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CHANGELOG
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# -*- tab-width: 2; indent-tabs-mode: nil; coding: utf-8 -*-
======================
MDAnalysis CHANGELOG
======================
The rules for this file:
* entries are sorted newest-first.
* summarize sets of changes - don't reproduce every git log comment here.
* don't ever delete anything.
* keep the format consistent (79 char width, M/D/Y date format) and do not
use tabs but use spaces for formatting
* accompany each entry with github issue/PR number (Issue #xyz)
* release numbers follow "Semantic Versioning" https://semver.org
-------------------------------------------------------------------------------
??/??/?? IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy,
marinegor
* 2.9.0
Fixes
* Add support for TPR files produced by GROMACS 2024.4
* Fixes invalid default unit from Angstrom to Angstrom^{-3} for convert_density() function. (Issue #4829)
* Fixes deprecation warning Array to scalar convertion. Replaced atan2() with np.arctan2() (Issue #4339)
* Replaced mutable defaults with None and initialized them within
the function to prevent shared state. (Issue #4655)
Enhancements
* Addition of 'water' token for water selection (Issue #4839)
* Enables parallelization for analysis.density.DensityAnalysis (Issue #4677, PR #4729)
* Enables parallelization for analysis.contacts.Contacts (Issue #4660)
* Enable parallelization for analysis.nucleicacids.NucPairDist (Issue #4670)
* Add check and warning for empty (all zero) coordinates in RDKit converter (PR #4824)
* Added `precision` for XYZWriter (Issue #4775, PR #4771)
Changes
* Changed `fasteners` dependency to `filelock` (Issue #4797, PR #4800)
* Codebase is now formatted with black (version `24`) (PR #4886)
Deprecations
11/11/24 IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher,
yuxuanzhuang, PythonFZ, laksh-krishna-sharma, orbeckst, MattTDavies,
talagayev, aya9aladdin
* 2.8.0
Fixes
* Allows bond/angle/dihedral connectivity to be guessed additively with
`to_guess`, and as a replacement of existing values with `force_guess`.
Also updates cached bond attributes when updating bonds. (Issue #4759, PR #4761)
* Fixes bug where deleting connections by index would only delete
one of multiple, if multiple are present (Issue #4762, PR #4763)
* Changes error to warning on Universe creation if guessing fails
due to missing information (Issue #4750, PR #4754)
* Adds guessed attributes documentation back to each parser page
and updates overall guesser docs (Issue #4696)
* Fix Bohrium (Bh) atomic mass in tables.py (PR #3753)
* set `n_parts` to the total number of frames being analyzed if
`n_parts` is bigger. (Issue #4685)
* Catch higher dimensional indexing in GroupBase & ComponentBase (Issue #4647)
* Do not raise an Error reading H5MD files with datasets like
`observables/<particle>/<property>` (part of Issue #4598, PR #4615)
* Fix failure in double-serialization of TextIOPicklable file reader.
(Issue #3723, PR #3722)
* Fix failure to preserve modification of coordinates after serialization,
e.g. with transformations
(Issue #4633, PR #3722)
* Fix PSFParser error when encoutering string-like resids
* (Issue #2053, Issue #4189 PR #4582)
* Fix `MDAnalysis.analysis.align.AlignTraj` not accepting writer kwargs
(Issue #4564, PR #4565)
* Fix #4259 via removing argument `parallelizable` of `NoJump` transformation.
* Fix doctest errors of analysis/pca.py related to rounding issues
(Issue #3925, PR #4377)
* Convert openmm Quantity to raw value for KE and PE in OpenMMSimulationReader.
* Atomname methods can handle empty groups (Issue #2879, PR #4529)
* Add support for TPR files produced by Gromacs 2024.1 (PR #4523)
* Remove mutable data from ``progressbar_kwargs`` argument in ``AnalysisBase.run()``
(PR #4459)
* Fix ChainReader `__repr__()` method when sub-reader is MemoryReader
(Issue #3349, PR #4407)
* Fix bug in PCA preventing use of `frames=...` syntax (PR #4423)
* Fix `analysis/diffusionmap.py` iteration through trajectory to iteration
over `self._sliced_trajectory`, hence supporting
`DistanceMatrix.run(frames=...)` (PR #4433)
* Fix doctest errors of lib/picklable_file_io.py (Issue #3925, PR #4371)
* Fix deploy action to use the correct version of the pypi upload action.
* Fix groups.py doctests using sphinx directives (Issue #3925, PR #4374)
Enhancements
* Removed type and mass guessing from all topology parsers (PR #3753)
* Added guess_TopologyAttrs() API to the Universe to handle attribute
guessing (PR #3753)
* Added the DefaultGuesser class, which is a general-purpose guesser with
the same functionalities as the existing guesser.py methods (PR #3753)
* Added is_value_missing() to `TopologyAttrs` to check for missing
values (PR #3753)
* Added guessed `Element` attribute to the ITPParser to preserve old mass
partial guessing behavior from being broken (PR #3753)
* MDAnalysis now supports Python 3.13 (PR #4732)
* Introduce parallelization API to `AnalysisBase` and to `analysis.rms.RMSD` class
(Issue #4158, PR #4304)
* Enables parallelization for analysis.gnm.GNMAnalysis (Issue #4672)
* Explicitly mark `analysis.pca.PCA` as not parallelizable (Issue #4680)
* Enables parallelization for analysis.bat.BAT (Issue #4663)
* Enable parallelization for analysis.dihedrals.{Dihedral,Ramachandran,Janin}
(Issue #4673)
* Enables parallelization for analysis.dssp.dssp.DSSP (Issue #4674)
* Enables parallelization for analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis (Issue #4664)
* Improve error message for `AtomGroup.unwrap()` when bonds are not present.(Issue #4436, PR #4642)
* Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)
* Added a tqdm progress bar for `MDAnalysis.analysis.pca.PCA.transform()`
(PR #4531)
* Improved performance of PDBWriter (Issue #2785, PR #4472)
* Added parsing of arbitrary columns of the LAMMPS dump parser. (Issue #3504)
* Documented the r0 attribute in the `Contacts` class and added the
`n_initial_contacts` attribute, with documentation. (Issue #2604, PR #4415)
* Implement average structures with iterative algorithm from
DOI 10.1021/acs.jpcb.7b11988. (Issue #2039, PR #4524)
Changes
* Relicense code contributions from GPLv2+ to LGPLv2.1+
and the package from GPLv3+ to LGPLv3+ (PR #4794)
* only use distopia < 0.3.0 due to API changes (Issue #4739)
* The `fetch_mmtf` method has been removed as the REST API service
for MMTF files has ceased to exist (Issue #4634)
* MDAnalysis now builds against numpy 2.0 rather than the
minimum supported numpy version (PR #4620)
* As per SPEC0 the minimum supported Python version has been raised
to 3.10 (PR #4502)
* MDAnalysis.analysis.hole2 is now directly imported from the mdakit
mdahole2. This module is deprecated and will be fully removed in
MDAnalysis version 3.0 (PR #4464)
* Testsuite packaging now uses a pyproject.toml file (PR #4463)
* Improvement of setuptools packaging, including deduplication of
dependency lists (PR #4424)
* As per NEP29, the minimum version of numpy has been raised to 1.23.
We have opted to pin to 1.23.2 to ensure the same minimum numpy version
is used from python 3.9 to 3.11 (Issue #4401, PR #4402)
* updated tests that used assert_almost_equal(..., decimal={N}) with
equivalent assert_allclose(... rtol=0, atol=1.5e-{N}) (issue modernize
testing code #3743, PR Replaced numpy.testing.assert_almost_equal to
numpy.testing.assert_allclose #4438)
Deprecations
* The `guess_bonds`, `vdwradii`, `fudge_factor`, and `lower_bound` kwargs
are deprecated for bond guessing during Universe creation. Instead,
pass `("bonds", "angles", "dihedrals")` into `to_guess` or `force_guess`
during Universe creation, and the associated `vdwradii`, `fudge_factor`,
and `lower_bound` kwargs into `Guesser` creation. Alternatively, if
`vdwradii`, `fudge_factor`, and `lower_bound` are passed into
`Universe.guess_TopologyAttrs`, they will override the previous values
of those kwargs. (Issue #4756, PR #4757)
* MDAnalysis.topology.guessers is deprecated in favour of the new
Guessers API and will be removed in version 3.0 (PR #4752)
* MDAnalysis.topology.tables is deprecated in favour of
MDAnalysis.guesser.tables and will be removed in version 3.0 (PR #4752)
* Element guessing in the ITPParser is deprecated and will be removed in version 3.0
(Issue #4698)
* Unknown masses are set to 0.0 for current version, this will be depracated
in version 3.0.0 and replaced by :class:`Masses`' no_value_label attribute(np.nan)
(PR #3753)
* The MDAnalysis.anaylsis.encore module has been deprecated in favour of the
mdaencore MDAKit and will be removed in version 3.0.0 (PR #4737)
* The MMTF Reader is deprecated and will be removed in version 3.0
as the MMTF format is no longer supported (Issue #4634)
* The MDAnalysis.analysis.waterdynamics module has been deprecated in favour
of the waterdynamics MDAKit and will be removed in version 3.0.0 (PR #4404)
* The MDAnalysis.analysis.psa module has been deprecated in favour of
the PathSimAnalysis MDAKit and will be removed in version 3.0.0
(PR #4403)
12/26/23 IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith,
richardjgowers, lilyminium, ALescoulie, hmacdope, HeetVekariya,
JoStoe, jennaswa, ljwoods2
* 2.7.0
Fixes
* Fix doctest errors of lib/transformations.py (Issue #3925, PR #4370)
* Fix documentation building errors due to `html_static_path` and unindented
block of code (Issue #4362, PR #4365)
* Updated cimport for numpy to maintain cimport consistency (Issue #3908)
* Fix `NoJump` unwrapping for jumps on the second frame in a
trajectory (PR #4258, Issue #4257)
* Deprecated np.float_ and np.NaN aliases have been replaced with
their original type value (np.float64 and np.nan) (PR #4272)
* Fixes a case where qcprot.CalcRMSDRotationalMatrix would return a
RMSD of None
* Fixes hydrogenbonds tutorial path to point to hbonds (Issue #4285, PR #4286)
* Fix atom charge reading in PDBQT parser (Issue #4282, PR #4283)
* Fix doctests failing from separated blocks of imports and
execution and incorrectly formatted test output (Issue #3925, PR #4366)
Enhancements
* Added a reader for GROMOS11 TRC trajectories (PR #4292 , Issue #4291)
* Document the usage of NoDataError in its docstring (Issue #3901, PR #4359)
* Refactor c_distances backend to have a cython .pxd header and expose in
libmdanalysis (Issue #4315, PR #4324)
* Add faster nucleic acid Major and Minor pair distance calculators using
AnalysisBase for updated nucleicacids module (Issue #3720, PR #3735)
* Adds external sidebar links (Issue #4296)
* Updated lib.qcprot.CalcRMSDRotationalMatrix to accept either float32 or float64
inputs (PR #4273, part of #3927)
* Added a warning about charge neutrality to the documentation of
`DielectricConstant` (Issue #4262, PR #4263)
* Add support for reading chainID info from prmtop amber topologies (PR #4007)
* Add support for reading chainID info from GROMACS TPR topologies
(Issue #3994, PR #4281)
* Add support for reading chainID info from Autodock PDBQT files (Issue #4207,
PR #4284)
Changes
* Biopython is now an optional dependency (Issue #3820, PR #4332)
* Networkx is now an optional dependency (Issue #3822).
* High memory tests (enabled through the environment variable
`ENABLE_HIGH_MEM_UNIT_TESTS` are now only enabled if the environment variable
is set to "true") (PR #4295)
* The `mda-xdrlib` module is now a core dependency of MDAnalysis
replacing the now deprecated `xdrlib` core Python library
(PR #4271)
* ConverterBase class moved from coordinates/base.py to converters/base.py (Issue #3404)
* Results for WatsonCrickDist nucleic acids analysis are now stored in
`analysis.nucleicacids.WatsonCrickDist.results.distances` (Issue #3720, PR #3735)
Deprecations
* The `asel` argument to timeseries will be renamed to `atomgroup` in 3.0.0.
(Issue #3911)
* MDAnalysis.lib.util is deprecated and will be removed in version 3.0
(Issue #3649)
* The TRZ reader & writer are deprecated and will be removed in version 3.0
(PR #4335)
* X3DNA has been deprecated and will be removed in 3.0.0 (Issue #3788)
* coordinates.base.ConverterBase has been deprecated and will be removed in 3.0.0;
use converters.base.ConvertBase instead (Issue #3404)
* In `nucleicacids.WatsonCrickDist`, accepting lists of `Residue` objects was deprecated
in favor of using `ResidueGroup`: using `List[Residue]` will be removed in release
3.0.0; instead use a `ResidueGroup` (Issue #3720, PR #3735)
* In `nucleicacids.WatsonCrickDist` the result `results.pair_distances` was
deprecated and will be removed in 3.0.0; use `results.distances` (Issue #3720,
PR #3735)
08/28/23 IAlibay, hmacdope, pillose, jaclark5, tylerjereddy
* 2.6.1
Fixes
* Fix Atom type guessing error (PR #4168, Issue #4167)
Enhancements
* Allow `set_dimensions` transformation to handle NPT trajectories (PR #4258)
Changes
* Reverts PR #4108, builds are now again made using the oldest
supported NumPy version.
* NumPy `in1d` replaced with `isin` in preparation for NumPy
`2.0` (PR #4255)
* Update documentation for SurvivalProbabilty to be more clear
(Issue #4247)
* Cython DEF statments have been replaced with compile time integer constants
as DEF is deprecated as of Cython>=3.0 (Issue #4237, PR #4246)
Deprecations
08/15/23 IAlibay, jaclark5, MohitKumar020291, orionarcher, xhgchen,
ztimol, orbeckst, Shubx10
* 2.6.0
Fixes
* Fix AtomGroup.center_of_charge(..., unwrap=True) giving
inconsistent (but scientifically correct) results on Intel macOS
(Issue #4211)
* Fix Boltzmann typo in `units.py` (PR #4214, Issue #4213)
* Fix deletion of bond/angle/dihedral types (PR #4003, Issue #4001)
* CRD, PQR, and PDBQT writers now write BZ2 and GZ files if requested
(PR #4163, Issue #4159)
Enhancements
* Added a `exclude_same` kwarg to InterRDF (PR #4161)
* LAMMPSDump Reader use of `continuous` option to stitch trajectories
(Issue #3546)
Changes
* Package builds are now made using NumPy 1.25 or higher. This provides
backwards runtime compatibility with older NumPy builds within the limit
of NEP29 (PR #4108).
* Removed `-ffast-math` compiler flag to avoid potentially incorrect
floating point results in MDAnalysis *and* other codes when
MDAnalysis shared libraries are loaded --- see
https://moyix.blogspot.com/2022/09/someones-been-messing-with-my-subnormals.html
(Issues #3821, #4211)
* Atom ID representation order updated to match that of associated
AtomGroup indices.
(PR #4191, Issue #4181)
* Package license has been updated to GPLv3+ to better reflect the
compatibility of GPLv2+ with Apache and GPLv3 licenced codes (PR #4219).
* All new contributions are now made under LGPLv2.1+ (PR #4219).
* Support for GSD is now limited to version 3.0.1 and above. Alongside this
change, support for schema 1.3 files has been dropped (PR #4153)
* Add definition of ts.data['time'] in LAMMPSDump Reader (Issue #3546)
* As per NEP29 the minimum supported version has been raised to 1.22. We
have opted to pin to a minimum of 1.22.3 to avoid known issues on some
platforms.
* GSD is no longer a core dependency of MDAnalysis. It must be installed
independently if you wish to read HOOMD trajectory files.
(PR #4174, Issue #3819)
Deprecations
* Incorrectly spelt Boltzmann unit entry will be removed in version 2.8.0
(PR #4230, Issue #4229)
* The hole2 module is deprecated in favour of the the MDAKit:
https://github.com/MDAnalysis/hole2-mdakit (Issue #4179, PR #4200)
* MDAnalysis no longer officially supports 32 bit installations (they are
no longer tested in our continuous integration pipelines). Note: whilst
no code changes have been made to disable 32 bit, although it is known that
new versions of most MDAnalysis core dependencies no longer release
32 bit compatible versions. (Issue #3858, PR #4176)
05/28/23 IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae,
ooprathamm, MeetB7, BFedder, v-parmar, MoSchaeffler, jbarnoud, jandom,
xhgchen, jaclark5, DrDomenicoMarson, AHMED-salah00, schlaicha,
SophiaRuan, g2707, p-j-smith, tylerjereddy, xiki-tempula, richardjgowers,
cbouy, DanielJamesEvans, jvermaas, egormarin
* 2.5.0
Fixes
* Fixed using 'rb' mode inside GSDReader to avoid FutureWarning from GSDFile (Issue #4152)
* Fixed ChainReader performing transformations correctly across boundaries in the individual trajectories
(Issue #3657 #4008 PR #3906)
* Fix the `heavy` distance_type for water bridge analysis where distance
is not correctly assigned when more than one hydrogen is bonded to a
heavy atom (Issue #4040, PR #4066).
* PDB topology parser no longer fails when encountering unknown formal
charges and instead simply does not populate attribute (Issue #4027)
* Added support for Cython 3.0.0b2 (PR #4129)
* Ensure 'HydrogenBondAnalysis' returns the correct distances when using the
'between' keyword (PR #4092)
* Skip tests artificially checking for readonly or PermissionError cases
when running at root user on linux systems (Issue #4112, PR #4120)
* Fix chi1_selections() ignored atom names CG1 OG OG1 SG and incorrectly returned
None for amino acids CYS, ILE, SER, THR, VAL (Issue #4108)
* Fix parsing of box vector in H5MD reader (Issue #4076)
* Fix the misleading 'AtomGroup.guess_bonds()' docs and passed missing
arguments (PR #4059)
* Fix for NetCDF trajectories without `time` variable (Issue #4073)
* Allows shape_parameter and asphericity to yield per residue quantities
(Issue #3002, PR #3905)
* Add tests for "No path data" exception raise in test_psa.py (Issue #4036)
* Fix uninitialized `format` variable issue when calling
`selections.get_writer` directly (PR #4043)
* Fix tests should use results.rmsf to avoid DeprecationWarning (Issue #3695)
* Fix EDRReader failing when parsing single-frame EDR files (Issue #3999)
* Fix test clobbering in lib/test_util.py (PR #4000)
* Fix MSD docs to use the correct error metric in example (Issue #3991)
* Add 'PairIJ Coeffs' to the list of sections in LAMMPSParser.py
(Issue #3336)
Enhancements
* ARM64 (osx and linux) wheels now uploaded on release (Issue #4054)
* Add simple atomic distance analysis to `analysis.atomicdistances` with
new class `AtomicDistances` (Issue #3654)
* Add kwarg `n_frames` to class method `empty()` in
`MDAnalysis.core.universe`, enabling creation of a `Universe` with
multiple frames from scratch (PR #4140)
* PDBReader now populates ts.data['tempfactor'] with the tempfactor for
each atom *for each frame*. If an entry is missing for a given atom,
this will default to a `1.0` value. Note, this does not affect the
topology (i.e. `AtomGroup.tempfactors` is not dynamically updated.
(Issue #3825, PR #3988)
* Add writing u.trajectory.ts.data['molecule_tag'] as molecule tags to LAMMPS data file (Issue #3548)
* Improved speed of chi1_selection (PR #4109)
* Add `progressbar_kwargs` parameter to `AnalysisBase.run` method, allowing
to modify description, position etc of tqdm progressbars.
* Add a nojump transformation, which unwraps trajectories so that particle
paths are continuous. (Issue #3703, PR #4031)
* Added AtomGroup TopologyAttr to calculate gyration moments (Issue #3904,
PR #3905)
* Add support for TPR files produced by Gromacs 2023 (Issue #4047)
* Add distopia distance calculation library bindings as a selectable backend
for `calc_bonds` in `MDA.lib.distances`. (Issue #3783, PR #3914)
* AuxReaders are now pickle-able and copy-able (Issue #1785, PR #3887)
* Add pickling support for Atom, Residue, Segment, ResidueGroup
and SegmentGroup. (PR #3953)
Changes
* As per NEP29 the minimum supported Python version has been raised to 3.9
(PR #4115).
* einsum method for Einstein summation convention introduced to increase
performance (Issue #2063, PR #4089)
* Add progress bars to track the progress of _conclude() functions
(_conclude_simple() and _conclude_fft()) in msd.py (Issue #4070, PR #4072)
* As per NEP29 the minimum supported NumPy version has been raised to 1.21
(note: in practice later versions of NumPy may be used depending on your
architecture, operating system, or Python version) (PR #3983)
* The deprecated direct indexing and `times` from the `results` attribute of
analysis.nucleicacids' NucPairDist and WatsonCrickDist classes has been
removed. Please use the `results.pair_distances` and `times` attributes
instead (Issue #3744)
* RDKitConverter changes (part of Issue #3996):
* moved some variables (`MONATOMIC_CATION_CHARGES `and
`STANDARDIZATION_REACTIONS`) out of the related functions to allow users
fine tuning them if necessary.
* changed the sorting of heavy atoms when inferring bond orders and
charges: previously only based on the number of unpaired electrons, now
based on this and the number of heavy atom neighbors.
* use RDKit's `RunReactantInPlace` for the standardization reactions, which
should result in a significant speed improvement as we don't need to use
bespoke code to transfer atomic properties from the non-standardized mol
to the standardized one.
03/29/23 richardjgowers, IAlibay
* 2.4.3
Fixes
* Fixed DCD reading for large (>2Gb) files (Issue #4039). This was broken
for versions 2.4.0, 2.4.1 and 2.4.2
* Fix element parsing from PSF files tests read via Parmed (Issue #4015)
01/04/23 IAlibay
* 2.4.2
Fixes
* np.histogramdd calls in :class:`DensityAnalysis` now pass the `density`
argument rather than the NumPy 1.24 removed `normed` (PR #3976)
* visualization.streamlines_3D and visualization.streamlines no longer
rely on the scalar return of an numpy array elementwise comparison which
is no longer supported as of NumPy 1.25 (PR #3977)
12/17/22 IAlibay
* 2.4.1
Fixes
* Fixes pyproject.toml minimum pin for biopython
12/16/22 IAlibay, Luthaf, hmacdope, rafaelpap, jbarnoud, BFedder, aya9aladdin,
jaclark5, jfennick, lilyminium, orbeckst, Hakarishirenai
* 2.4.0
Fixes
* Update hbond analysis doc string to use exclusive bound language
(Issue #3847)
* XTC and TRR readers now fail with IOError when a status except EOK (=0) is
detected on reading a frame instead of silently continuing
* Consolidate license files across MDAnalysis library packages (PR #3939)
* Kwargs passed through to `MemoryReader` when using `transfer_to_memory()`
and `in_memory=True`.
* NoDataError raised on empty atomgroup provided to `DCDReader.timeseries`
was changed to ValueError (see #3901). A matching ValueError was added to
`MemoryReader.timeseries`(PR #3890).
* Removes ``pbc`` kwarg from ``AtomGroup.wrap`` (Issue #3909)
* LAMMPSDump Reader translates the box to the origin (#3741)
* hbond analysis: access hbonds results through new results member in count_by_ids() and count_by_type()
* Auxiliary; determination of representative frames: Removed undefined
behaviour for cutoff values < -1 (PR # 3749)
* Fixes distances.between not always returning AtomGroup (Issue #3794)
* Upgrade to chemfiles 0.10.3 (Issue #3798)
* fixes guessed_attributes and read_attributes methods of the Topology class, as
those methods were giving unexpected results for some topology attributes
(e.g. bonds, angles) (PR #3779).
Enhancements
* Added dipole and quadrupole moment topology methods to AtomGroup
(Issue #3841, PR #3842)
* MDAnalysis now follows PEP621 (PR #3528)
* Added a reader for GROMACS TNG files based on PyTNG (PR #3765,
Issue #3237, partially addressing Issue #865)
* Added ability for hbond analysis to use types when resnames are not
present (Issue #3847)
* Added explanatory warnings when hbond analysis doesn't find any hbonds
(Issue #3847)
* Improve C content of libxdr Cython, add `read_direct` methods to read
coordinates, velocities and forces directly into memoryviews of `Timestep`
attributes, make `TRR` timestep have positions, velocities and forces on
`__init__`. (Issue #3891 PR #3892).
* Improve C content of libdcd Cython (Issue #3882, PR #3888)
* The timeseries method for exporting coordinates from multiple frames to a
NumPy array was added to ProtoReader (PR #3890)
* MDAnalysis now officially supports py3.11 (Issue #3878)
* LAMMPSDump Reader optionally unwraps trajectories with image flags upon
loading (Issue #3843)
* LAMMPSDump Reader now imports velocities and forces (Issue #3843)
* Minimum NumPy version for py3.11 is now set to 1.23.2.
* Added decorator to check for an empty atom group, applied in topological
attributes(Issue #3837)
* AuxReaders now have a memory_limit parameter to control when memory usage
warnings are issued. (PR # 3749)
* MDAnalysis.units now has a lookup dictionary called MDANALYSIS_BASE_UNITS
where unit types like length or speed are mapped to their base units in
MDAnalysis (i.e. "A" or "A/ps") (PR # 3749)
* A new AuxReader for the GROMACS EDR file format was implemented.
(Issue # 3629, PR # 3749)
* Added benchmarks for bonds topology attribute (Issue #3785, PR #3806)
* Added isolayer selection method (Issue #3845)
Changes
* Minimum numpy version for python 3.10 and Windows has been raised to 1.22.3
(PR #3903)
* Replaced deprecated Bio.pairwise2 with Bio.align.PairwiseAligner in
MDAnalysis.analysis.align.sequence_alignment (Issue #3950)
* Increased minimal version of biopython to 1.80 (Issue #3950)
* Moved `libmdanalysis` cython header to `lib`(Issue #3912, PR #3913)
* Auxiliary; determination of representative frames: The default value for
cutoff is now None, not -1. Negative values are now turned
to None. (PR #3749)
* `MDAnalysis.coordinates.base.add_auxiliary()` now supports adding of
multiple auxiliary data points at the same time. To this end, the API was
rewritten and now expects dictionaries of `desired attribute name`:
`name in auxiliary data file` as input. Adding all data found in the
auxiliary data source is possible by omitting the dictionary and explicitly
passing the AuxReader instance as `auxdata`. (PR #3749)
* The "AMBER" entry in setup.py's extra_requires has now been removed. Please
use `pip install ./package[extra_formats]` instead (PR #3810)
* `Universe.empty` emmits less warnings (PR #3814)
* adding element attribute to TXYZParser if all atom names are valid element symbols (PR #3826)
Deprecations
* Direct indexing of results in analysis.nucleicacids' NucPairDist
and WatsonCrickDist classes is deprecated and will be removed in 2.5.0.
Please use `results.pair_distances` instead (Issue #3744)
* Deprecated analysis.align.sequence_alignment() for removal in 3.0 (#3950)
* Add deprecation warning for `timestep` copying in DCDReader
(Issue #3889, PR #3888)
* Add deprecation warning for inclusive stop indexing in
MemoryReader.timeseries (PR #3894)
08/29/22 IAlibay, PicoCentauri, orbeckst, hmacdope, rmeli, miss77jun, rzhao271,
yuxuanzhuang, hsadia538, lilyminium
* 2.3.0
Fixes
* Fixes awk call in deploy.yaml tests for macos runners (Issue #3693)
* add a 0.5 for correct midpoints in hole analysis (Issue #3715)
* Fix reading error when PDB CONECT records are corrupt. (Issue #988)
* Fix writing unusable PDB CONECT records with index>100000. (Issue #988)
Enhancements
* Add a new `formalcharge` attribute for storing formal charges (PR #3755)
* Add the ability to read & write formal charges from PDB files (PR #3755)
* Change functions in `lib.distances` to accept AtomGroups as well as NumPy
arrays (CZI Performance track PR #3730)
* Add `norm` parameter to InterRDF, InterRDF_s to normalize as rdf,
number density or do not normalize at all. (Issue #3687)
* Additional logger.info output when per-frame analysis starts (PR #3710)
* Timestep has been converted to a Cython Extension type
(CZI Performance track, PR #3683)
* Refactor make_downshift_arrays with vector operation in numpy(PR #3724)
* Optimize topology serialization/construction by lazy-building _RA and _SR.
Changes
* To add additional optional packages for different file formats when
using `pip` use the new "extra_formats" extras_require target as in
`pip install ./package[extra_formats]` (Issue #3701, PR #3711)
* Minimum supported NumPy version is now 1.20 (1.21 for macosx-arm64)
as per NEP29 (PR #3737)
* Narrowed variable scope to reduce use of OpenMP `private` clause (PR #3706, PR
#3728)
Deprecations
* The extras_requires target "AMBER" for `pip install ./package[AMBER]`
will be removed in 2.4. Use "extra_formats". (Issue #3701, PR #3711)
* Deprecate `density` parameter in favor of `norm` in InterRDF_s
(Issue #3687)
06/01/22 IAlibay, BFedder, inomag, Agorfa, aya9aladdin, shudipto-amin, cbouy,
HenokB, umak1106, tamandeeps, Mrqeoqqt, megosato, AnirG, rishu235,
mtiberti, manishsaini6421, Sukeerti1, robotjellyzone, markvrma, alescoulie,
mjtadema, PicoCentauri, Atharva7K, aditi2906, orbeckst, yuxuanzhuang,
rsexton2, rafaelpap, richardjgowers, orioncohen, mdpoleto
* 2.2.0
Fixes
* Fixed issue where Reader.copy() did not preserve optional arguments
and kwargs passed to the original class (Issue #3664, PR #3685)
* Iterating a SingleFrameReaderBase trajectory now rewinds the
reader, resetting any modified trajectory attributes to those
read from file. Fixes behavior that was previously undefined (Issue #3423)
* Fixed Reader.copy() did not preserve convert_units=False (see PR #3642)
* Fix the competition when generating offsets from multiple processes by
using a interprocess file lock. (Issue #1988, PR #3375)
* Fix the error when trying to load a corrupted offset file (Issue #3230
PR #3375)
* Fixed `OpenMMTopologyParser` not working when some or none of the elements
are present in the openmm topology (Issue #3317, PR #3511).
* Remove None from filenames in analysis.hole.HoleAnalysis (PR #3650)
* Fixed Numpy deprecation warnings about elementwise comparisons.
(Issue #3535, PR #3619)
* Fixed encore.covariance.covariance_matrix not working when providing
an external reference (Issue #3539, PR #3621)
* Fixed LinearDensity not working with grouping='residues' or 'segments'
(Issue #3571, PR #3572)
* LinearDensity now uses the definition of Avogadro's number from
MDAnalysis.units, which has more significant digits.
(Issue #3571, PR #3572)
* MOL2 can read files without providing optional columns:
subst_id, subst_name and charge. (Issue #3385, PR #3598)
* When converting an AtomGroup to an RDKit molecule (PR #3044):
- the atoms are now in the same order
- the output of `atom.GetMonomerInfo().GetName()` now follows the
guidelines for PDB files while the original name is still available
through `atom.GetProp("_MDAnalysis_name")`
- using `NoImplicit=False` should no longer throw a `SanitizationError`
* Contacts can now accept static AtomGroups as well as selection texts.
(Issue #2666, PR #3565)
* Fixed DumpReader triclinic box dimensions reading. (Issue #3386, PR #3403)
* Updated the badge in README of MDAnalysisTest to point to Github CI Actions
* Fixed FrameIteratorIndices doesn't rewind. (Issue #3416)
* Fixed BAT method Cartesian modifies input data. (Issue #3501)
Enhancements
* Add smarts_kwargs to allow greater flexiblity with smarts atom selection
(Issue #3469, PR #3470).
* Added DL_POLY Classic support. Now HISTORY files from DL_POLY Classic can be
* used. (Issue #3678)
* Wheels and dist now get automatically built and deployed on release
triggers (Issue #1300, PR #3680)
* Added equations for `center_of_mass` and `center_of_geometry`to
documentation (PR #3671)
* Added `center_of_charge` attribute (PR #3671)
* Added `frames` argument to AnalysisBase.run to allow analysis to run on
arbitrary list of frames (Issue #1985)
* LinearDensity now works with updating AtomGroups (Issue #2508, PR #3617)
* Link PMDA in documentation (PR #3652)
* Added MSD example where multiple replicates are combined(Issue #3578
PR #3633)
* PCA class now has an inverse-PCA function. The inverse transform can
also be extrapolated to certain non-PCA atoms. (PR #3596, Issue #2703)
* `DistanceMatrix` class in MDAnalysis.analysis.diffusionmap now also
accepts `AtomGroup` as a valid argument (Issue #3486, PR #3541)
* Improves the RDKitConverter's accuracy (PR #3044): AtomGroups containing
monatomic ion charges or edge cases with nitrogen, sulfur, phosphorus and
conjugated systems should now have correctly assigned bond orders and
charges.
* New optimized AnalysisBase derived Watson-Crick distance analysis class in
analysis.nucleicacids
* CRD extended format can now be explicitly requested with the `extended`
keyword (Issue #3605)
* Added benchmarks in lib.distances for enhancement (Issue #3205, PR #3641)
Changes
* smarts selection's `maxMatches` now defaults to max(1000, n_atoms*10)
instead of the standard RDKit default of 1000 (Issue #3469, PR #3470).
* `fasteners` package is now a core dependency (Issues #3230, #1988, PR #3375)
* The minimm Python, NumPy, and SciPy versions (following NEP29) are now 3.8,
1.19, and 1.5.0; GSD now also has a minimum version of 1.9.3 and networkx
has minimum version 2.0 (Issue #3665)
* LinearDensity now saves the histogram bin edges for easier plotting as
"hist_bin_edges" for each dimension xyz in the results dictionary.
(Issue #2508, PR #3617)
* ITPParser no longer adds an angle for water molecules that have the SETTLE
constraint applied to them. This mirrors the way the constraint is handled
in AMBER. (Issue #2417, PR #3564)
Deprecations
* The old results attributes for LinearDensity are now deprecated and will be
removed in version 3.0.0. (Issue #2508, PR #3617)
- "pos" is now "mass_density",
- "char" is now "charge_density"
- "std" entries are now "stddev"
03/06/22 IAlibay, melomcr, mdd31, ianmkenney, richardjgowers, hmacdope,
orbeckst, scal444, p-j-smith, edisj, Atharva7K, ojeda-e, jbarnoud,
yangtcai
* 2.1.0
Fixes
* Use uint64_t loop counters in C level distance functions to avoid overflow
for large arrays (Issue #3512, PR #3513).
* Prevents attempts to close an already closed NamedStream (Issue #3386)
* Added missing exe_err import in hole.py. Fixed a bug in HoleAnalysis where
kwarg was passed instead of object to generate path (Issue #3493, PR #3496)
* Fixes creation of vmd surfaces in hole2 when using non-contiguous frames
with start/stop/step (Issue #3476)
* Allow empty strings to be passed to HydrogenBondAnalysis (Issue #3453).
* Avoid integer overflow in NSGrid with too many grids (Issue #3183)
* Fix ITPParser charge reading (Issue #3419).
* TRRWriter preserves timestep data (Issue #3350).
* Fixed Universe creation from a custom object which only provided a topology,
previously raised a TypeError. (Issue #3443)
* Documentation fixes (Issues #3224, #2667)
* Fixed string attributes (e.g. resname, segid) not working on Residues and Segments
created using add_Residue and add_Segment (Issue #3437)
Enhancements
* Added dielectric analysis module (PR #2118)
* Supports TPR files produced by Gromacs 2022 (PR #3514)
* Add support for millisecond and microsecond units (Issue #3473, PR #3491)
* Adds :meth:`parse_n_atoms` to H5MD reader (Issue #3465)
* Add option for custom compiler flags for C/C++ on build and remove march
option from setup.cfg (Issue #3428, PR #3429).
* Added R/S Chirality support to RDKit parsed molecules
* Added MDAnalysis.lib.distances.minimize_vectors
Changes
* `packaging` is now a core dependency for MDAnalysis
* Indexing a group (AtomGroup, ResidueGroup, or SegmentGroup) with None
raises a TypeError (Issue #3092, PR #3517)
* TRZReader now defaults to a `dt` of 1.0 (instead of 0.0 previously) when
it cannot be obtained from file (Issue #3257)
* Dropped python 3.6 support and raised minimum numpy version to 1.18.0
(NEP29)
Deprecations
* Deprecated the 'pbc' kwarg for various Group methods, the 'wrap' kwarg
should be used instead. (Issue #1760)
08/21/21 tylerjereddy, richardjgowers, IAlibay, hmacdope, orbeckst, cbouy,
lilyminium, daveminh, jbarnoud, yuxuanzhuang, VOD555, ianmkenney,
calcraven，xiki-tempula, mieczyslaw, manuel.nuno.melo, PicoCentauri,
hanatok, rmeli, aditya-kamath, tirkarthi, LeonardoBarneschi, hejamu,
biogen98, orioncohen, z3y50n, hp115, ojeda-e, thadanipaarth, HenryKobin,
1ut, sulays, ahy3nz, fiszczyp, fiona-naughton
* 2.0.0
Fixes
* Added an `rdkit_kwargs` parameter to pass arguments to the RDKitConverter
from the `select_atoms` method (Issue #3319, PR #3324)
* Fixes AtomGroup.unique, ResidueGroup.unique, SegmentGroup.unique not
sorting the output atoms. The returned group is now always a copy.
(Issue #3364, Issue #2977, PR #3368)
* Only GRO files with unit cells defined with 3 or 9 entries are now
supported (Issue #3305)
* Ensures that reading and writing of GRO files with missing unit cell
information is consistently treated (Issue #3305)
* Fixed sometimes wrong sorting of atoms into fragments when unwrapping
(Issue #3352, PR #3353)
* Fixed missing array flatten preventing PCA from running when mean positions
provided and bugs causing tests to incorrectly pass (Issue #2728, PR #3296)
* DL_POLY HISTORY file may contain unit cell dimensions even if there are
no periodic boundary conditions (imcom=0) (Issue #3314, PR #3312).
* New RDKitConverter cache system to fix issue #2958 (PR #2942)
* Fixed OpenMM converter documentation not showing up in the Converters
section (Issue #3262, PR #2882)
* WaterBridgeAnalysis double counts the water (Issue #3119, PR #3120)
* NCDFReader now defaults to a dt value of 1.0 ps when it cannot estimate
it from the first two frames of the file (Issue #3166)
* Get chi1_selection to match canonical gamma atoms (Issue #2044)
* ITPParser now accepts relative paths (Issue #3037, PR #3108)
* Fixed issue with unassigned 'GAP' variable in fasta2algin function when
resids are provided in input (Issue #3124)
* Improve diffusionmap coverage (Issue #3208)
* Removed deprecated parameters `n_jobs` and `precompute_distances` of
sklearn.cluster.KMeans (Issue #2986)
* Helix_analysis coverage raised to 100% and `from __future__ import`
removed (Issue #3209)
* Fixed 'sphzone', 'sphlayer', 'cyzone', and 'cylayer' to return empty if the
zone/layer is empty, consistent with 'around' (Issue #2915)
* A Universe created from an ROMol with no atoms returns now a Universe
with 0 atoms (Issue #3142)
* PDBParser will check for the presence of the chainID attribute of an
atom group and use these values instead of just using the end of segid.
If no chainID attribute is present, then a default value will be
provided. If the chainID for an atom is invalid (longer than one character,
not alpha-numeric, blank) it will be replaced with a default. (Issue #3144)
* ValueError raised when empty atomgroup is given to DensityAnalysis
without a user defined grid. UserWarning displayed when user defined
grid is provided. (Issue #3055)
* Fixed import of several `__all__` lists (PR #3013)
* atommethods (_get_prev/next_residues_by_resid) returns empty residue group
when given empty residue group (Issue #3089)
* MOL2 files without bonds can now be read and written (Issue #3057)
* Write `CONECT` record only once in multi-model PDB files (Issue #3018)
* Add '.nc' as a recognised extension for the NCDFWriter (Issue #3030)
* PDB parser now assigns empty records for partially missing/invalid elements
instead of not assigning the elements attribute at all (Issue #2422)
* PDB writer now uses elements attribute instead of guessing elements from
atom name (Issue #2423)
* Cleanup and parametrization of test_atomgroup.py (Issue #2995)
* The methods provided by topology attributes now appear in the
documentation (Issue #1845)
* AtomGroup.center now works correctly for compounds + unwrapping
(Issue #2984)
* Avoid using deprecated array indexing in topology attributes
(Issue #2990, PR #2991)
* ParmedParser no longer guesses elements if they are not recognised, instead
empty strings are assigned (Issue #2933)
* Instead of using ATOM for both ATOM and HETATM, HETATM record type
keyword is properly written out by PDB writer (Issue #1753, PR #2880).
* Change referenced PDB standard version to 3.3 (Issue #2906).
* Fixed reading in masses and charges from a hoomdxml file
(Issue #2888, PR #2889)
* Bond attribute is no longer set if PDB file contains no CONECT records
(Issue #2832)
* ResidueAttrs now have Atom as a target class by default; ICodes and
Molnums now have default target_classes (#2803, PR #2805)
* Selections on emtpy AtomGroups now return an empty AtomGroup instead of an
error (Issue #2765)
* TOPParser no longer guesses elements when missing atomic number records
(Issues #2449, #2651)
* Testsuite does not any more matplotlib.use('agg') (#2191)
* In ChainReader, read_frame does not trigger change of iterating position.
(Issue #2723, PR #2815)
* TRZReader now checks `n_atoms` on reading. (Issue #2817, PR #2820)
* TRZWriter now writes `n_atoms` to the file. (Issue #2817, PR #2820)
* rdf.InterRDF_s density keyword documented and now gives correct results for
density=True; the keyword was available since 0.19.0 but with incorrect
semantics and not documented and did not produce correct results (Issue
#2811, PR #2812)
* In hydrogenbonds.hbond_analysis.HydrogenbondAnalysis an AttributeError
was thrown when finding D-H pairs via the topology if `hydrogens` was an
empty AtomGroup (Issue #2848)
* Fixed performance regression on select_atoms for string selections (#2751)
* Fixed the DMSParser, allowing the creation of multiple segids sharing
residues with identical resids (Issue #1387, PR #2872)
* H5MD files are now picklable with H5PYPicklable (Issue #2890, PR #2894)
* Fixed Janin analysis residue filtering (include CYSH) (Issue #2898)
* libmdaxdr and libdcd classes in their last frame can now be pickled
(Issue #2878, PR #2911)
* AtomGroup now are pickled/unpickled without looking for its anchored
Universe (PR #2893)
* ensure that unistd.h is included on macOS when compiling ENCORE's spe.c
(Issue #2934)
* Fix tests for analysis.bat that could fail when run in parallel and that
would create a test artifact (Issue #2979, PR #2981)
* Fix syntax warning over comparison of literals using is (Issue #3066)
* new `Results` class now can be pickled/unpickled. (PR #3309)
Enhancements
* LAMMPSDumpReader can now read coordinates in all the different LAMMPS
coordinate conventions. Both LAMMPSDumpReader and LAMMPSDumpParser are no
longer hardcoded to a set column layout (Issue #3358, PR #3360).
* Add a ``sort`` keyword to AtomGroup.select_atoms for ordered selections
(Issue #3364, PR #3368)
* Adds AtomGroup.asunique, ResidueGroup.asunique, SegmentGroup.asunique
with optional sorting. The returned group may or may not be a copy
if it is already unique and/or sorted. (Issue #3364, PR #3368)
* Adds ``issorted`` property (PR #3368)
* MOL2 parser populates elements attribute from SYBYL atom types (Issue #3062)
* Added guessers for aromaticity and Gasteiger partial charges (Issue #2468,
PR #2926)
* Added `Results` class for storing analysis results (#3115, PR #3233)
* Added intra_bonds, intra_angles, intra_dihedrals etc. to return only
the connections involving atoms within the AtomGroup, instead of
including atoms outside the AtomGroup (Issue #1264, #2821, PR #3200)
* Added del_TopologyAttr function (PR #3069)
* Switch GNMAnalysis to AnalysisBase (Issue #3243)
* Adds python 3.9 support (Issue #2974, PR #3027, #3245)
* Added an MDAnalysis shields.io badge to the README (Issue #3227, PR #3229)
* Added sort method to the atomgroup (Issue #2976, PR #3188)
* ITPParser now reads [ atomtypes ] sections in ITP files, used for charges
and masses not defined in the [ atoms ] sections
* Add `set_dimensions` transformation class for setting constant
box dimensions for all timesteps in trajectory (Issue #2691)
* Added a ValueError raised when not given a gridcenter while
providing grid dimensions to DensityAnalysis, also added
check for NaN in the input (Issue #3148, PR #3154)
* Read TPR files from Gromacs 2021 (Issue #3180)
* Adds preliminary support for the ppc64le platform with minimal
dependencies (Issue #3127, PR #3149)
* Caches can now undergo central validation at the Universe level, opening
the door to more useful caching. Already applied to fragment caching
(Issue #2376, PR #3135)
* Code for operations on compounds refactored, centralized and optimized for
performance (Issue #3000, PR #3005)
* Added automatic selection class generation for TopologyAttrs,
FloatRangeSelection, and BoolSelection (Issues #2925, #2875; PR #2927)
* Added 'to' operator, negatives, scientific notation, and arbitrary
whitespace for ranges (Issue #3054, PR #2927)
* Added `atol` and `rtol` keywords for float comparison (PR #2927)
* Improved performance of the ParmEd converter (Issue #3028, PR #3029)
* Improved analysis class docstrings, and added missing classes to the
`__all__` list (PR #2998)
* The PDB writer gives more control over how to write the atom ids
(Issue #1072, PR #2886)
* Preliminary support for the Linux ARM64 platform with minimal
dependencies (PR #2956)
* Refactored analysis.helanal into analysis.helix_analysis
(Issue #2452, PR #2622)
* Improved MSD code to accept `AtomGroup` and reject `UpdatingAtomGroup`
and improved docs (Issue #2784)
* Added the RDKitParser which creates a `core.topology.Topology` object from
an `rdkit.Chem.rdchem.Mol` object, and the RDKitReader to read coordinates
from RDKit conformers (Issue #2468, PR #2707)
* Added the `Aromaticities` topology attribute, and the `aromatic` selection
token (Issue #2468, PR #2707)
* Added the `from_smiles` classmethod to the Universe (Issue #2468, PR #2707)
* Added computation of Mean Squared Displacements (#2438, PR #2619)
* Improved performances when parsing TPR files (PR #2804)
* Added converter between Cartesian and Bond-Angle-Torsion coordinates (PR #2668)
* Added Hydrogen Bond Lifetime via existing autocorrelation features (PR #2791)
* Added Hydrogen Bond Lifetime keyword "between" (PR #2791)
* Added lib.pickle_file_io module for pickling file handlers. (PR #2723)
* Added pickle function to `Universe` and all Readers (without transformation)
(PR #2723)
* Dead code removed from the TPR parser and increased test coverage (PR #2840)
* TPR parser exposes the elements topology attribute (PR #2858, see Issue #2553)
* Added `H5MDReader` to coordinate readers (Issue #762, PR #2787)
* Added new kwargs `select_remove` and `select_protein` to
analysis.dihedrals.Janin analysis to give user more fine grained control
over selections (PR #2899)
* Improved performance of select_atoms on strings (e.g. name, type, resname) and
'protein' selection (#2751 PR #2755)
* Added an RDKit converter that works for any input with all hydrogens
explicit in the topology (Issue #2468, PR #2775)
* Added `TransformationBase`. Implemented threadlimit and add an attribute for
checking if it can be used in parallel analysis. (Issue #2996, PR #2950)
* Improved performance of H5MDReader by using h5py.Dataset.read_direct()
to transfer data from HDF5 file into timestep. (PR #3293)
* Added `H5MDWriter` to coordinate writers (Issue #2866, PR #3189)
Changes
* NCDFWriter now allows for the writing of `scale_factor` attributes for
trajectory variables. Default writing is no `scale_factor` except for
velocities where it is 20.455 (Issue #2327)
* Update the API for coordinate writers to reflect practice:
start. stop, step are not required anymore (#3392)
* Aliased bfactors to tempfactors (Issue #1901, PR#3345)
* The RDKitParser now raises an error if only part of the atoms have metadata
on residues (Issue #3318, PR #3325)
* `analysis.pca.PCA` class now stores `p_components`, `variance`,
`cumulated_variance` and `mean_atoms` using the
`analysis.base.Results` class (Issues #3275 #3285)
* Timestep now stores information in 'C' memory layout instead of
the previous 'F' default (PR #1738)
* `analysis.rdf.InterRDF` and `analysis.rdf.InterRDF_s` now store
their result attributes using the `analysis.base.Results` class
(Issue #3276, #3261)
* Adds a `force` parameter to the RDKitConverter to allow conversion of
molecules with no hydrogen atom, and a `set_converter_cache_size` function
to change how many items are retained in the cache (PR #2942)
* `hydrogenbonds.WaterBridgeAnalysis.generate_table()` now returns the table; as previously,
it also generates the `table` attribute but the attribute will be removed in 3.0.0.
* `hydrogenbonds.WaterBridgeAnalysis` now stores data using the
`hydrogenbonds.WaterBridgeAnalysis.results` attribute
(Issue #3261, Issue #3270)
* Introduces a new converter API with all converters in MDAnalysis.converters
(Issue #2790, PR #2882)
* The ParmEd classes were moved to the `converters` module (PR #2882)
* The `convert_to` method of the AtomGroup is now case-insensitive and
passes keyword arguments to the underlying converter. It can also be used
as `convert_to.lowercase_pkg_name()` for tab-completion (PR #2882)
* `analysis.polymer.PersistenceLength` class now stores `lb`,
`lp` and `fit` using the `analysis.base.Results` class
(Issues #3289, #3291)
* `analysis.hole2.HoleAnalysis` now stores ``sphpdbs``, ``outfiles``
and ``profiles`` in the `analysis.base.Results` class (Issues #3261, #3269)
* `analysis.diffusionmap.DistanceMatrix` class now stores `dist_matrix`
using the `analysis.base.Results` class (Issues #3288, #3290)
* `helix_analysis.HELANAL` now uses the `analysis.base.Results` class to
store results attributes (Issue #3261, #3267)
* `analysis.align.AlignTraj` and `analysis.align.AverageStructure` now store
their result attributes using the `analysis.base.Results` class
(Issues #3278 and #3261)
* `analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalyis` now stores
`hbonds` data using the `analysis.base.Results class (Issues #3271, #3261)
* `analysis.rms.RMSD` and `analysis.rms.RMSF` classes now store `rmsd` and
`rmsf` data using the `analysis.base.Results` class (Issues #3274 #3261)
* `analysis.dihedrals` classes now store angle data using the
`results.angles` attribute (Issue #3261)
* `msd.EinsteinMSD` now uses the `analysis.base.Results` class to store
analysis results (Issue #3261)
* `bat.BAT` now uses the `analysis.base.Results` class to store the `bat`
results attribute (Issue #3261, #3272)
* `contacts.Contacts` now stores data using the `Contacts.results.timeseries`
attribute. `Contacts.timeseries` is now deprecated (Issue #3261)
* `DensityAnalysis` now uses the `results.density` attribute for storing
data. The `DensityAnalysis.density` attribute is now deprecated
(Issue #3261)
* Deprecated analysis.hbonds.hbond_analysis has been removed in favour of
analysis.hydrogenbonds.hbond_analysis (Issues #2739, #2746)
* `GNMAnalysis`, `LinearDensity`, `PersistenceLength` and
`AnalysisFromFunction` use the `results` attribute.
* Fixed inaccurate docstring inside the RMSD class (Issue #2796, PR #3134)
* TPRParser now loads TPR files with `tpr_resid_from_one=True` by default,
which starts TPR resid indexing from 1 (instead of 0 as in 1.x) (Issue #2364, PR #3152)
* Introduces encore specific C compiler arguments to allow for lowering of
optimisations on non-x86 platforms (Issue #1389, PR #3149)
* Continuous integration uses mamba rather than conda to install the
dependencies (PR #2983)
* removes deprecated `as_Universe` function from MDAnalysis.core.universe,
as a result :class:`MDAnalysis.analysis.leaflet.LeafletFinder` now only
accepts Universes for its `universe` argument (Issue #2920)