Changelog for python-MDAnalysis-0.15.0-1.4.x86_64.rpm :
Thu Nov 17 13:00:00 2016 alinm.elenaAATTgmail.com
- updated to version 0.15.0

* 0.15.0
Metadata

* link download_url to GitHub releases so that Depsy recognizes
contributors (issue #749)

* a __version__ variable is now exposed; it is built by setup.py from the
AUTHORS file (Issue #784)
API Changes

* rmsd doesn\'t superimpose by default anymore. The superposition
is controlled by the \'superposition\' keyword now. (see issue #562, #822)
Enhancements

* Add conda build scripts (Issue #608)

* Added read-only property giving Universe init kwargs (Issue #292)

* Added \'crdbox\' as AMBER Trj format extension (Issue #846)

* Iteration and seeking in PDB files made faster (Issue #848)
Fixes

* ENT file format added to PDB Readers/Writers/Parsers (Issue #834)

* rmsd now returns proper value when given array of weights (Issue #814)

* change_release now finds number and dev (Issue #776)

* units.py now correctly prints errors for unknown units.

* test_shear_from_matrix doesn\'t fail for MKL builds anymore (Issue #757)

* HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)

* MOL2 files without substructure section can now be read (Issue #816)

* MOL2 files can be written without substructure section (Issue #816)

* GRO files with an incomplete set of velocities can now be read (Issue #820)

* Fixed Atom.position/velocity/force returning a view onto Timestep array
(Issue #755)

* PDB files can now read a CRYST entry if it happens before model headers
(Issue #849)

* Fixed HistoryReader returning 1 based frame indices (Issue #851)
Changes

* Added zero_based indices for HBondsAnalysis. (Issue #807)

* Generalized contact analysis class `Contacts` added. (Issue #702)

* Removed Bio.PDBParser and sloppy structure builder and all of
MDAnalysis.coordinates.pdb (Issue #777)

* PDB parsers/readers/writers replaced by \"permissive\"/\"primitive\"
counterparts (formerly known as PrimitivePDBReader); the
\'permissive\' keyword for Universe is now ignored and only the
native MDAnalysis PDBReader is being used (Issue #777)

* PDBReader only opens a single file handle in its lifetime,
previously opened & closed handle each frame (Issue #850)
Deprecations (Issue #599)

* Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
Writer/Parser (Issue #777)

* Deprecated all `get_
*` and `set_
*` methods of Groups.

* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.

* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).

* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).

* Deprecated Atom number, pos, centroid, universe setter

* Deprecated AtomGroup serials, write_selection

* Deprecated Residue name, id

* Deprecated Segment id, name

* Deprecated as_Universe function; not needed

* Deprecated ContactAnalysis and ContactAnalysis1 classes
02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy

* 0.14.0
API Changes

* Offsets files for Gromacs trajectory formats have been changed to a numpy
style format \'.npz\'. Offsets files will be regenerated when you load a
xtc/trr trajectory again. (Issue #441)

* rotation_matrix now accepts array-likes as input
Enhancement

* XDR file seeking errors now report system errno. (PR #678)

* Offsets reading for xtc/trr files has been sped up. (Issue #441)

* select_atoms now implicitly ORs multiple values after a keyword for
many types of selections (Issue #345)

* Performance improvements for the PDBReader of about 10%

* LinearDensity analysis module added, which allows to compute linear mass
and charge density profiles along the three cartesian axes of the cell.
Works for orthorombic, fixed volume cells only. (Issue #670)

* Trajectories can now be sliced using a boolean array (Issue #725)
Changes

* xdrlib was rebranded libmdaxdr. (Issue #679)

* xdrlib has been ported to cython. (Issue #441)

* util.NamedStream no longer inherits from basestring (Issue #649)

* Short TRZ titles are striped from trailing spaces. A friendlier error
message is raised when the TRZ writer is asked to write a title longer
than 80 characters. (Issue #689)

* PDB doesn\'t save charge information anymore

* coordinates.core.get_writer_for uses the user defined format if provided
before trying to deduce the format from file extension. (Issue #712)
Fixes

* Syntax error corrected in psa.py (Issue #738)

* XDR file seeking and telling working again for large files (Issue #677).

* ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)

* Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)

* The \'atom\' selection keyword returns an empty selection rather than an
error when no atoms are are found. (Issue #644)

* nucleic selection will now detect nucleic residue names suffixed with 3 or 5
(Issue #461)

* Fixed Reader returning all frames with stop in slice was 0 (Issue #672)

* Fixed NCDFReader not reading dt (Issue #676)

* Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)

* Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)

* Fixed cyzone selection failing in orthogonal systems (Issue #710)

* Fixed Error in calculation of average grid density (Issue #716)

* Fixed indexing an AtomGroup using a list of bools now working (Issue #729)
01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,
orbeckst, Balasubra

* 0.13.0
API Changes

* ChainReader `delta` keyword deprecated in favor of `dt`. (Issue #522)

* XYZWriter can now be used as a container format for different protein models
as well as a normal trajectory. If `n_atoms` is None (default) MDAnalysis
assumes that it is used as a container and won\'t give a warning if the
number of atoms differs between frames.

* GROWriter.fmt strings updated to use format style (Issue #494)

* removed MDAnalysis.lib.parallel.distances; use the new backend=\"OpenMP\"
keyword for the functions in MDAnalysis.lib.distances (Issue #530)
Enhancement

* ChainReader now reports times properly summed over sub-readers (Issue #522)

* GRO file reading approximately 50% faster for large files (Issue #212)

* GRO file writing now will write velocities where possible (Issue #494)

* Added bonded selection (Issue #362)

* Spherical layer and spherical zone selections now much faster (Issue #362)

* new keyword \"backend\" for accelerated functions in MDAnalysis.lib.distances
to select \"serial\" or \"OpenMP\"-enabled versions of the code; the default
is \"serial\" so old code will behave as before (see Issue #530)

* Lammps data file parsing improved greatly. Should now support all files,
and triclinic geometry. (Issue #139)

* Added analysis.polymer, currently with PersistenceLength tool (Issue #460)

* Added analysis.rdf, with InterRDF tool. (Issue #460)

* Made Reader.check_slice_indices a public method (Issue #604)

* analysis.helanal.helanal_main() now returns results as dict

* Added keyword to update selection every frame in density calculation (Issue #584)

* New keywords start, stop, step for density.density_from_Universe()
to slice a trajectory.

* MOL2Reader now reads molecule and substructure into ts.data

* All subclasses of ProtoReader, Writer and TopologyReader are automatically
added to the MDAnalysis directory of I/O (Issue #431)
Changes

* built html doc files are no longer version controlled (Issue #491)

* The lib._distances and lib_distances_openmp libraries now have a
OPENMP_ENABLED boolean flag which indicates if openmp was used in
compilation. (Issue #530)

* analysis.helanal.helanal_trajectory() and helanal_main() now use a
logger at level INFO to output all their computed values instead
of printing to stdout

* default offset for ProgressMeter was changed from 0 to 1 (to match
the change from 1- to 0-based ts.frame counting)

* removed superfluous analysis.density.density_from_trajectory();
use density_from_Universe(TOPOL, TRAJ) instead.

* MOL2Writer.write now only writes a single frame (Issue #521)
Fixes

* Fixed select_atoms requiring a trajectory be loaded (Issue #270)

* AtomGroup timesteps no longer cached (Issue #606)

* GROWriter now truncates atom numbers over 99999 (Issue #550)

* AMBER netcdf writer now correctly uses float32 precision (Issue #518)

* Fixed a numpy incompatibility in `analysis.leaflet.LeafletFinder`.
(Issue #533)

* Cleaned up `MDAnalysis.Writer` docs regarding `dt` usage. (Issue #522)

* Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)

* Fixed unpickling errors due to lingering dead universes. (Issue #487)

* Fixed analysis.density modules requiring the defunct `skip` attribute
on trajectories. (Issue #489)

* ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)

* ten2eleven will now convert numatoms to n_atoms argument
for writer() functions (Issue #470)

* Fixed non-compliant Amber NCDFWriter (Issue #488)

* Fixed many Timestep methods failing when positions weren\'t present
(Issue #512)

* Fixed PointSelection using KDTree (Issue #362)

* Fixed GROParser getting tripped up by some file (Issue #548)

* Fixed writing dx files from analysis.density.density_from_Universe()
(Issue #544 and #410)

* Fixed base.Reader._check_slice_indices not liking numpy ints
(Issue #604)

* Fixed broken analysis.helanal.helanal_trajectory() and
helanal_main()

* Fixed lib.util.greedy_splitext() (now returns full path)

* Fixed MOL2Reader not reading molecule and substructure on init
(Issue #521)

* Fixed MOL2Writer rereading frames when writing them (Issue #521)

* Fixed PDBWriter not writing occupancies from atoms (Issue #620)
10/08/15

* 0.12.1 kain88-de, orbeckst, richardjgowers
API Changes
Enhancements
Changes
Fixes

* Fixed OpenMP detection on Linux/OSX #459

* Fixed reading of LAMMPS trajectory times: default unit ought
to be fs and not ps

* Fixed setting of dt for DCDReader (and LAMMPS DCDReader) with
keyword argument Universe(..., dt=

)

* Fixed a bug in topology.core.guess_atom_element where a
single digit atom name would raise an IndexError (#476)

* Fixed numpy -> np in LeafletFinder
10/04/15 kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud

* 0.12.0
API Changes

* PrimitivePDBReader now imports occupancies into the `TimeStep` object.
(Issue #396)

* Atoms without a Universe now return NoDataError instead of
AttributeError

* AtomGroups of zero length or containing Atoms with no Universe raise
a NoDataError when trying to access Universe

* Atoms now keep a strong reference to Universe, meaning they
do not become orphaned when the Universe goes out of scope (Issue #297)
Enhancements

* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)

* XYZReader now supports frame indexing (Issue #428)

* Reader objects can now be sliced using lists and arrays of indices
(Issue #437)

* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor plotting method (Issue #438)

* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis (Issue #438)

* `PSAnalysis` can now generate annotated heat maps (Issue #438)

* Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)

* Additional getters added to `Path` and `PSAnalysis` (Issue #438)

* MSD matrix function now globally available in MDAnalysis.analysis.psa
(Issue #438)

* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa (Issue #438)

* TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)

* Setup.py now looks for some configuration values in a config file. Each
config option can also be changed via environment variables if they are
prefixed with \'MDA_\'. Current options are \'use_cython\', \'ues_openmp\', \'debug_cflags\'
Changes

* An AtomGroup with 0 atoms now yields an `IndexError` on call to
`AtomGroup.write` (Issue #434)

* `PSA` changed to `PSAnalysis` to reduce namespace clutter (Issue #438)

* To build with debug-symbols use \'MDA_DEBUG_CFLAGS\' instead of \'MDA_DEBUG_CFLAGS\'
Fixes

* Fixed minor issue in lib.mdamath.make_whole where if all bonds
were correctly sized, it wouldn\'t notice that multiple fragments
had been given. (Issue #445)

* Fixed issue with PDB Topology parsing where if serials went
over 100k, they wrapped to \'
*
*
*\', breaking the parser (Issue #446)

* Fixed AtomGroup.sequence() (Issue #451)

* Fixed PrimitivePDBParser not detecting when resids had looped over
10,000. The original resid is stored as Atom.resnum (Issue #454)

* Fixed TPR topology parser to treat all bonded interactions available in
Gromacs 5.1 (Issue #222 and #352, pull request #463).
09/07/15 tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl,
manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de,
gormanstock

* 0.11.0
This release brings large changes to many parts of the API and might
break many existing scripts. For a full guide on the API changes,
please see:
https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-0.11-unifying-release-user-guide
Migrating old scripts has been made easier with the introduction of
the ten2eleven tool which is part of the package.
Details on how to use this are available at:
https://github.com/MDAnalysis/mdanalysis/wiki/Migrating-MDAnalysis-code-with-ten2eleven.py
API Changes

* Changed AtomGroup counting methods to properties with different
names: numberOfAtoms() to n_atoms, numberOfResidues() to
n_residues, numberOfSegments() --> n_segments (Issue #376)

* Changed trajectory reader numframes to n_frames (Issue #376)

* Changed Timestep.numatoms to n_atoms (Issue #376)

* Deprecated the use of the \'fullgroup\' selection keyword (Issue #268)

* Changed atom.number attribute to atom.index (Issue #372)

* Changed many AtomGroup methods to properties. These are: indices,
masses, charges, names, types, radii, resids, resnames, resnums,
segids (Issue #372)

* Timestep can now only init using an integer argument (which
represents the number of atoms) (Issue #250)

* Added from_timestep and from_coordinates construction methods
to base.Timestep (Issue #250)

* Removed KDTree and CoordinateNeighbor from MDAnalaysis. If you
want to search in cartesian coordinates directly for nighboring
points use the BioPython KDTree or scikit-learn Neighbors module.
The AtomNeighborSearch class has been ported to use the BioPython
KDTree and is now located in MDAnalaysis.lib.NeighborSearch.
MDAnalaysis.KDTree still exists in this version so load the
NeighborSearch module but is deprecated and will be removed in
1.0. (Issue #383)

* Moved MDAnalysis.core.transformations to
MDAnalysis.lib.transformations (Issue #287)

* Moved MDAnalysis.core.util to MDAnalysis.lib.util (Issue #287)

* Moved MDAnalysis.core.log to MDAnalysis.lib.log (Issue #287)

* Moved MDAnalysis.core.units to MDAnalysis.units (Issue #287)

* Moved MDAnalysis.core.distances to MDAnalysis.lib.distances
(Issue #287)

* Moved MDAnalysis.core.parallel to MDAnalysis.lib.parallel
(Issue #287)

* Moved norm, normal, angle, stp and dihedral from lib.util to
lib.mdamath (Issue #287)

* AtomGroup.bond .angle .dihedral and .improper now return the
corresponding TopologyObject rather than performing the calculation
(Issue #373)

* All TopologyObjects now have a \"value\" method to evaluate them
(Issue #373)

* TopologyGroup now has a \"values\" methods to evaluate all contained
bonds (Issue #373)

* MDAnalysis.lib.distances.calc_torsions renamed to calc_dihedrals
(Issue #373)

* TopologyGroup.selectBonds renamed to select_bonds (Issue #389)

* deprecated camelCase AtomGroup methods in favour of underscore_style
(Issue #389)

* deprecate lib.distances.applyPBC in favour of apply_PBC (Issue #389)

* AtomGroup.res[names,ids,nums] and AtomGroup.segids now give arrays
of equal size to AtomGroup (Issue #385)

* ResidueGroup.segids now gives arrays of equal size to ResidueGroup
(Issue #385)

* AtomGroup setters `set_` now plural for consistency with
property names (Issue #385)

* DCDReader no longer supports the \"skip\" keyword. Use slicing
on reader iteration to achieve same affect. (Issue #350)

* All Readers have a default \"dt\" of 1.0 ps. This applies also to
single frame readers, these would previously raise an error on
accessing dt. (Issue #350)

* NCDF Reader no longer has a default skip_timestep of 1 (Issue #350)
Enhancements

* Added the \'global\' selection keyword (Issue #268)

* Added Jmol selection writer (Issue #356)

* Added reading of Hoomd XML files (Issue #333)
These can only act as topology information for now

* Tests can now detect memleaks on a per-test basis (Issue #323)

* AtomGroups can now be pickled/unpickled (Issue #293)

* Universes can have a __del__ method (not actually added) without
leaking (Issue #297)

* Added reading of DL_Poly format CONFIG and HISTORY files, these can
both act as both Topology and Coordinate information (Issue #298)

* Timestep objects now have __eq__ method (Issue #294)

* coordinates.base.Timestep now can handle velocities and forces
(Issue #294)

* Waterdynamics analysis module added, including five analysis
classes: Hydrogen Bond Lifetimes, Water Orientational Relaxation,
Angular Distribution, Mean Square Displacement and Survival
Probability. Documentation and test are included. (Issue #300)

* RMSF class added to rms analysis module

* ProgressMeter now outputs every
*interval
* number of ``update``
calls (Issue #313)

* Created lib.mdamath for common mathematical functions. (Issue #287)

* All Timesteps have the has_positions has_velocities and has_forces
boolean flags (Issue #213)

* Timesteps can now allocate velocities and forces if they weren\'t
originally created with these through the use of the has_ flags.
(Issue #213)

* Timesteps now store \'dt\' and \'time_offset\' if passed to them by
Reader to calculate time attribute (Issues #306 and #307)

* MDAnalysis.selection: can also be written to a NamedStream

* Added function lib.mdamath.make_whole to \"unbreak\" molecules
over periodic boundaries. (Issue #355)

* Added triclinic_dimensions to Timestep, returns representation of
unit cell as triclinic vectors (Issue #276)

* Added setter to bfactors property (Issue #372)

* Added AtomGroup altLocs and serials properties with setters.
(Issue #372)

* MDAnalysis.core.AtomGroup.Merge now copies across bonding
information (Issue #249)
Changes

* numpy >= 1.5 required

* A ProtoReader class intermediate between IObase and Reader was added
so specific Readers can be subclassed without __del__ (the
ChainReader and SingleFrameReader), thus preventing memleaks
(Issue #312).

* Atoms (and all container classes thereof) are now bound to Universes
only via weakrefs. If Universes are not explicitly kept in scope
Atoms will become orphaned. (Issue #297)

* Removed FormatError, now replaced by ValueError (Issue #294)

* base.Reader now defines __iter__ and __iter__ removed from many
Readers (now use base.Reader implementation) (Issue #350)

* Timestep._x _y and _z are now read only (Issue #213)

* moved MDAnalysis.selections.base.get_writer() to
MDAnalysis.selections.get_writer() to break a circular import. This
should not affect any code because
MDAnalysis.selections.get_writer() already existed.

* distances.contact_matrix now treats the particle distance with
itself as a contact for sparse matrices and numpy arrays. The
progress reporting for sparse calculations has been removed.
(Issue #375)

* TopologyObjects and TopologyGroup moved to core.topologyobjects
module (Issue #373)

* Consolidated coordinates.guess_format and topology.guess_format to
lib.util.guess_format (Issue #336)
Fixes

* All Writers now refer to time between written Timesteps as \"dt\",
was previously \"delta\" in some Writers. (Issue #206)

* Topology files can now be compressed (Issue #336)

* Fixed PDB Parser and Reader requiring occupancy field (Issue #396)

* Amber TRJ and NCDF Reader & Writers now use \'dt\' instead of \'delta\'
to refer to time elapsed between timesteps. (Issue #350 and #206)

* Fixed TPRParser considering LJ 1..4 exclusions as bonds (Issue #351)

* ChainReaders no longer cause memory leak (Issue #312)

* analysis.hbonds.HydrogenBondAnalysis performs a sanity check for
static selections (Issue #296)

* Fixed TRZWriter failing when passed a non TRZTimestep (Issue #302)

* relative imports are now banned in unit testing modules
(Issue #189)

* Fixed bug and added DivisionByZero exception in
analysis/waterdynamics.py in SurvivalProbability. (Issue #327)

* Fixed parsing of PDB header data for PrimitivePDBReader (Issue #332)

* Fixed contact_matrix handles periodic boundary conditions correctly
for sparse matrices. (Issue #375)

* Fixed analysis.hole not using CPOINT (Issue #384)

* Fixed XTC/TRR .dt rewinding the trajectory (Issue #407)

* Fixed TopologyGroup.from_indices not guessing topology object class
(Issue #409)

* Fixed TopologyGroup.__contains__ failing if different instance of
same bond was queried. (Issue #409)
06/01/15 richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst,
sseyler

* 0.10.0
Enhancements

* Improved performance of PDB Reading. Up to 3x faster. (Issue #212)

* Added the \'same ... as\' selection keyword (Issue #217)

* Added guess_bonds keyword argument to Universe creation. This will attempt to
guess all topology information on Universe creation. (Issue #245)

* Added guess_bonds method to AtomGroup. (Issue #245)

* All TopologyObjects (Bond, Angle etc) now have is_guessed attribute

* TopologyGroup now has alternate constructor method, .from_indices()

* Added TopologyObject.indices property

* Amber netCDF4 Reader will now read Forces (Issue #257)

* Amber netCDF4 Writer will now write Velocities and Forces

* Added Amber coordinate/restart file reader (Issue #262)

* Structural superpositions (MDAnalysis.analysis.align) can work
with partial matches of atoms.

* new path similarity analysis module MDAnalysis.analysis.psa

* AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays
works identically to numpy masks. (Issue #282)
Changes

* TopologyGroup can now have zero length, and will evaluate to False
when empty.

* Renamed TopologyGroup.dump_contents to \"to_indices\"

* Deprecated \'bonds\' keyword from Universe and replaced with \'guess_bonds\'

* PrimitivePDBReader now requires the numatoms keyword

* Structural superpositions (MDAnalysis.analysis.align) use partial
matches of atoms by default (use strict=True for old behavior)

* Function rmsd() was removed from MDAnalysis.analysis.align name
space and should be accessed as MDAnalysis.analysis.rms.rmsd()
Fixes

* bynum selections now work from AtomGroup instances (Issue #275)

* Cylinder selections now work from AtomGroup instances and honor
PBC (Issue #274)

* NetCDFWriter previously always wrote velocities/forces if found
in timestep, rather than following how the Writer was created.
04/20/15 tyler.je.reddy, richardjgowers, orbeckst

* 0.9.2
Enhancements

* Can now set velocity from Atom object. (Issue 221)

* Atom object now has force attribute for getting/setting forces (requires a
trajectory with forces) (Issue 221)

* Added wrap method. Wrap allows the centers of groups of atoms to be
moved within the primary unit cell without breaking up the group. (Issue 190)
Changes

* The MDAnalysis project moved from Google Code to GitHub: the new
website is http://www.mdanalysis.org and the new source code
repository is at https://github.com/MDAnalysis/mdanalysis

* \"applications\" were removed from the mdanalysis source code
repository and now exist as independent repositories under
https://github.com/MDAnalysis/

* Using a non-existent atom name as an instant selector now raises
AttributeError instead of SelectionError (Issue 220)
Fixes

* trajectory objects are now properly closed in unit tests (Issue 256)
03/27/15 manuel.nuno.melo, richardjgowers, comconadin

* 0.9.1
Enhancements

* XYZ file format can be used without an associated topology file.

* GAMESS output files can be read as trajectories for calculations of
type ``SURFACE\'\' and ``OPTIMIZE\'\' (work wit both GAMESS-US and Firefly)
Changes

* removed undocumented MDAnalysis.builder module
Fixes

* TRR coordinate access via _y and _z now works properly (Issue 224)
03/15/15 richardjgowers, tyler.je.reddy, orbeckst, e.jjordan12, zhuyi.xue,
bala.biophysics, dotsdl, sebastien.buchoux

* 0.9.0
Enhancements

* offsets for XTC and TRR trajectories now stored and retrieved
automatically; improves init times for large trajectories (Issue 208)

* docs now use secure mathjax CDN (Issue 182)

* minor improvements to helanal docstring

* Support for reading altloc records in PDB files

* Cap proteins with ACE and NMA terminal caps

* MOL2 read and write support

* 2D streamplot code no longer uses deprecated matplotlib.nxutils module

* core.distances.calc_angles and calc_torsions now accept an optional box
argument to consider periodic boundary conditions in their calculation
(Issue 172)

* TopologyGroup angles and torsions methods both have a pbc flag, (default
False) to toggle consideration of periodic boundaries

* XYZWriter (write simple XYZ trajectories)

* TRZReader upgrades, seeking and numframes faster

* PQRWriter (write PQR files)

* HydrogenBond analysis: new keyword distance_type to alternatively
look at the distance between heavy atoms (Issue 185)

* TopologyGroup/TopologyDict system overhauled. (Issue 194)

* TopologyObject class created, Bonds/Angles/etc nicer to work with.

* Topology information is now loaded lazily into Universe, can be forced to
load all with u.load_topology(). All topology information is now stored in
.bonds .angles .torsions and .impropers attributes.

* Added support for improper torsions.

* AtomGroup now has .bonds .angles .torsions and .impropers attributes which
retrieve relevant TopologyGroups

* Increased performance of topology.core.guess_bonds greatly

* Added topology.core.guess_angles guess_torsions and guess_improper_torsions
which given accurate bond information can calculate the rest of the
topology info.

* Universe topology information is now settable after initialisation using lists of indices
such as those provided by the guess_
* functions.

* Added LAMMPS data parser for topology files with the .data suffix. Can also
read single frame coordinate & velocity information from these files.
(Issue 139)

* Added Fragments. Fragments are continuously bonded groups of atoms.
These are lazily built, and accessible via the Atom.fragment and AtomGroup.fragments
attributes.
(Issue 190)

* Added ability to remove items from Universe cache with _clear_caches.

* Added ability to define dimensions from AtomGroup, Universe and Timestep for most
formats.
(Issue 203)

* streamIO: many readers can directly use gzip- or bzip2 compressed
files or a stream (such as cStringIO.StringIO) wrapped in
util.NamedStream; currently supported: PDB, PSF, CRD, PQR, PDBQT,
GRO, MOL2, XYZ

* Added hydrogen bonding time autocorrelation analysis module
(analysis.hbonds.HydrogenBondAutoCorrel)

* Added energy units to core.units (Issue 214)

* New AtomGroup.split() method to produce a list of AtomGroups for each atom,
residue, or segment

* New AtomGroup.sequence() method to extract a protein sequence.

* Can pass subclasses of Reader and Topology reader to Universe init to allow
custom readers to be defined. (Issue 198)

* Added Atom.bonded_atoms property. This returns an AtomGroup of the Atoms
that are bonded to a given Atom. (Issue 219)

* Added atom selections to ContactAnalysis (Issue 169)
Changes

* DCD unitcell format changed: MDAnalysis will now read it as [A,
gamma, B, beta, alpha, C] instead of [A, alpha, B, beta, gamma,
C]. The new CHARMM box vector unitcell format is heuristically guessed.
(see Issue 187 for a full discussion and implications).

* __getstate__() and __setstate__() raise an NotImplementedError for
Universe and AtomGroup; before they were silently accepted on
pickling and a cryptic \"TypeError: AtomGroup is not callable\" was
raised (see also Issue 173 for detailed explanation)

* XTC/TRR reader raise IOError with errorcode EIO (instead of
ENODATA) when the last frame is reached and EBADF (instead of
EFAULT) for any other issues (partially addresses Issue 150,
Windows compatibility)

* Universe.bonds now returns a TopologyGroup not a list. TopologyGroup can be
iterated over; list(universe.bonds) should provide a fix to legacy code.

* PQR reader will now set segid to a chainID if found in the PQR
file (previously, the segid would always be set to \'SYSTEM\').

* util.anyopen() only returns the stream and not the tuple (stream,
filename) anymore; it tries to set stream.name instead

* topology reading now done via classes (similar to trajectory reading)
rather than functions.
(Issue 210)
Fixes

* fixed DCD triclinic unit cell reading and writing (although the new CHARMM
format with the box matrix is not supported for writing) (Issue 187)
ATTENTION: Support for triclinic boxes from DCDs was BROKEN prior to this fix!

* fixed creation of residues and segments in Merge()

* resolves Issue 188 regarding Helanal Finish Argument

* fixed Issue 184 (TPR files with double precision)

* fixed Issue 199 (FutureWarning in pyqcprot)
04/01/14 orbeckst, jandom, zhuyi.xue, xdeupi, tyler.je.reddy,
manuel.nuno.melo, danny.parton, sebastien.buchoux, denniej0,
rmcgibbo, richardjgowers, lennardvanderfeltz, bernardin.alejandro
matthieu.chavent

* 0.8.1
(Note: 0.8.0 contains a subset of these changes; 0.8.0 is deprecated)
Enhancements

* Named selections can now be passed to selectAtoms (Issue 174)

* (experimental) MDAnalysis.visualization namespace added along with
2D/3D streamplot modules & documentation for them

* TRR file handling is now fully aware of missing coordinate/velocity/force
information when reading and writing frames.

* MDAnalysis.analysis.contacts.ContactAnalysis1 run() method
now allows trajectory slicing (Issue 161)

* 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([inplace=True])

* 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

* added calc_bonds, calc_angles and calc_torsions cython functions to
core.distances for quickly calculating bond information

* added applyPBC(coords, box) function to core.distances to move
coordinates to within the primary unit cell

* many AtomGroup methods now support \'pbc\' flag to move atoms to within
primary unitcell before calculation. This behaviour can also be
toggled using the core.flags[\'use_pbc\'] flag (Issue 156)

* MDAnalysis.analysis.rms.rmsd(): new center keyword so that one can
immediately calculate the minimum rmsd of two rigid-body superimposed
structures
Changes

* libxdrfile2 is now used instead of libxdrfile. libxdrfile2 is distributed
under GPLv2

* 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)

* AtomGroup.velocities is now a (managed) attribute and not a method
anymore: replace \'ag.velocities()\' with \'ag.velocities\'

* changed the name of the flag \'convert_gromacs_lengths\' to \'convert_lengths\'
Fixes

* asUniverse now also accepts any instance that inherits from
MDAnalysis.Universe (Issue 176)

* fixed XDR writer incorrect use of delta parameter (Issue 154)

* 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)

* fixed AtomGroup.ts Timestep instance not containing all available
information (Issue 163)

* fixed Timestep copy method returning a base Timestep rather than
appropriate format (Issue 164)

Thu Oct 24 14:00:00 2013 speilickeAATTsuse.com
- Require python-setuptools instead of distribute (upstreams merged)

Sun Jan 13 13:00:00 2013 p.drouandAATTgmail.com
- Update to 0.7.7 version:

* 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)

Wed Jan 18 13:00:00 2012 toddrme2178AATTgmail.com
- Updated BuildRequires and Requires to match new dependency names

Wed Jan 11 13:00:00 2012 toddrme2178AATTgmail.com
- Cleaned up spec file

Thu Sep 8 14:00:00 2011 alinm.elenaAATTgmail.com
- initial commit