MDAnalysis is a Python library to analyze molecular dynamics simulations.
In line with ongoing attempts to align with NEP29, this version of MDAnalysis drops support for Python 3.6 and raises the minimum NumPy version to 1.18.0.
Please note that at time of release whilst all the MDAnalysis core functionality supports Python 3.10, some optional modules do not due to a lack of support by dependencies which they require. We hope that this support will gradually be added as more of these dependencies release new versions compatible with Python 3.10.
Supported python versions:
See the CHANGELOG and our release blog post for more changes and details.
minimize_vectors
, has been introduced (PR #3472)add_Segment
or add_Residue
(Issue #3437).packaging
is now a core dependency of MDAnalysis.None
now raises a TypeError
. Prior to this indexing by None
would incorrectly return the whole Group but claim to have a length of 1 atom (Issue #3092).dt
value of 1.0 ps instead of the previous 0.0 ps (Issue #3257).pbc
keyword argument for various Group methods has been deprecated in favor of wrap
. The deprecated keyword will be removed in version 3.0.0 (Issue #1760).pytest-xdist
and more than 4 workers
This is the first version of MDAnalysis to solely support python 3.6+
Supported python versions:
Please note that starting with the next minor version, MDAnalysis will be following NEP29.
Results
class for storing analysis results (Issue #3115)intra_bonds
,intra_angles
, intra_dihedrals
, etc... methods to return connections involve atoms within AtomGroups instead of including atoms outside of it (Issue #1264, #2821, PR #3200)analysis.helix_analysis
(Issue #2452)from_smiles
Universe generator method, and the aromatic and smarts selection.pickled
paving the way to easier parallel analyses (Issue #2723)select_atom
, AtomGroup.unique, ResidueGroup.unique, and SegmentGroup.unique did not sort the output atoms (Issues #3364 #2977)density
keyword for rdf.InterRDF_s
(Isuse #2811)hbonds.hbond_analysis
has been remove din favour of hydrogenbonds.hbond_analysis
(Issues #2739, #2746)tpr_resid_from_one=True
by deafult, which starts TPR resid indexing from 1 (instead of 0 as in previous MDAnalysis versions) (Issue #2364, PR #3152)analysis.hole
has now been removed in favour of analysis.hole2.hole
(Issue #2739)Writer.write(Timestep)
and Writer.write_next_timestep
have been removed. Please use write()
instead (Issue #2739)waterdynamics.HydrogenBondLifetimes
(PR #2842)hbonds.WaterBridgeAnalysis
has been moved to hydrogenbonds.WaterBridgeAnalysis
(Issue #2739 PR #2913)bfactors
attribute is now aliased to tempfactors
and will be removed in 3.0.0 (Issue #1901)WaterBridgeAnalysis.generate_table()
now returns table information, with the table
attribute being deprecatedResults
will be deprecated in 3.0.0 (Issue #3261)MDAnalysis.converters
moduleSee the CHANGELOG for more changes and details.
MDAnalysisTests.lib.test_augment
tests. To our knowledge this does not significantly affect results (as all other tests pass). We will aim to fix this in version 2.1.0.Python support is kept the same as 1.0.0, with python 3.9 not supported.
Supported python versions:
Please note that python 2.7 and 3.5 support will be dropped in the upcoming 2.0.0 release.
Bug fixes
Deprecations:
scale_factor
writing behaviour will change in 2.x (Issue #2327)tempfactors
and bfactors
will stop being separate (Issue #1901)MDAnalysis.analysis.hbonds.WaterBridgeAnalysis
will be moved to MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis
in 2.x (PR #3111)tpr_resid_from_one
keyword has been added to modify this behaviour (Issue #2364)Enhancements:
get_connections
method has been added to more easily get bonds, angles, dihedrals, etc.. for a group (Issues #1264 #2821)See the CHANGELOG for more changes and details.
MDAnalysisTests.lib.test_augment
tests. To our knowledge this does not significantly affect results (as all other tests pass). We will aim to fix this in version 2.0.os.path
). As far as we know they do not affect the validity of the code. The following tests are affected:
MDAnalysisTests.analysis.test_base::test_analysis_class_decorator
MDAnalysisTests.analysis.test_dihedrals::TestRamachandran::test_protein_ends
MDAnalysisTests.analysis.test_helanal::test_warnings
MDAnalysisTests.coordinates.test_chainreader::TestChainReaderContinuous::test_easy_trigger_warning
MDAnalysisTests.utils.test_streamio::TestNamedStream_filename_behaviour::test_func[abspath]
Python support is kept the same as 1.0.0, with python 3.9 not supported. Supported python versions:
Bug fixes
capped_distance
code due to a bug affecting accuracy (#2930)n_atoms
(#2817)rdf.InterRDF_s
is now documented and has been fixed to give correct results (#2811)Deprecations:
waterdynamics.HydrogenBondLifetimes
will be replaced with hydrogenbonds.HydrogenBondAnalysis.lifetime
in 2.0.0 (#2547)analysis.helanal
will be removed in 2.0.0 and will be replaced with analysis.helix_analysis
(#2622)lib.util.echo
and core.universe.as_Universe
will be removed in 2.0.0.analysis.leaflets.LeafletFinder
will no longer accept non-Universe inputs as of version 2.0.0.Performance improvements:
select_atoms
(#2751)See the CHANGELOG for more changes and details.
setup.py
. We aim to fix this for the upcoming 1.0.2 release (#3129)As detailed in the 1.0.0 release, the 1.x releases only include bug fix changes. New features are being developed for MDAnalysis 2.x.
First major stable release of MDAnalysis. The API will be stable for all 1.x releases.
See the CHANGELOG for details.
Note that 1.x will not be further developped, with only occasional bug fixes being backported as described in the Roadmap.
The main development is geared towards MDAnalysis 2.x, which will only support Python 3.x and remove any code that was deprecated in 1.0.
Major enhancements and fixes.
See CHANGELOG for details.
(Note: 0.20.1 fixed an installation issue with 0.20.0 so there's no published 0.20.0 release.)
Added full support for Windows platform.
See CHANGELOG for details.