MDAnalysis/mdanalysis release-2.0.0

MDAnalysis 2.0.0

on GitHub

Release 2.0.0 of MDAnalysis

This is the first version of MDAnalysis to solely support python 3.6+

Supported python versions:

• 3.6, 3.7, 3.8, 3.9

Please note that starting with the next minor version, MDAnalysis will be following NEP29.

Notes:

• This is a major release and introduces major advertised API breaks. Caution is advised when upgrading to 2.0.0.

Major changes:

Enhancements:

• LAMMPSDumpReader can now read coordinates in all different LAMMPS coordinate conventions (Issue #3358)
• New Results class for storing analysis results (Issue #3115)
• New OpenMM coordinate and topology converters (Issue #2863, PR #2917)
• New 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)
• Support for Groamcs 2021 TPR files (Issue #3180)
• Adds preliminary support for ppc64le and aarch64 [ARM] (Issue #3127, PR #2956 #3149)
• New selection operators (Issue #3054, PR #2927)
• New refactor of helix analysis class as analysis.helix_analysis (Issue #2452)
• New converter between RDKit molecules and MDAnalysis AtomGroup objects (Issue #2468). Also includes from_smiles Universe generator method, and the aromatic and smarts selection.
• New analysis method for calculating Mean Squared Dsiplacements (Issue #2438)
• New converter between Cartesian and Bond-Angle-Torsion coordinates (PR #2668)
• Universes and readers can now be pickled paving the way to easier parallel analyses (Issue #2723)
• New H5MDReader and H5MDWriter (Issue #762, #2866)

Fixes:

• Fixes an issue where select_atom, AtomGroup.unique, ResidueGroup.unique, and SegmentGroup.unique did not sort the output atoms (Issues #3364 #2977)
• GRO files now only support unit cells defined with 3 or 9 entries (Issue #3305)
• Fixes the sometimes wrong sorting of atoms into fragments when unwrapping (Issue #3352)
• Fixes issue when atttempting to use/pass mean positions to PCA analysis (Issue #2728)
• Fixes support for DL_POLY HISTORY files that contain cell information even if there are no periodic boundary conditions (Issue #3314)
• Fixes issue with WaterBridgeAnalysis double counting waters (Issue #3119)
• PDBWriter will use chainID instead of segID (Issue #3144)
• PDBParser and PDBWriter now assign and use the element attribute (Issues #3030 #2422)
• AtomGroup.center now works correctly for compounds + unwrapping (Issue #2984)
• Documents and fixes the density keyword for rdf.InterRDF_s (Isuse #2811)
• Fixed Janin analysis residue filtering, including CYSH (Issue #2898)

Changes:

• New converter API for all MDAnalysis converters under MDAnalysis.converters
• Timestep now stores information in 'C' memory layout instead of the previous 'F' default (PR #1738)
• hbonds.hbond_analysis has been remove din favour of hydrogenbonds.hbond_analysis (Issues #2739, #2746)
• TPRParser now loads TPR files with 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)
• Removes deprecated density_from_Universe, density_from_PDB, Bfactor2RMSF, and notwithin_coordinates_factory from MDAnalysis.analysis.density (Issue #2739)
• Changes the minimum numpy supported version to 1.16.0 (Issue #2827)
• Removes deprecated waterdynamics.HydrogenBondLifetimes (PR #2842)
• hbonds.WaterBridgeAnalysis has been moved to hydrogenbonds.WaterBridgeAnalysis (Issue #2739 PR #2913)

Deprecations:

• The 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 deprecated
• Various analysis result attributes which are now stored in Results will be deprecated in 3.0.0 (Issue #3261)
• In 3.0.0 the ParmEd classes will only be accessible from the MDAnalysis.converters module
• In 2.1.0 the TRZReader will default to a dt of 1.0 ps when failing to read it from the input TRZ trajectory

See the CHANGELOG for more changes and details.

Known issues:

• Windows builds
  • For some compilers (seen on MVC v.19xx), differences in floating point precision leads to PBC wrapping differing from expected outcomes. This leads to failures in the 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.