Improved online documentation

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/topology.html#topoaa-module>`
 """
 # Import here what you need
 from pathlib import Path

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/analysis.html#alascan-module>`
 """
 
 from pathlib import Path

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/analysis.html#caprieval-module>`
 """
 
 

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/analysis.html#clustfcc-module>`
 """
 
 import os

src/haddock/modules/analysis/clustrmsd/__init__.py

@@ -17,17 +17,19 @@
 * `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
 `clustrmsd` modules (possibly with different parameters) on the same RMSD
 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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/analysis.html#clustrmsd-module>`
+"""
 from pathlib import Path
 
 from haddock import log

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/analysis.html#contactmap-module>`
 """
 
 from copy import deepcopy

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/analysis.html#filer-module>`
 """
 
 from pathlib import Path

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/analysis.html#ilrmsdmatrix-module>`
 """
 
 import os

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/analysis.html#rmsdmatrix-module>`
 """
 
 import contextlib

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/analysis.html#seletop-module>`
 """
 from pathlib import Path
 

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/analysis.html#seletopclusts-module>`
 """
 
 from pathlib import Path

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/refinement.html#emref-module>`
 """
 
 from pathlib import Path

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/refinement.html#flexref-module>`
 """
 
 from pathlib import Path

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/refinement.html#mdref-module>`
 """
 
 from pathlib import Path

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/refinement.html#openmm-module>`
 """
 import os
 import shutil

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/sampling.html#lightdock-module>`
+"""
 import shutil
 import subprocess
 from pathlib import Path

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/sampling.html#rigidbody-module>`
 """
 
 from pathlib import Path

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/scoring.html#emscoring-module>`
 """
 
 from pathlib import Path

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/scoring.html#mdscoring-module>`
 """
 
 from pathlib import Path

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/scoring.html#prodigyligand-module>`
 """
 
 from pathlib import Path

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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/scoring.html#prodigyprotein-module>`
 """
 
 from pathlib import Path

src/haddock/modules/topology/topoaa/__init__.py

@@ -19,8 +19,22 @@
 and carbohydrates ... see `detailed list of supported molecules
 <https://wenmr.science.uu.nl/haddock2.4/library>`_),
 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
+<https://www.bonvinlab.org/haddock3-user-manual/modules/topology.html#topoaa-module>`
 """
 
 import operator