02 Sep 2023
We are happy to release version 2.6.1 of MDAnalysis!
(This blog post describes 2.6.1 and the initial release in the 2.6 series, 2.6.0.)
This is a minor update to the MDAnalysis library.
This release of MDAnalysis is packaged under a GPLv3+ license.
Additionally all contributions made from commit 44733fc
onwards are made under the LGPLv2.1+ license. More details about these license changes
will be provided in an upcoming blog post.
In line with NEP 29, the minimum required NumPy version has
been raised to 1.22.3.
Supported Python versions: 3.9, 3.10, 3.11
Supported Operating Systems:
Upgrading to MDAnalysis version 2.6.1
To update with conda from the conda-forge channel run
conda update -c conda-forge mdanalysis
To update from PyPi with pip run
python -m pip install --upgrade MDAnalysis
For more help with installation see the installation instructions in the User Guide. Make sure you are using a Python version compatible with MDAnalysis before upgrading (Python >= 3.9).
Notable changes
For a full list of changes, bugfixes and deprecations see the CHANGELOG.
Fixes:
- Fix to element guessing code to more accurately interpret atom names split by
numbers (i.e. N0A is now recognised as N rather than NA) [Issue #4167, PR #4168]
- The -ffast-math compiler flag is no longer used by default at build time,
avoiding inconsistent (although still scientifically correct) results seen
in Intel MacOS systems when calling
AtomGroup.center_of_charge(..., unwrap=True).
This also avoids potentially incorrect floating point results. (PR #4220)
- DATAWriter, CRD, PQR, and PDBQT files can now be correctly written to
compressed files. Before this change, any attempt to write to a compressed
format (gzip or bzip2) would lead to writing out an uncompressed file. (PR #4163)
- Prevent accidental merging of bond/angle/dihedral types when they are
defined as LAMMPS style string integers instead of tuples. This was leading
to an incorrect number of bond/angle/dihedral types being written to lammps
data files. (PR #4003)
Enhancements:
- An
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. (PR #4161)
- LAMMPS reader now supports the
continuous ChainReader option. (PR #4170)
- AtomGroup representation now returns atom indices in the same order
as they are stored in the AtomGroup. (PR #4191)
Changes:
- As per NEP29, the minimum supported runtime version of NumPy has
been increased to 1.22.3. (PR #4160)
- The GSD package is now an optional dependency. (PR #4174)
- The MDAnalysis package now only supports GSD versions 3.0.1 or
above. (PR #4153)
- MDAnalysis no longer officially supports 32 bit installations,
(they are no longer tested in our continuous integration pipelines).
Note: 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. (PR #4176)
- The package license has been updated to GPLv3+
to better reflect the compatibility of GPLv2+ with Apache and GPLv3 licensed
codes. Additionally all new contributions from commit 44733fc
onwards are made under the LGPLv2.1+ license. (PR #4219)
Deprecations:
- The misspelt
Boltzman_constant entry in MDAnalysis.units is now
deprecated in favour the correctly spelt Boltzmann_constant. (PRs #4230 and #4214)
-
MDAnalysis.analysis.hole2 is now deprecated in favour of a new
HOLE2 MDAKit. (PR #4200)
Author statistics
This release was the work of 10 contributors, 4 of which are new contributors.
Our new contributors are:
@MohitKumar020291
@Shubx10
@ztimol
@pillose
Acknowledgements
MDAnalysis thanks NumFOCUS for its continued support as our fiscal sponsor and the Chan Zuckerberg Initiative for supporting MDAnalysis under EOSS4 and EOSS5 awards.
— The MDAnalysis Team
17 Aug 2023
MDAnalysis is excited to to have participated this year as a host organization for the Station1 Frontiers Fellowship program for the first time. We thank Station1 for supporting two outstanding students, John Ong and Karen Bekhazi, who have been working with us to understand the evolution of heterogeneity between objects in the Protein Data Bank (PDB) PDBx/mmCIF file format. John and Karen’s research will help inform MDAnalysis’s planned extension of interoperability between MDAnalysis and the PDBx/mmCIF format. Keep reading to learn more about John and Karen’s experience, and download their capstone poster here.
John Ong
Hello everyone, my name is John Ong, and I was one of the Station1 interns working with MDAnalysis this summer. I am a soon-to-be third-year undergraduate student at the University of Utah studying mathematics and computer science.
MDAnalysis is used widely in the biomolecular sciences and thus is important in research that ultimately aims at improving human health. The PDB is an international repository for experimentally-determined 3D structures of biomolecules, such as proteins and nucleic acids. However, data representation techniques for structures on the PDB often differ, despite the same master format (PDBx/mmCIF). Hence, there exists “dialects” within the PDB’s files.
This summer, Karen and I explored the reasons for the existence of these dialects. Through literature reviews and interviews we’ve carried out with both key members within the PDB and PDB user(s), we’ve found experimental methods, knowledge of proteins, data processing methods, and user error to be the most common contributors to these dialects. We also studied the motivations for format changes and regulations (and the lack thereof) within the PDB and its user base.
All in all, this was a rewarding summer. While we did not achieve as many technical results as we would have liked, studying change has been interesting. I’m honored to have been a mentee of @richardjgowers and @hmacdope, and to have had the support of MDAnalysis and its community this summer.
You can find me on GitHub, LinkedIn and my website!
I hope to be able to continue contributing to this incredible community!
Karen Bekhazi
Molecular dynamics simulations are capable of generating new trajectory analyses in their own specific output format. This consequently challenges the tools’ further development and widespread use since they are limited to specific formats that can’t be accessed by all users. This summer, our work has mostly focused on the effects of the lack of a standardized format on molecular dynamics’ scientific and social impact. We evaluated the creation of different PDB file formats by drawing parallels between them and notions in the field of linguistics, such as dialects and stemmatics. Our research was also supported by further study of both the PDB and MDAnalysis’s stakeholders.
I am a rising junior at Smith College. I am studying Engineering Sciences and Chemistry, with an interest in biochemistry, biomaterials, and the intersection of biophysics and chemistry. Originally from Beirut, Lebanon, I enjoy running, reading, and watching movie commentaries in my free time.
Here are my LinkedIn and GitHub profiles.
Thank you to the amazing MDAnalysis community and to our mentors, @richardjgowers and @hmacdope, for this summer!
11 Aug 2023
MDAnalysis is excited to be kicking off a series of free online training workshops in Fall 2023. The first will be held on October 25, 2023 from 15:00-18:30 UTC.
This online workshop will consist of an introduction to the MDAnalysis Python library, as well as an opportunity for hands-on learning through basic MDAnalysis tutorials. The workshop will be delivered to a small group to allow interactive discussions, questions, and participant engagement. It is designed for beginners to MDAnalysis who already have a working knowledge of Python and know how use shell and notebook environments.
Register soon (places limited)
If you are interested in participating in this workshop, fill out this short application form before September 30, 2023. Selected participants will be notified in early October.
We have a small number of bursaries to enable participation for researchers from underrepresented groups who are facing financial barriers; these can be applied for when completing the application form.
We are looking into organizing the next workshop for Australasian time zones, so also keep an eye out for announcements of future workshops!
— The MDAnalysis Team