MDAnalysis is a Python library to analyze molecular dynamics simulations.
This a minor release of MDAnalysis.
This release of MDAnalysis is packaged under a GPLv3+ license, additionally all contributions made from commit 44733fc214dcfdcc2b7cb3e3705258781bb491bd
onwards are made under the LGPLv2.1+ license.
The minimum supported NumPy version is 1.22.3.
Supported Python versions:
See the CHANGELOG and our release blog post for more details.
chainID
from PDBQT files (PR #4284)chainID
from molblock
(PR #4281)libmdanalysis.pxd
(PR #4342)mda_xdrlib
as a core dependency to replace the now deprecated Python xdrlib
code (PR #4271)MDAnalysis.converters.base
(PR #4253)networkx
is now an optional dependency of MDAnalysis (PR #4331)BioPython
is now an optional dependency of MDAnalysis (PR #4332)analysis.nucleicacids.WatsonCrickDist.results.distances
(PR #3735)MDAnalysis.coordinates.base
will not be possible after MDAnalysis 3.0 (PR #4253)MDAnalysis.lib.util.which
method (PR #4340)asel
argument of the timeseries
attribute of Readers is now deprecated in favour of the atomgroup
argument (PR #4343)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
(PR #3735)nucleicacids.WatsonCrickDist
the result results.pair_distances
was deprecated and will be removed in 3.0.0; use results.distances
instead (PR #3735)This is a bugfix release of the 2.6.x version branch of MDAnalysis, it serves as an amendment to the earlier released version 2.6.0.
See the CHANGELOG for more details.
in1d
have been replaced with isin
in prepartion for NumPy 2.0 [PR #4255]This a minor release of MDAnalysis.
This release of MDAnalysis is packaged under a GPLv3+ license, additionally all contributions made from commit 44733fc214dcfdcc2b7cb3e3705258781bb491bd onwards are made under the LGPLv2.1+ license. More details about these license changes will be provided in an upcoming blog post.
The minimum supported NumPy version has been raised to 1.22.3 as per NEP29. Please note that package builds are now made with NumPy 1.25+ which offer backwards runtime compatibility with NEP29 supported versions of NumPy.
Supported Python versions:
See the CHANGELOG and our release blog post for more details.
exclude_same
argument has been added to InterRDF
allowing pairs of atoms that share the same residue, segment or chain to be excluded from the calculation. (https://github.com/MDAnalysis/mdanalysis/pull/4161)continuous
ChainReader option. (https://github.com/MDAnalysis/mdanalysis/pull/4170)Boltzman_constant
entry in MDAnalysis.units
is now deprecated in favour the correctly spelt Boltzmann_constant
. (https://github.com/MDAnalysis/mdanalysis/pull/4230 and https://github.com/MDAnalysis/mdanalysis/pull/4214)MDAnalysis.analysis.hole2
is now deprecated in favour of a new HOLE2 MDAKit. (https://github.com/MDAnalysis/mdanalysis/pull/4200)This a minor release of MDAnalysis.
The minimum Python version has been raised to 3.9 and NumPy to 1.21.0 as per NEP29. We also now package wheels for both linux and osx arm64 machines on PyPi.
Supported Python versions:
See the CHANGELOG and our release blog post for more details.
heavy
distance_type for WaterBridgeAnalysis
where distance was not correctly assigned when more than one hydrogen
was bonded to a heavy atom (Issue #4040, PR #4066).between
keyword of HydrogenBondAnalysis
led to incorrect donor-atom distances being returned (PR #4092, Issue #4091)None
for amino acids CYS, ILE, SER, THR, VAL
(Issue #4108, PR #4109)None
as the
dimensions (Issue #4075, PR #4076)time
variable defined (Issue #4073, PR #4074)analysis.atomicdistances.AtomicDistances
to provide distances between two atom groups over a trajectory.
(Issue #3654, PR #4105)n_frames
to class method empty()
in
MDAnalysis.core.universe
, enabling creation of a blank Universe
with
multiple frames (PR #4140)1.0
value. Note, this does not affect the
topology, i.e. AtomGroup.tempfactors
is not dynamically updated.
(Issue #3825, PR #3988)progressbar_kwargs
parameter to AnalysisBase.run
method, allowing
to modify description, position etc of tqdm progressbars. (PR #4085)calc_bonds
in MDA.lib.distances
. (Issue #3783, PR #3914)mds.EinsteinMSD
_conclude()
methods (_conclude_simple() and _conclude_fft()) (Issue #4070, PR #4072)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)MONATOMIC_CATION_CHARGES
and
STANDARDIZATION_REACTIONS
) out of the related functions to allow users
fine tuning them if necessary.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.This is a bugfix release of the 2.4.x version of MDAnalysis, it serves as an amendment to the earlier released version 2.4.2.
This is a bugfix release of the 2.4.x version of MDAnalysis, it serves as an amendment to the earlier released version 2.4.1.
MDAnalysis.analysis.DensityAnalysis
were not compatible with the 1.24 release of NumPy (PR #3976)MDAnalysis.visualization.streamlines_3D
and MDAnalysis.visualization.streamlines
where incorrect comparison of the truth of arrays would have led to failures (PR #3977)This a minor release of MDAnalysis, as per our once-every-three-months schedule.
The minimum NumPy and Python versions remain largely unchanged, however the minimum version of biopython
has been raised to 1.80. This is also the first release to officially support Python 3.11.
Supported Python versions:
See the CHANGELOG and our release blog post for more details.
extra_requires
AMBER
entry has been removed in favor of extra_formats
(PR #3810)MDAnalysis.analysis.align.sequence_alignment
now uses Bio.Align.PairwiseAligner instead of the deprecated Bio.pairwise2 (PR #3951)sequence_aligment()
method has been deprecated and will be removed in version 3.0.0 (PR #3951)results.pair_distances
(PR #3958)This a minor release of MDAnalysis, as per our once-every-three-months schedule.
The minimum NumPy version has been raised to 1.20.0 (1.21 for macosx-arm64) in line with NEP29.
Supported python versions:
See the CHANGELOG and our release blog post for more details.
formalcharge
attribute (PR #3755).norm
parameter for the InterRDF
and InterRDF_s
analysis methods (Issue #3687).pip install ./package[extra_formats]
(Issue #3701, PR #3711).extra_requires
target AMBER
for pip install ./package[AMBER]
will be removed in 2.4.0. Use extra_formats
(Issue #3701, PR #3711).A series of performance improvements to the MDAnalysis library's backend have been made as per planned work under MDAnalysis' CZI EOSS4 grant. Further details about these will be provided in a future blog post.
MDAnalysis.lib.distances
now accepts AtomGroups
as well as NumPy arrays (PR #3730).In line with NEP29, this version of MDAnalysis drops support for Python 3.7 and raises the minimum NumPy version to 1.19.0. Minimum version support has also been changed for the following packages; networkx>=2.0
, scipy>=1.5.0
, gsd>=1.9.3
. Further details on MDAnalysis future support strategy and NEP29 will be released shortly.
Supported python versions:
See the CHANGELOG and our release blog post for more changes and details.
frames
argument was added to AnalysisBase-derived classes (i.e. modern analysis classes) allowing for specific frames to be defined when running an analysis. (PR #3415)center_of_charge
attribute for AtomGroups (PR #3671)copy
method of Readers did not preserve optional arguments (Issue #3664, PR #3685)subst_id
, subst_name
and charge
) not to be provided (Issue #3385, PR #3598)atom.GetMonomerInfor().GetName()
now follows the guidelines for PDB filesNoImplicit=False
no longer throws a SanitizationError
smarts_kwargs
can now also be passed
to override this behaviour (Issue #3469, PR #3470)fasteners
package is now a core dependency (PR #3375)pos
is now mass_density
char
is now charge_density
std
entries are now stddev