v2.1.0 - 2026-01-20

Welcome to new contributors: talagayev, yuyuan871111, nilay-v3rma, VAKozyrev, H-EKE, weitse-hsu, amorehead, maabuu, tanii1125 👋

Summary

This release has been staggered for a very long time and so it's quite massive, here's a TL;DR

• New WaterBridge interaction 💧
• Performance enhancements for parallelisation 🚀
• New utility functions split_molecule and select_over_trajectory ✂️
• Adjustments to the Hydrophobic and HBond SMARTS patterns 🎯
• Type-hints ℹ️

Added

• Added a new queue parallelization strategy for trajectories, alongside the
  existing chunk strategy, and some simple heuristics to decide
  between the two. Users can also force the usage of one strategy or the other
  through the parallel_strategy parameter.
• Added split_molecule to split a molecule into components based on a predicate
  function.
• Added select_over_trajectory to easily make AtomGroup distance-based selections
  (including recursive selections) over the whole trajectory rather than just the first
  frame. This helps making optimised selections when a protein is highly flexible
  instead of using protein and byres around X group ligand with a very large X.
• Support for WaterBridge interactions (PR #229 with @talagayev).
• Refactored the LigNetwork plotting code (PR #268 by @nilay-v3rma).
• Type-checking and related pipelines:
  • poe pipeline using preconfigured mypy (PR #254 by @nilay-v3rma).
  • script for viewing current the progress on type hints (PR #257 by H-EKE).
  • type hints (PR #259 by @VAKozyrev, PR #263).
• Support for FrameIteratorIndices as trajectories in fp.run (PR #246 by @wehs7661).
• LigNetwork now optionally displays the percentage of interaction occurence when
  show_interaction_data is enabled. The type of data shown on both the label and
  hover title can be modified (PR #234 by @talagayev).
• VdWContact now accepts a preset parameter to easily use different van der Waals
  radii values: one of mdanalysis (default), rdkit, or csd. Documented in PR #253
  by @yuyuan871111.
• IFP.interactions() iterator that yields all interaction data for a given frame in
  a single flat structure. This makes iterating over the fp.ifp results a bit
  easier / less nested.
• Complex3D and fp.plot_3d now have access to only_interacting and
  remove_hydrogens parameters to control which residues and hydrogen atoms are
  displayed. Non-polar hydrogen atoms that aren't involved in interactions are now
  hidden by default.
• LigNetwork.save_png to save the displayed plot to a PNG file through JavaScript
  (Issue #163).
• Complex3D.save_png to save the displayed plot to a PNG file through JavaScript.
• fp.plot_3d and fp.plot_lignetwork now return the underlying LigNetwork or
  Complex3D object which has been enhanced with rich display functionality. From the
  user's perspective, nothing changes apart from being able to do
  view = fp.plot_*(...); view.save_png() to display a popup window for saving the
  image.
• cleanup_substructures parameter now accessible in mol2_supplier to skip
  sanitization based on atom types.
• sanitize parameter now available for the mol2_supplier and sdf_supplier classes.
• ruff linter and formatter.
• uv and poethepoet for running local and automated CI pipelines.

Fixed

• ResidueGroup resnumbers are now declared as uint32 instead of uint16 (PR #315,
  Issue #313).
• SMARTS pattern for Hydrophobic were not matching as expected due to the presence of
  explicit hydrogens in the molecules. The SMARTS have been rewritten to account for
  this.
• ProLIF can now use the segment number as a ResidueId chain. This should help with
  solvated systems that may reuse the same resname, resnumber and chain and were using
  the segment number/identifier to distinguish them in the topology file.
• Sorting ResidueId objects where a subset of residues had no chain was raising a
  TypeError, it will now put cases without a chain first (PR #235 by @amorehead).
• display_residues was sanitizing each residue while preparing them for display, which
  could make debugging faulty molecules difficult. This is now disabled.
• Deprecation warnings

Changed

• For trajectory analysis, unless a number of jobs is specified through n_jobs
  in Fingerprint.run, ProLIF will now use up to a maximum of 10 processes instead of
  all available cores. The cap can be modified through the PROLIF_MAX_N_JOBS
  environment variable.
• Fingerprint.run now exposes a parallel_strategy parameter (chunk, queue, or
  None).
• Unpin the numpy version (PR #306 by @maabuu).
• Hydrophobic SMARTS pattern now excludes all carbon linked to
  nitrogen/oxygen/fluoride from being hydrophobic, previous versions were allowing such
  carbons if they were aromatic.
• HBond SMARTS patterns now removes charged aromatic nitrogen, triazolium, and
  guanidine/anidine-like from acceptors, and enables the charged nitrogen from
  histidine as donor.
• Strip whitespaces in ResidueId name and chain.
• Improved parsing for less standard residue names in ResidueId.