ReleaseNotes076

Tyler Reddy edited this page May 5, 2015 · 2 revisions

CHANGELOG

Enhancements

  • GRO file velocities may be accessed as AtomGroup.velocities() or Atom.velocity (Issue 102)
  • PrimitivePDBReader can be sliced
  • AMBER NetCDF (binary trajectory) reader and writer, supporting coordinates and velocities; requires netcdf4-python (Issue 109)
  • additional attributes and methods for AtomGroup to consolidate the interface to the Timestep: attribute 'positions' and 'get_positions()' can be used instead of the 'coordinates()' method. get/set methods for both positions and velocities.
  • almost all Readers now support some form of slicing; unsupported slicing operations will raise a TypeError
  • additional analysis for Nucleic Acid order parameters (MDAnalysis.analysis.nuclinfo)
  • AMBER TOPParser now able to do both amber10 and amber12 formats (Issue 100)

Changes

  • HydrogenBondAnalysis: multiple enhancements and changes (Issue 103)
    • many new analysis functions (see docs)
    • run() does not return the results anymore; results are simply stored as attribute timeseries (similar to other analysis tools)
    • only write per-frame debugging messages to the logfile when the new verbose keyword is set to True
    • more reliable detection of hydrogens bonded to heavy atoms
    • remove duplicate hydrogen bonds from the output
  • removed CHO and EAM (formyl and ethanol termini of gA in CHARMM) from the set of residues recognized as protein (collision with commonly used CHO for cholesterol)
  • PrimitivePDBWriter: special segid SYSTEM is translated to empty chainID
  • In order to write multi frame PDB files, the multiframe=True keyword must be supplied or use the MultiPDBWriter
  • empty AtomGroup can be constructed or can result from a selection without matches; it does not raise NoDataError anymore (Issue 12)
  • all single frame readers denote the first (and only) frame as frame number 1 (i.e. ts.frame == 1); it used to be 0 but 1 is consistent with the way this is is handled with real trajectories
  • requires Biopython >= 1.51 (fixes for Issue 112 and Issue 113)
  • Atom.type is always stored as a string.

Fixes

  • HydrogenBondAnalysis: NH1 and NH2 were not recognized
  • GROWriter: enforce maximum resname and atomname length of 5 chars
  • Universe.load_new() raised a NameError (thanks to JiyongPark.77)
  • fixed Issue 105 (trajectory snapshots could not be written to PDB)
  • fixed Issue 107 (NAMD/VMD space delimited PSF files can be autodetected and read); important when using CGENFF atom types (thanks to JiyongPark.77 for initial patch)
  • fixed Issue 101 (could not write single frame to trr file)
  • fixed: permissive=True flag was ignored in Universe and hence the PrimitivePDBReader was always selected even if the Biopython one was desired
  • fixed Issue 112 (used removed Biopython constructs in MDAnalysis.analysis.align.fasta2select; thanks to francesco.oteri for a test case and fix)
  • fixed failing 'type' selection for topology formats that read an atom type as an integer (such as the AMBER parser)
  • fixed Issue 111 (NAN in pycpqrot and RMSD calculation)
  • fixed Issue 113 (replaced outdated Biopython to call ClustalW)

Authors

orbeckst, joshua.adelman, andy.somogyi, tyler.je.reddy, lukas.grossar, denniej0

Project Information

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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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