ReleaseNotes074

Oliver Beckstein edited this page Sep 26, 2015 · 4 revisions

The 0.7.4 release of MDAnalysis has considerably shrunk in size: Instead of a 20 MB tar file it is now about 1 MB because all the trajectories and files for testing have been moved into a separate package, MDAnalysisTestData (file MDAnalysisTestData-0.7.4.tar.gz), which is to be installed separately. For more details see Issue 28 and MDAnalysisTestData.

Changes

0.7.4 release

Enhancements

  • Universe() got new keywords topology_format and format to allow the user to specify the file formats instead of deriving it from the extensions (does not work with "chained" files at the moment); thanks to Michael Lerner for the suggestion
  • Chain trajectory reader allows frame indexing.
  • Issue 75: additional donors and acceptors keywords for H-bond analysis
  • structural alignment functions alignto() and rms_fit_traj() can also take a list of selection strings in order to define atom groups with fixed atom order and alignto() preserves the order of supplied AtomGroups for the special select values "all" and None.
  • new set_* methods for AtomGroup allows changing of Atom attributes for all members of the group (such as the segid) (EXPERIMENTAL)
  • new Atom and Residue attribute resnum that can be used to store the canonical PDB residue number (EXPERIMENTAL)

Fixes

  • fixed Issue 74 (bug in AMBER topology parser which would show up for certain numbers of input lines; thanks to htaoyu1)
  • fix for Issue 48 (sparse contact_matrix in distances.py was slow as written in pure Python; was optimized in C code using scipy.weave)
  • HydrogenBondingAnalysis: donor atom name CO --> O (proper backbone oxygen) and acceptor NH -> N; without the fix one misses most of the backbone H-bonds
  • alignto() and rms_fit_traj(): order of mobile and reference selection was reversed when supplied as a tuple (sel1, sel2)

Changes

  • replaced analysis.util.progress_meter() with class core.log.ProgressMeter
  • Issue 28: split off test data trajectories and structures from MDAnalysis/tests/data into separate package MDAnalysisTestData, which is required to run the UnitTests from release 0.7.4 onwards. Numbering matches the earliest MDAnalysis release for which the data is needed. Any later releases of MDAnalysis will also use these test data unless a MDAnalysisTestData package with a higher release number is available

Authors

orbeckst, dcaplan, jandom

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Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
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