ReleaseNotes073

Changes

• 0.7.3 release

Removals

• completely removed the old core.rms_fitting module (and thus we also do not depend on the LAPACK library anymore, which should simplify installation); use the functions accessible through MDAnalysis.analysis.align (which are faster and use QCPROT)

Enhancements

• PDBQT (AutoDOCK) format added (reading and writing of single frames)
• new attributes universe.trajectory.frame and universe.trajectory.time: report the current frame number and time (e.g. in ps) of the current frame of the trajectory
• new attribute Timestep.volume (unit cell volume)
• HELANAL helix analysis in MDAnalysis.analysis.helanal; Python implementation of helanal.f from http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html (Benjamin Hall, used under GPL v2+)
• hydrogen bonds analysis in MDAnalysis.analysis.hbonds
• MDAnalysis.analysis.distances.dist() for calculating distances between matching atoms in two groups
• MDAnalysis logo by Christian Beckstein from the LogoCompetition (and reformatting of the online docs to match the logo theme)

Change of behaviour

• alignto() and rms_fit_trj(): changed keyword 'select' default from 'backbone' to 'all'

Fixes

• fixed alignto() (raised KeyError)
• fixed Issue 57 (check for illegal coordinates when writing PDB and GRO)
• use spaces everywhere and no TABs and tell emacs and vim to keep it that way (Issue 69)
• fixed Issue 70 (problems with instant atom selections)

Authors

orbeckst, jandom, Benjamin Hall, Paul Rigor, dcaplan, Christian Beckstein (logo), denniej0