From 4f6e0532d42120c13d78ab25b3e001e288c04056 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 15 Jun 2026 23:20:46 +0100 Subject: [PATCH 1/2] docs: fix lignetwork not showing in API docs --- docs/source/modules/plotting.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/modules/plotting.rst b/docs/source/modules/plotting.rst index 60e2b749..06fe9c75 100644 --- a/docs/source/modules/plotting.rst +++ b/docs/source/modules/plotting.rst @@ -7,4 +7,4 @@ Plotting .. automodule:: prolif.plotting.complex3d -.. automodule:: prolif.plotting.network +.. automodule:: prolif.plotting.network.lignetwork From 431447bb327b75066f2e2c597069cbd1044adcc2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 15 Jun 2026 23:50:07 +0100 Subject: [PATCH 2/2] chore: other small docs adjustments --- docs/source/installation.rst | 2 +- prolif/io/cif.py | 3 +-- prolif/molecule.py | 9 +++++++++ 3 files changed, 11 insertions(+), 3 deletions(-) diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 40a3c2f4..7e582577 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -1,7 +1,7 @@ Installation ------------ -The recommanded way to install ProLIF is to use `conda`_. +The recommended way to install ProLIF is to use `conda`_. These first steps are optional and will create a separate environment for ProLIF:: diff --git a/prolif/io/cif.py b/prolif/io/cif.py index 1f7f91b1..d78e5cea 100644 --- a/prolif/io/cif.py +++ b/prolif/io/cif.py @@ -4,8 +4,7 @@ This module provides a wrapper around `gemmi` for reading Crystallographic Information File (CIF) format. -.. versionchanged:: 2.2.0 - Replaced the custom CIF parser with a thin wrapper around ``gemmi``. +.. versionadded:: 2.2.0 """ from pathlib import Path diff --git a/prolif/molecule.py b/prolif/molecule.py index 917e63de..6e286272 100644 --- a/prolif/molecule.py +++ b/prolif/molecule.py @@ -146,6 +146,15 @@ def from_mda( mol = prolif.Molecule.from_mda(protein) mol + Since MDAnalysis v2.10.0, it is possible to directly control how bond orders and + charges are inferred from the topology using the ``inferrer`` parameter:: + + >>> from MDAnalysis.converters.RDKitInferring import TemplateInferrer + >>> from rdkit import Chem + >>> ligand_template = Chem.MolFromSmiles("NC(c2nc(=Cc1ccc([O-])cc1)c(=O)n2CC=O)C(C)O") + >>> ligand_inferrer = TemplateInferrer(ligand_template) + >>> mol = prolif.Molecule.from_mda(u, "resname LIG", inferrer=ligand_inferrer) + .. versionchanged:: 2.1.0 Added `use_segid`. """