Haddock3 v2025.8.0 - Hot summer release (#13)

* adding info about how to use molecule specific parameters in topoaa

* adding random removal haddock3-restraints subcommand info

* add indexing to random removal

* 5' end on nucleic acids `[topoaa.molX]` molecule parameters

* add notes for termini in topoaa

* adding the restrain_ligand haddock3-restraints subcommand

* fix equation display in ab-initio - issue #12

* migrate GenTBL to haddock-restraints generate restraints

* GenTBL to HADDOCK Restraints Generator

* upgrade topoaa and molecule specific documentation / example

* tweak airs

* fix missing text in intro_restraints

* add toc in intro_restraints

* add new file obtain_active_resiudes

* imporve seletopclusts

* keep_hetatm described in caprieval

Author: VGPReys

src/SUMMARY.md

@@ -20,8 +20,9 @@
   - [Tools to manipulate structures](./pdbtools.md)
 
 - [Generating restraints for HADDOCK](./intro_restraints.md)
-
-  - [haddock3-restraints](./restraints_cli.md)
+  - [Introduction to restraints in HADDOCK](./intro_restraints.md)
+  - [Obtaining a set of interacting residues](./obtain_active_resiudes.md)
+  - [The haddock3-restraints CLI](./restraints_cli.md)
   - [Automated restraints generation](./automated_restraints.md)
     - [Symmetry restraints](./automated_restraints.md)
     - [DNA & RNA restraints](./automated_restraints.md)

src/abinitio_docking.md

@@ -19,11 +19,15 @@ To calculate the upper distance limit for the restraints, the height, width, and
 
 - If `cmtight=true`: The 'molecule distance' for each molecule is calculated as the average of the two smallest dimensions, each divided by 2. For example:
 
-![equ](https://latex.codecogs.com/gif.latex?Molecule\;Distance = \frac{1}{2} \left( \frac{\text{width}}{2} + \frac{\text{depth}}{2} \right))
+<figure style="text-align: center;">
+<img width="100%" src="./images/cmrest_cmtight_true.png">
+</figure>
 
 - If `cmtight=false`: The 'molecule distance' is the average of all three half-dimensions:
 
-![equ](https://latex.codecogs.com/gif.latex?Molecule\;Distance = \frac{1}{3} \left( \frac{\text{height}}{2} + \frac{\text{width}}{2} + \frac{\text{depth}}{2} \right))
+<figure style="text-align: center;">
+<img width="100%" src="./images/cmrest_cmtight_false.png">
+</figure>
 
 
 - For DNA, RNA, small ligands, or glycans: The 'molecule distance' is set to 0.  

src/airs.md

@@ -67,7 +67,7 @@ In general, an AIR is defined as an ambiguous intermolecular distance between an
 This procedure can be performed:
 
 - locally using the `haddock3-restraints active_passive_to_ambig` command line
-- online using [GenTBL server](https://rascar.science.uu.nl/gentbl/)
+- online using [HADDOCK Restraints Generator web server](https://wenmr.science.uu.nl/haddock-restraints/)
 
 Using ambiguous restraints for docking is described in several tutorials:
 
@@ -247,7 +247,7 @@ In [BonvinLab](https://www.bonvinlab.org), a number of complementary web servers
 
 [ARCTIC-3D](https://wenmr.science.uu.nl/arctic3d/), standing for Automatic Retrieval and Clustering of Interfaces in Complexes, is a data mining algorithm that searches for experimental interfaces in the PDB and cluster interaction sites together. It is also able to directly generate AIRs for haddock3.
 
-### [CPORT](http://alcazar.science.uu.nl/services/CPORT/)
+### [CPORT](https://wenmr.science.uu.nl/services/CPORT/)
 
 [CPORT](http://alcazar.science.uu.nl/services/CPORT/) is an algorithm for the prediction of protein-protein interface residues. It combines six interface prediction methods into a consensus predictor.
 

src/bpg/restraints.md

@@ -5,6 +5,13 @@ Various types of restraints are available, namely **Ambiguous**, **Unambiguous**
 Restraints are defined using the CNS syntax, basically defining two selections and a pseudo-distance that must be satisfied.
 In case of unsatisfied restraints, a pseudo-energetical penalty is applied to the HADDOCK scoring function, therefore enabling to rank lower complexes that do not respect the restraints.
 
+Table of content:
+
+- [Definition of distance restraints in CNS](#distance-restraints)
+- [Ambiguous interaction restraints (AIRs)](#ambiguous-distance-restraints)
+- [*Un*ambiguous interaction restraints](#unambiguous-distance-restraints)
+- [Hydrogen distance restraints](#hydrogen-distance-restraints)
+
 ## Distance restraints
 
 In the definition of restraints, we define two type of selection, *active* (first selection) and *passive* (second selection) and a pseudo-distance to be satisfied.
@@ -22,8 +29,8 @@ Where:
 * `active selection`: is the first selection statement.
 * `passive selection`: is the second selection statement.
 * `distance`: is the pseudo-distance where we hope to find the two selections together
-* `lower_boundary`:
-* `upper_boundary`: is the upper
+* `lower_boundary`: value by which the distance can be lowered and still be in the acceptable range
+* `upper_boundary`: value by which the distance can be increased and still be in the acceptable range
 
 Basically, a restraint is satisfied if the pseudo-distance is found between `distance - lower_boundary` and `distance + upper_boundary` (`distance - lower_boundary` <= pseudo-distance <= `distance - upper_boundary`).
 
@@ -33,7 +40,7 @@ By default, we usually use the following values:
 * lower_boundary = 2.0
 * upper_boundary = 0.0
 
-therefore expecting the find the pseudo-distance under 2.0 between the two selections for a restraint to be satisfied.
+therefore expecting the find the pseudo-distance under 2.0 A between the two selections for a restraint to be satisfied.
 
 For a detailed explanation of the distance restraints, please refer to the following articles: