From f542cbb8a6988b84aa20e7b4ba8d79779f61b8e6 Mon Sep 17 00:00:00 2001
From: Rodrigo V Honorato <r.vargashonorato@uu.nl>
Date: Tue, 13 Aug 2024 15:05:10 +0200
Subject: [PATCH] update docs

---
 docs/src/SUMMARY.md |  1 +
 docs/src/usage.md   |  2 ++
 docs/src/z.md       | 21 +++++++++++++++++++++
 3 files changed, 24 insertions(+)
 create mode 100644 docs/src/z.md

diff --git a/docs/src/SUMMARY.md b/docs/src/SUMMARY.md
index 7e55082..2184b7f 100644
--- a/docs/src/SUMMARY.md
+++ b/docs/src/SUMMARY.md
@@ -9,4 +9,5 @@
   - [`ti`](./ti.md)
   - [`restraint`](./restraint.md)
   - [`interface`](./interface.md)
+  - [`z`](./z.md)
 - [Development](./development.md)
diff --git a/docs/src/usage.md b/docs/src/usage.md
index f8afc21..74e5910 100644
--- a/docs/src/usage.md
+++ b/docs/src/usage.md
@@ -9,3 +9,5 @@
 - [`restraint`: Generate _unambiguous restraints_ to keep molecules together during docking](./restraint.md)
 
 - [`interface`: List residues in the interface](./interface.md)
+
+- [`z`: Generate restraints to keep the molecule aligned to the Z-axis](./z.md)
diff --git a/docs/src/z.md b/docs/src/z.md
new file mode 100644
index 0000000..9be169b
--- /dev/null
+++ b/docs/src/z.md
@@ -0,0 +1,21 @@
+# Generate `z` restraints to keep the molecule aligned to the Z-axis
+
+This subcommand generates restraints to keep the molecule aligned to the Z-axis. This is useful when you want to keep the molecule in a specific orientation during docking.
+
+As input you need to pass at least one selection of residues, this will be used to define a plane perpendicular to the Z-axis. The restraints will be generated to keep the molecule aligned to this plane.
+
+## Usage
+
+To run the `z` subcommand, you need to provide the path to the PDB file, the selection of residues, the output file which will contain the shape beads, the number of beads to generate, and the distance between the beads. For example:
+
+```bash
+./haddock-restraints z \
+  --residues 19,83,145,119,167 \
+  path/to/the/input.pdb \
+  path/to/the/output/shape.pdb \
+  20 \ # spacing between the beads in angstrom - 20A
+  6 \  # grid size in dimension - 6x6
+  > z_restraints.tbl
+```
+
+Further, follow the HADDOCK documentation **\<pending\>** to use the generated restraints in the docking protocol.