All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
IFP.interactions()
iterator that yields all interaction data for a given frame in a single flat structure. This makes iterating over thefp.ifp
results a bit easier / less nested.Complex3D
andfp.plot_3d
now have access toonly_interacting
andremove_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
andfp.plot_lignetwork
now return the underlyingLigNetwork
orComplex3D
object which has been enhanced with rich display functionality. From the user's perspective, nothing changes apart from being able to doview = fp.plot_*(...); view.save_png()
to display a popup window for saving the image.cleanup_substructures
parameter now accessible inmol2_supplier
to skip sanitization based on atom types.sanitize
parameter now available for themol2_supplier
andsdf_supplier
classes.ruff
linter and formatter.
display_residues
was sanitizing each residue while preparing them for display, which could make debugging faulty molecules difficult. This is now disabled.- Deprecation warnings
- The SMARTS pattern for halogen bond acceptors was not allowing carbonyles and other groups with double bonds to match (PR #190 by @asiomchen).
Maintenance update:
PROLIF_N_JOBS
environment variable to control multiprocessing during the documentation build.
- Updated CI pipelines to test on Python 3.8, 3.10 and 3.12.
- Packaging maintenance to fix the
tests/
directory being included as a module rather than as plain data files. This could interfere withpytest
during test collection in other packages.
- In
Complex3D
you can now use thecompare
method to display two 3D structures side by side.
- The barcode plot would display artifacts due to downsampling in the underlying
matplotlib
imshow
call when generating the plot for large fingerprints. Interpolation has been disabled to address the issue. - The barcode plot would skip labelling the second residue on the Y axis.
- Parsing residue names/number was broken for TIP3 water molecules and others.
This is a post-release to fix releases not containing the complete test suite.
This is a post-release to fix an issue with the conda build not being able to run the tests.
- Added a
display_residues
function to quickly visualize the residues in aMolecule
object. - Added a
Complex3D
class for plotting interactions in 3D. Added the correspondingFingerprint.plot_3d
method to generate the plot directly from an FP object. - Added a
Barcode
class for plotting interactions. Added the correspondingFingerprint.plot_barcode
method to generate the plot directly from an FP object. - Added a
count
argument inFingerprint
. Ifcount=True
, enumerates all groups of atoms that satisfy interaction constraints (instead of stopping at the first one), allowing users to generate a count-fingerprint. TheFingerprint.to_dataframe
method has been modified accordingly, and aFingerprint.to_countvectors
method has been added to generate a list of RDKit'sUIntSparseIntVect
from the count-fingerprint. The visualisation scripts have been updated to display the occurence with the shortest distance when a count-fingerprint is being used. - Added a
parameters
argument inFingerprint
to easily update the parameters used by an interaction, instead of defining a new interaction class (Issue #118). - Added new abstract interaction classes
SingleAngle
andDoubleAngle
to more easily create custom interactions. - Added the
vdwradii
parameter to theVdWContact
interaction class to update the radii it uses. - Added the
Fingerprint.plot_lignetwork
method to generate aLigNetwork
plot directly. - Added
LigNetwork.from_fingerprint
to generate the ligplot from aFingerprint
instance. Added adisplay_all
parameter for displaying all interactions instead of only the shortest one for a given pair of residues. Addeduse_coordinates
andflatten_coordinates
to control how the ligand structure is displayed. - Added support for displaying peptides with the
LigNetwork
. - Added
Fingerprint.metadata
to generate a dictionary containing metadata about interactions between two residues. ReplacesFingerprint.bitvector_atoms
. - Added a
vicinity_cutoff
parameter inFingerprint
to control the distance cutoff used to automatically restrict the IFP calculation to residues within the specified range of the ligand. - Added a
metadata
method to the baseInteraction
class to easily generate metadata for custom interactions. - Added an
Interaction.invert_class
classmethod to easily invert the role of the ligand and protein residues in an interaction, e.g. to create a donor class from an acceptor class.
- The tutorials have been overhauled and should now be much easier to navigate.
- The multiprocessing and pickling backends have been switched to
multiprocess
anddill
respectively, and the parallel implementation has been improved. Users should now be able to define custom interactions in Jupyter notebooks, IPython and so on without any issue (Issue #117, Issue #86). - The
LigNetwork
plot now displays the distance for each interaction on mouse hover. - Changed the format of the
Fingerprint.ifp
attribute to be a dictionary indexed by frame/structure index. The values are customIFP
dictionaries that can be more easily indexed by using residue identifier strings (e.g.ALA216.A
) rather thanResidueId
objects. Each entry contains complete interaction metadata instead of just atom indices. - All interaction classes now return more complete details about the interaction (e.g. distances, angles, atom indices in the residue and parent molecule).
- Changed the default color for
VanDerWaals
interactions in the builtin plots. - Converting the IFP to a dataframe with atom indices has been optimized and now runs about 5 times faster (Issue #112, PR #113 by @ReneHamburger1993). Note: discarded by the subsequent updates to the codebase which removed the ability to have atom indices in the dataframe.
- Various changes related to packaging, code formatting, linting and CI pipelines (PR #114).
- Fixed pickling properties on RDKit molecules for Windows.
- Removed the
return_atoms
argument inFingerprint.to_dataframe
. Users should directly useFingerprint.ifp
instead (the documentation's tutorials have been updated accordingly). - Removed the
Fingerprint.bitvector_atoms
method, replaced byFingerprint.metadata
. - Removed the
__wrapped__
attribute on interaction methods that are available from theFingerprint
object. These methods now accept ametadata
parameter instead. - Removed
LigNetwork.from_ifp
in favor ofLigNetwork.from_fingerprint
. - Removed the
match3D
parameter inLigNetwork
. Replaced byuse_coordinates
andflatten_coordinates
to give users more control and allow them to provide their own 2D coordinates.
Fingerprint.run
now has aconverter_kwargs
parameter that can pass kwargs to the underlying RDKitConverter from MDAnalysis (Issue #57).- Formatting with
black
.
- The SMARTS for the following groups have been updated to a more accurate definition
(Issue #68, PR #73 by @DrrDom, and PR #84):
- Hydrophobic: excluded F, Cl, tetracoordinated C and S, C connected to N, O or F.
- HBond donor: exclude charged O, S and charged aromatic N, only accept nitrogen that is in valence 3 or ammonium
- HBond acceptor: exclude amides and some amines, exclude biaryl ethers and alkoxy oxygen from esters, include some aromatic oxygen and nitrogen,
- Anion: include resonance forms of carboxylic, sulfonic and phosphorus acids,
- Cation: include amidine and guanidine,
- Metal ligand: exclude amides and some amines.
- The Pi stacking interactions have been changed for a more accurate implementation (PR #97, PR #98).
- The Van der Waals contact has been added to the default interactions, and the
tolerance
parameter has been set to 0. - The
pdbqt_supplier
will not add explicit hydrogen atoms anymore, to avoid detecting hydrogen bonds with "random" hydrogens that weren't in the PDBQT file (PR #99). - When using the
pdbqt_supplier
, irrelevant warnings and logs have been disabled (PR #99). - Updated the minimal RDKit version to
2021.03.1
- Dead link in the quickstart notebook for the MDAnalysis quickstart (PR #75, @radifar).
- The
pdbqt_supplier
now correctly preserves hydrogens from the input PDBQT file (PR #99). - If no interaction was detected,
to_dataframe
would error without giving a helpful message. It now returns a dataframe with the correct number of frames in the index and no column.
- Support for multiprocessing, enabled by default (Issue #46). The number of processes can
be controlled through
n_jobs
infp.run
andfp.run_from_iterable
. - New interaction: van der Waals contact, based on the sum of vdW radii of two atoms.
- Saving/loading the fingerprint object as a pickle with
fp.to_pickle
andFingerprint.from_pickle
(Issue #40).
- Molecule suppliers can now be indexed, reused and can return their length, instead of being single-use generators.
- ProLIF can now be installed through pip and conda (Issue #6).
- If no interaction is detected in the first frame,
to_dataframe
will not complain about aKeyError
anymore (Issue #44). - When creating a
plf.Fingerprint
, unknown interactions will no longer fail silently.
- Added our J. Cheminformatics article to the citation page of the documentation and the
CITATION.cff
file.
- Improved the documentation on how to properly restrict interactions to ignore the
protein backbone (Issue #22), how to fix the empty dataframe issue when no bond
information is present in the PDB file (Issue #15), how to save the LigNetwork diagram
(Issue #21), and some clarifications on using
fp.generate
- Mixing residue type with interaction type in the interactive legend of the LigNetwork would incorrectly display/hide some residues on the canvas (#PR 23)
- MOL2 files starting with a comment (
#
) would lead to an error
- Custom interactions must return three values: a boolean for the interaction, and the indices of residue atoms responsible for the interaction
- Custom interactions that only returned a single value instead of three would raise an uninformative error message
- LigNetwork: an interaction diagram with atomistic details for the ligand and residue-level details for the protein, fully interactive in a browser/notebook, inspired from LigPlot (PR #19)
fp.generate
: a method to get the IFP between twoprolif.Molecule
objects (PR #19)
- Default residue name and number:
UNK
and0
are now the default values ifNone
or''
is given - The Hydrophobic interaction now uses
+0
(no charge) instead of!$([+{1-},-{1-}])
(not negatively or positively charged) for part of its SMARTS pattern (PR #19) - Moved the
return_atoms
parameter from therun
methods toto_dataframe
to avoid recalculating the IFP if one wants to display it with atomic details (PR #19) - Changed the values returned by
fp.bitvector_atoms
: the atom indices have been separated in two lists, one for the ligand and one for the protein (PR #19)
- Residues with a resnumber of
0
are not converted toNone
anymore (Issue #13) - Fingerprint instantiated with an unknown interaction name will now raise a
NameError
- Integration with Zenodo to automatically generate a DOI for new releases
- Citation page
- Docking section in the Quickstart notebook (Issue #11)
- PDBQT, MOL2 and SDF molecule suppliers to make it easier for users to use docking results as input (Issue #11)
Molecule.from_rdkit
classmethod to easily prepare RDKit molecules for ProLIF
- The visualisation notebook now displays the protein with py3Dmol. Some examples for creating and displaying a graph from the interaction dataframe have been added
- Updated the installation instructions to show how to install a specific release
- The previous repr method of
ResidueId
was easy to confuse with a string, especially when trying to access theFingerprint.ifp
results by string. The new repr method is now more explicit. - Added the
Fingerprint.run_from_iterable
method, which uses the new supplier functions to quickly generate a fingerprint. - Sorted the output of
Fingerprint.list_available
Fingerprint.to_dataframe
is now much faster (Issue #7)ResidueId.from_string
method now supports 1-letter and 2-letter codes for RNA/DNA (Issue #8)
- Reading input directly from RDKit Mol as well as MDAnalysis AtomGroup objects
- Proper documentation and tests
- CI through GitHub Actions
- Publishing to PyPI triggered by GitHub releases
- All the API and the underlying code have been modified
- Repository has been moved from GitHub user @cbouy to organisation @chemosim-lab
- Custom MOL2 file reader
- Command-line interface
- Interactions not detected properly
Base version for this changelog