./wip/py-mdanalysis, Library to analyze and manipulate molecular dynamics trajectories

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Branch: CURRENT, Version: 0.15.0, Package name: py39-mdanalysis-0.15.0, Maintainer: jihbed.research

MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics
trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber.

It allows one to read molecular dynamics trajectories and access the atomic
coordinates through numpy arrays. This provides a flexible and relatively fast
framework for complex analysis tasks. In addition, CHARMM-style atom selection
commands are implemented. Trajectories can also be manipulated (for instance,
fit to a reference structure) and written out.


Required to run:
[devel/py-setuptools] [wip/biopython] [math/py-networkx] [math/py-numpy] [lang/py-six] [lang/python37]

Required to build:
[devel/py-nose] [pkgtools/cwrappers]

Master sites:

RMD160: b06d6ef3d2ab33cb94b8a074be2e1e9c0b43af3e
Filesize: 2186.122 KB

Version history: (Expand)


CVS history: (Expand)


   2014-05-09 09:38:42 by Thomas Klausner | Files touched by this commit (229)
Log message:
Mark packages that are not ready for python-3.3 also not ready for 3.4,
until proven otherwise.
   2014-01-26 16:49:50 by Thomas Klausner | Files touched by this commit (121)
Log message:
Mark packages as not python-3.x ready where appropriate.
   2014-01-03 22:28:42 by Kamel Derouiche | Files touched by this commit (3) | Package updated
Log message:

	Update new version
	------------------------------------------------------------------------------
??/??/13  orbeckst, jandom, zhuyi.xue, xdeupi, tyler.je.reddy,
          manuel.nuno.melo, danny.parton, sebastien.buchoux, denniej0,
	  rmcgibbo, richardjgowers, lennardvanderfeltz, alejandro.bernardin

  * 0.8.0

  Enhancements

  * Merge AtomGroups into a new Universe (Issue 157)
  * TPR parser (currently limited to versions 58, 73 and 83 of the
    Gromacs TPR format (Gromacs 4.0 to 4.6.1), see Issue 2)
  * fast XTC seeking (Issue 127)
  * changing resid (set_resid()) or segid (set_segid()) changes the
    topology and lists of resids/segids can be assigned to 
    groups of objects (AtomGroup, ResidueGroup)
  * helanal: additional output of local bend and unit twist angles
    (Issue 133)
  * added support for reading DMS files (DESRES molecular structure)
  * bond connectivity information can be guessed from a PDB file if
    the bond=True keyword is set in Universe (Issue 23)
  * MDAnalysis.analysis.rms.RMSD: calculation of additional RMSDs
  * Plugin to generate nucleic acid helicoidal parameters using X3DNA;
    (must install working version 2.1 of X3DNA independently)
  * can use advanced slicing (with arbitrary lists or arrays) at all
    levels of the hierarchy (Issue 148)
  * coordinate readers and writers can be used as context managers
    with the 'with' statement
  * Can load multiple trajectories as Universe(topology, traj2, traj2,
    ...) in addition to providing all trajectories as a list,
    i.e. Universe(topology, [traj1, traj2, ...])
  * added support for YASP and IBIsCO formats (.trz) (Issue 152)
  * new methods for AtomGroup: packintobox() (only orthorhombic boxes)
  * added non-standard "extended" PDB format (XPDB) that reads
    five-digit residue numbers
  * util.convert_aa_code() recognizes non-standard residue names such
    as HSE, GLUH, GLH, ...
  * added new geometrics selections: sphlayer, sphzone, cylayer, cyzone
  * added TopologyDict and TopologyGroup classes for bond analysis

  Changes

  * dropped support for Python 2.5; minimum requirement is Python 2.6
    (Issue 130)
  * almost all methods of AtomGroup return NumPy arrays
  * slicing and indexing of AtomGroup, Residue, ResidueGroup, Segment,
    SegmentGroup will now always return an appropriate object and
    never a simple list
  * removed Timeseries.principleAxis (probably was never working)
  * dependent on Biopython >= 1.59 (Issue 147)
  * Hydrogen bond analysis defaults to updating selection 1 and 2 for
    every timestep in order to avoid unexpected behavior (Issue 138)

  Fixes

  * fixed incorrect computation of distances in serial and parallel 
    distance_array() with PBC (Issue 151)
  * fixed Issue 129 (hole.py module pipe/file closure)
  * fixed array comparison bug in MDAnalysis.analysis.helanal
    and various enhancements to the helanal module
  * fixed MDAnalysis.analysis.rms.RMSD.run(): gave incorrect results
    if ref_frame != 0
  * alignto() now checks that the two selections describe the same
    atoms (fixes Issue 143)
  * slicing of ResidueGroup will now produce a ResidueGroup, and
    slicing of a SegmentGroup will produce a SegmentGroup, not a list
    as before (fixes Issue 135)
  * detect OpenMP-capable compiler during setup (Issue 145), which should allow
    users of Mac OS X 10.7 and 10.8 to build MDAnalysis using Apple's
    C-compiler (clang) (Issue 142) although they will not get a parallel
    version of distance_array.
  * PDB with blank lines gave IndexError (Issue 158)
 

12/24/12 danny.parton, jandom, orbeckst, jjlights03, jphillips, \ 
naveen.michaudagrawal, andy.somogyi, sebastien.buchoux

  * 0.7.7

  Enhancements

  * multithreaded distance_array() (Issue 80, experimental); see the 
    new core.parallel.distance module
  * MDAnalysis.analysis.rms for simple RMSD analysis
  * format of input coordinates can be set as (filename, format)
    tuples (Issue 76) 
  * new AtomGroup.asphericity() and AtomGroup.shapeParameter()   
    methods to compute shape descriptors.
  * access to forces (AtomGroup.forces with get_forces() and set_forces();
    the default unit for force is kJ/(mol*A) and it is automatically 
    converted from/to native). Currently, only the TRR Reader/Writer
    support forces.
  * all element masses
  * logger reports current version when starting

  Fixes

  * fixed Issue 115 (GROReader now uses fixed-column width format to read GRO files)
  * fixed Issue 116 (Failed to write AMBER netcdf trajectory from AtomGroup)
  * fixed Issue 117 (could not write Gromacs XTC/TRR from AMBER netcdf)
  * fixed Issue 120 (DCDWriter: wrote wrong unitcell information)
  * fixed Issue 121 (PSFParser would fail with IndexError for files without SEGID)
  * Issue 122 (made installation of netCDF4 library optional, which
    means that users of the AMBER netcdf Reader/Writer will have to
    manually install the library and its dependencies netcdf and HDF5, 
    see https://code.google.com/p/mdanalysis/wiki/netcdf)

06/30/12 orbeckst, joshua.adelman, andy.somogyi, tyler.je.reddy, lukas.grossar, \ 
denniej0, danny.parton

  * 0.7.6 

  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

  * selectAtoms: updated *nucleic* and *nucleicxstal* selection definition
    *nucleic* includes the two-letter NA code that follows gromacs topolgy
    format and *nucleicxstal* allows for the one-letter NA code that follows
    the PDB Database code.
  * 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)
   2013-12-02 10:59:25 by Kamel Derouiche | Files touched by this commit (3)
Log message:
UPGRADE Makefile

   2013-02-24 19:08:09 by Aleksej Saushev | Files touched by this commit (1)
Log message:
Don't accept python 3, biopython doesn't support it yet.
Fixes bulk build.
   2012-10-16 11:19:02 by Kamel Derouiche | Files touched by this commit (1)
Log message:
added dependency: wip/biopython

   2012-10-16 11:15:48 by Kamel Derouiche | Files touched by this commit (1)
Log message:
set PYTHON_VERSIONS_INCLUDE_3X=yes

   2012-10-07 14:25:12 by Aleksej Saushev | Files touched by this commit (52)
Log message:
Drop superfluous PKG_DESTDIR_SUPPORT, "user-destdir" is default these days.
Mark packages that don't or might probably not have staged installation.