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Fix lignetwork docs #356

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Merged
cbouy merged 2 commits into from
Jun 17, 2026
Merged

Fix lignetwork docs #356

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4f6e053
docs: fix lignetwork not showing in API docs
cbouy Jun 15, 2026
431447b
chore: other small docs adjustments
cbouy Jun 15, 2026
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2 changes: 1 addition & 1 deletion docs/source/installation.rst
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Original file line number Diff line number Diff line change
@@ -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::

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2 changes: 1 addition & 1 deletion docs/source/modules/plotting.rst
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Expand Up @@ -7,4 +7,4 @@ Plotting

.. automodule:: prolif.plotting.complex3d

.. automodule:: prolif.plotting.network
.. automodule:: prolif.plotting.network.lignetwork
3 changes: 1 addition & 2 deletions prolif/io/cif.py
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Expand Up @@ -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
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9 changes: 9 additions & 0 deletions prolif/molecule.py
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Expand Up @@ -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`.
"""
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