acde35d382ac7cbffdcc24221634d4ac3d79ed67 Mon Sep 17 00:00:00 2001 From: VGPReys Date: Wed, 8 Apr 2026 13:59:28 +0200 Subject: [PATCH 3/3] reviewed pr --- devtools/build_defaults_rst.py | 2 +- .../_template_cat/_template_mod/__init__.py | 4 +-- .../modules/analysis/alascan/__init__.py | 4 +-- .../modules/analysis/caprieval/__init__.py | 4 +-- .../modules/analysis/clustfcc/__init__.py | 4 +-- .../modules/analysis/clustrmsd/__init__.py | 4 +-- .../modules/analysis/contactmap/__init__.py | 4 +-- .../modules/analysis/filter/__init__.py | 29 ++++++++++++------- .../modules/analysis/ilrmsdmatrix/__init__.py | 4 +-- .../modules/analysis/rmsdmatrix/__init__.py | 4 +-- .../modules/analysis/seletop/__init__.py | 4 +-- .../analysis/seletopclusts/__init__.py | 4 +-- .../modules/refinement/emref/__init__.py | 4 +-- .../modules/refinement/flexref/__init__.py | 4 +-- .../modules/refinement/mdref/__init__.py | 12 ++++---- .../modules/refinement/openmm/__init__.py | 4 +-- .../modules/sampling/lightdock/__init__.py | 4 +-- .../modules/sampling/rigidbody/__init__.py | 4 +-- .../modules/scoring/emscoring/__init__.py | 4 +-- .../modules/scoring/mdscoring/__init__.py | 4 +-- .../modules/scoring/prodigyligand/__init__.py | 4 +-- .../scoring/prodigyprotein/__init__.py | 4 +-- .../modules/topology/topoaa/__init__.py | 4 +-- 23 files changed, 65 insertions(+), 58 deletions(-) diff --git a/devtools/build_defaults_rst.py b/devtools/build_defaults_rst.py index 88e0aca0d7..2529de657b 100644 --- a/devtools/build_defaults_rst.py +++ b/devtools/build_defaults_rst.py @@ -43,7 +43,7 @@ "sasascore": "Surface Accessibility Scoring module", "prodigyprotein": "Binding affinity prediction with PRODIGY", "prodigyligand": "Ligand binding affinity prediction with PRODIGY-lig", - "filter": "Filtering of models based on their score", + "filter": "Filtering module", } CATEGORY_TITLE_DICT = { diff --git a/src/haddock/modules/_template_cat/_template_mod/__init__.py b/src/haddock/modules/_template_cat/_template_mod/__init__.py index c6b4992ceb..16fc2c0c05 100644 --- a/src/haddock/modules/_template_cat/_template_mod/__init__.py +++ b/src/haddock/modules/_template_cat/_template_mod/__init__.py @@ -13,8 +13,8 @@ https://docutils.sourceforge.io/docs/user/rst/quickstart.html End this module docstring by providing a link to the haddock3-user-manual. e.g: -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ # Import here what you need from pathlib import Path diff --git a/src/haddock/modules/analysis/alascan/__init__.py b/src/haddock/modules/analysis/alascan/__init__.py index 1024cd458c..7658f9958c 100644 --- a/src/haddock/modules/analysis/alascan/__init__.py +++ b/src/haddock/modules/analysis/alascan/__init__.py @@ -41,8 +41,8 @@ >>> resdic_A = [1,2,3,4] >>> resdic_B = [2,3,4] -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ from pathlib import Path diff --git a/src/haddock/modules/analysis/caprieval/__init__.py b/src/haddock/modules/analysis/caprieval/__init__.py index c93d9ce0e4..9c595f829c 100644 --- a/src/haddock/modules/analysis/caprieval/__init__.py +++ b/src/haddock/modules/analysis/caprieval/__init__.py @@ -24,8 +24,8 @@ - **capri_ss.tsv**: a table with the CAPRI metrics for each model. - **capri_clt.tsv**: a table with the CAPRI metrics for each cluster of models (if clustering information is available). -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ diff --git a/src/haddock/modules/analysis/clustfcc/__init__.py b/src/haddock/modules/analysis/clustfcc/__init__.py index 0c873edc08..81298af8f2 100644 --- a/src/haddock/modules/analysis/clustfcc/__init__.py +++ b/src/haddock/modules/analysis/clustfcc/__init__.py @@ -9,8 +9,8 @@ Proteins: Struct. Funct. Bioinform. 80, 1810–1817 (2012)* -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ import os diff --git a/src/haddock/modules/analysis/clustrmsd/__init__.py b/src/haddock/modules/analysis/clustrmsd/__init__.py index 4e12aae2af..1fb871cdb4 100644 --- a/src/haddock/modules/analysis/clustrmsd/__init__.py +++ b/src/haddock/modules/analysis/clustrmsd/__init__.py @@ -27,8 +27,8 @@ .. _scipy routines: https://docs.scipy.org/doc/scipy/reference/cluster.hierarchy.html -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ from pathlib import Path diff --git a/src/haddock/modules/analysis/contactmap/__init__.py b/src/haddock/modules/analysis/contactmap/__init__.py index fd345fc396..20fd6ff65d 100644 --- a/src/haddock/modules/analysis/contactmap/__init__.py +++ b/src/haddock/modules/analysis/contactmap/__init__.py @@ -12,8 +12,8 @@ **Chordcharts** are describing only intermolecular contacts in circles, connecting with *chords* the two residues that are contacting. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ from copy import deepcopy diff --git a/src/haddock/modules/analysis/filter/__init__.py b/src/haddock/modules/analysis/filter/__init__.py index bd72855717..3c649f9e90 100644 --- a/src/haddock/modules/analysis/filter/__init__.py +++ b/src/haddock/modules/analysis/filter/__init__.py @@ -1,19 +1,26 @@ -"""Filter models based on their score. +"""Filtering module. -This module filters the input models based on their score using a threshold -value. Models having higher score than the threshold value are filtered out. +The ``[filter]`` module filters the input models based on their score using a +``threshold`` value. +Models having higher score than the threshold value are filtered out. The number of models to be selected is unknown, and is the set of models that -have a score below the defined threshold. -For this module to be functional, a score must be first computed. This can be -performed by running a CNS module or a scoring module. If scores are not -accessible, the workflow will terminate with an error message. +have a **score below the defined threshold**. -If the threshold value is too stringent, resulting in no models passed to the -next module, the workflow will stop with an error message. +**Important**: +For this module to be functional, a score must be first computed. +For this module to be functional, a score must be first computed. +This can be performed by running a CNS module or a scoring module. -For more details about this module, please `refere to the haddock3 user manual -` +**Program termination cases**: + +* If scores are not + accessible, the workflow will terminate with an error message. +* If the threshold value is too stringent, resulting in no models passed to the + next module, the workflow will stop with an error message. + +For more details about this module, please `refer to the haddock3 user manual +_` """ from pathlib import Path diff --git a/src/haddock/modules/analysis/ilrmsdmatrix/__init__.py b/src/haddock/modules/analysis/ilrmsdmatrix/__init__.py index 812fe927b9..7532a14e6e 100644 --- a/src/haddock/modules/analysis/ilrmsdmatrix/__init__.py +++ b/src/haddock/modules/analysis/ilrmsdmatrix/__init__.py @@ -15,8 +15,8 @@ chains, as no alignment is performed. The user must ensure that the numbering is coherent. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ import os diff --git a/src/haddock/modules/analysis/rmsdmatrix/__init__.py b/src/haddock/modules/analysis/rmsdmatrix/__init__.py index b66e380c2e..e0c957578d 100644 --- a/src/haddock/modules/analysis/rmsdmatrix/__init__.py +++ b/src/haddock/modules/analysis/rmsdmatrix/__init__.py @@ -25,8 +25,8 @@ thus telling the module to consider residues from 1 to 4 of chain A and from 2 to 4 of chain B for the alignment and RMSD calculation. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ import contextlib diff --git a/src/haddock/modules/analysis/seletop/__init__.py b/src/haddock/modules/analysis/seletop/__init__.py index 52bfbc9319..3d1636f470 100644 --- a/src/haddock/modules/analysis/seletop/__init__.py +++ b/src/haddock/modules/analysis/seletop/__init__.py @@ -7,8 +7,8 @@ In the standard HADDOCK protocol, this number is 200, which can be increased if more models should be refined. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ from pathlib import Path diff --git a/src/haddock/modules/analysis/seletopclusts/__init__.py b/src/haddock/modules/analysis/seletopclusts/__init__.py index 15b79acdec..c5abd9fe0e 100644 --- a/src/haddock/modules/analysis/seletopclusts/__init__.py +++ b/src/haddock/modules/analysis/seletopclusts/__init__.py @@ -8,8 +8,8 @@ keep a few models from all the clusters to have more diversity at the refinement stage(s). -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ from pathlib import Path diff --git a/src/haddock/modules/refinement/emref/__init__.py b/src/haddock/modules/refinement/emref/__init__.py index bb7c1cbf44..f7dc25eafb 100644 --- a/src/haddock/modules/refinement/emref/__init__.py +++ b/src/haddock/modules/refinement/emref/__init__.py @@ -6,8 +6,8 @@ Coordinates of the energy minimized structures are saved, and each complex is then evaluated using the HADDOCK scoring function. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ from pathlib import Path diff --git a/src/haddock/modules/refinement/flexref/__init__.py b/src/haddock/modules/refinement/flexref/__init__.py index 9a4426656f..577963214c 100644 --- a/src/haddock/modules/refinement/flexref/__init__.py +++ b/src/haddock/modules/refinement/flexref/__init__.py @@ -20,8 +20,8 @@ The temperature and number of steps for the various stages can be tuned. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ from pathlib import Path diff --git a/src/haddock/modules/refinement/mdref/__init__.py b/src/haddock/modules/refinement/mdref/__init__.py index f8c6bf1c40..0f9cbbe07d 100644 --- a/src/haddock/modules/refinement/mdref/__init__.py +++ b/src/haddock/modules/refinement/mdref/__init__.py @@ -7,10 +7,10 @@ surface residues. The `mdref` protocol is composed of 4 sequential steps: -- Short energy minimization -- 3 stages of molecular dynamics to reach 300K (at 100, 200 and 300K) -- Molecular dynamics at 300K. -- 3 stages of molecular dynamics, to reach 100K (at 300, 200 and 100K) +1. Short energy minimization +2. 3 stages of molecular dynamics to reach 300K (at 100, 200 and 300K) +3. Molecular dynamics at 300K. +4. 3 stages of molecular dynamics, to reach 100K (at 300, 200 and 100K) Using this protocol, with default parameters, no spectacular changes are expected, however, the scoring of the various structures might be improved. @@ -19,8 +19,8 @@ Number of MD steps can be modified using the ``waterheatsteps``, ``watersteps`` and ``watercoolsteps``. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ from pathlib import Path diff --git a/src/haddock/modules/refinement/openmm/__init__.py b/src/haddock/modules/refinement/openmm/__init__.py index 8d98be2624..815b937994 100644 --- a/src/haddock/modules/refinement/openmm/__init__.py +++ b/src/haddock/modules/refinement/openmm/__init__.py @@ -27,8 +27,8 @@ topologies by simply adding a `[topoaa]` step in the workflow. See examples in `examples/thirdparty/openmm` folder. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ import os import shutil diff --git a/src/haddock/modules/sampling/lightdock/__init__.py b/src/haddock/modules/sampling/lightdock/__init__.py index d87b352fc5..7827806330 100644 --- a/src/haddock/modules/sampling/lightdock/__init__.py +++ b/src/haddock/modules/sampling/lightdock/__init__.py @@ -1,7 +1,7 @@ """LightDock integration sampling module. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ import shutil import subprocess diff --git a/src/haddock/modules/sampling/rigidbody/__init__.py b/src/haddock/modules/sampling/rigidbody/__init__.py index 727a0ac6f6..9cb44bab91 100644 --- a/src/haddock/modules/sampling/rigidbody/__init__.py +++ b/src/haddock/modules/sampling/rigidbody/__init__.py @@ -28,8 +28,8 @@ diverse solutions will be obtained and the sampling should be increased to make sure to sample enough the possible interaction space. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ from pathlib import Path diff --git a/src/haddock/modules/scoring/emscoring/__init__.py b/src/haddock/modules/scoring/emscoring/__init__.py index d8c2339b17..56e07ddafb 100644 --- a/src/haddock/modules/scoring/emscoring/__init__.py +++ b/src/haddock/modules/scoring/emscoring/__init__.py @@ -3,8 +3,8 @@ This module performs energy minimization and scoring of the models generated in the previous step of the workflow. No restraints are applied during this step. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ from pathlib import Path diff --git a/src/haddock/modules/scoring/mdscoring/__init__.py b/src/haddock/modules/scoring/mdscoring/__init__.py index 2d1c2790f4..9825e26266 100644 --- a/src/haddock/modules/scoring/mdscoring/__init__.py +++ b/src/haddock/modules/scoring/mdscoring/__init__.py @@ -3,8 +3,8 @@ This module will perform a short MD simulation on the input models and score them. No restraints are applied during this step. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ from pathlib import Path diff --git a/src/haddock/modules/scoring/prodigyligand/__init__.py b/src/haddock/modules/scoring/prodigyligand/__init__.py index 32a9fa5bcf..31101a1db6 100644 --- a/src/haddock/modules/scoring/prodigyligand/__init__.py +++ b/src/haddock/modules/scoring/prodigyligand/__init__.py @@ -4,8 +4,8 @@ It predicts deltaG of the complex and can return predictions as either deltaG or pKd values. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ from pathlib import Path diff --git a/src/haddock/modules/scoring/prodigyprotein/__init__.py b/src/haddock/modules/scoring/prodigyprotein/__init__.py index 56431722ac..2a8349be59 100644 --- a/src/haddock/modules/scoring/prodigyprotein/__init__.py +++ b/src/haddock/modules/scoring/prodigyprotein/__init__.py @@ -6,8 +6,8 @@ Note that PRODIGY-protein is limited to natural amino-acids. -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ from pathlib import Path diff --git a/src/haddock/modules/topology/topoaa/__init__.py b/src/haddock/modules/topology/topoaa/__init__.py index 376e7fa905..6e64f4eda5 100644 --- a/src/haddock/modules/topology/topoaa/__init__.py +++ b/src/haddock/modules/topology/topoaa/__init__.py @@ -33,8 +33,8 @@ [topoaa.mol1] `` -For more details about this module, please `refere to the haddock3 user manual -` +For more details about this module, please `refer to the haddock3 user manual +_` """ import operator