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CVS commit: wip/py-mdanalysis
Module name: wip
Committed by: jihbed
Date: Fri Jan 3 21:28:42 UTC 2014
Modified Files:
wip/py-mdanalysis: Makefile PLIST distinfo
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)
02/16/12 sebastien.buchoux
* 0.7.5.1
Fixes
* added: missing files (Issue 95)
* removed: unused delaunay-related files
02/11/12 orbeckst, sebastien.buchoux, jandom, hallben, lukasgrossar
* 0.7.5
MDAnalysis can now be found on PyPI, allowing simple installation
from the internet. Metadata was added to setup to facilitate PyPI
upload and pages on the wiki describe how to do this.
In addition, Debian/Ubuntu packages are also available.
Note that in order to run UnitTests one needs the separate package
MDAnalysisTests (also release 0.7.5).
Enhancements
* new method OtherWriter() for trajectory readers to generate a
writer for any format that has been initialised for the common
basic values
* new simple Residue.chi1_selection() selection
* new distances.between() function (EXPERIMENTAL)
* support LAMMPS non-standard DCD files (Issue 84; EXPERIMENTAL)
* read and write multi-frame PDB files (Issue 77; EXPERIMENTAL)
* extend the PDB parsing, support CONECT and REMARK entries
* new GNM-based trajectory analysis module (Issue 90)
* Read/Write velocities with TRR, new attribute Atom.velocity
and AtomGroup.velocities() (Issue 91)
* hydrogen bond analysis detects a range of GLYCAM atom types
and utils.convert_aa_code will also accept GLYCAM-style residue
names (Issue 92)
* XYZ reader: can set timestep (Issue 92)
Changes
* The UnitTests are now integrated with the separate test data in a
separate Python package named MDAnalysisTests; to run the tests
for 0.7.5 one will need MDAnalysisTests-0.7.5 (Issue 87).
* install a range of analysis dependencies right away: networkx,
biopython, GridDataFormats (usually all painless); leave scipy and
matplotlib to the user and the local package manager
* When writing a trajectory and converting units, effectively a copy
of the timestep is made and the in-memory timestep is not
altered. In this way, analysis after writing a frame will still
see the coordinates in MDAnalysis units and not converted units.
Fixes
* analysis.align.rms_fit_traj(): can output fitted trajectory to any
supported format not just the input format
* fixed ProgressMeter: default format string was broken
* fixed: ResidueGroup and SegmentGroup indexing (did not work with
numpy.int64 etc) and now raise TypeError if it does not fit
* fixed HydrogenBondingAnalysis backbone donor list: had C but
should have been O (this was supposed to be fixed with r849 in
0.7.4 but a typo crept in). NOTE: analysis might have produced
partially wrong results.
* fixed: dihedral() and other methods using core.util.angle() sometimes
returned nan instead of +pi or -pi
* fixed: writing a trajectory from chained CRD files gave garbage
coordinates (Issue 81)
* fixed: support files for docs are now in included in the source
distribution (thanks to Sebastien Buchoux; Issue 82)
* fixed: core.util.iterable() would wrongly detect unicode strings
as "iterable"; this lead the Reader autodections and then the
ChainReader fail with "Runtime Error: Maximum recursion depth
exceeded" for single filenames provided as a unicode string.
* fixed: HBond analysis pickling of tables (Issue 92)
07/09/11 orbeckst, dcaplan, jandom
* 0.7.4
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 when
written in pure python; optimized in c code using scipy.weave)
* HydrogenBondingAnalysis: donor atom name CO --> O (proper backbone
oxygen); without the fix one misses most of the backbone H-bonds
* alignto() and rms_fit_trj(): 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
MDAnalaysis/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.
05/22/11 orbeckst, jandom, Benjamin Hall, Paul Rigor, dcaplan,
Christian Beckstein (logo), denniej0
* 0.7.3
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.frame:
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)
* new special methods of AtomGroup: bond(), angle(), improper() in
addition to the calculation of dihedral()
* 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 (and a 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)
03/31/11 orbeckst, dcaplan, naveen.michaudagrawal
* 0.7.2
* NOTE: minimum Python version required is 2.5 (since 0.6.3)
Enhancements
* loading from a PDB sets segid to the chain id if it exists
* PrimitivePDBWriter uses first letter of segid as PDB chain id
* aliased segment.name to segment.id
* new method AtomGroup.bbox() that returns the orthorhombic bounding box
* enhancements of the analysis.density module (build density
from B-factors)
* PQR radius is now an attribute of Atom; AtomGroup.radii() returns the
radii as a NumPy array; internally B-factor has also become an
attribute of each Atom.
* recognise many more OPLS/AA and Amber residue names as "protein"
* recognise more atom masses (taken from CHARMM27 and Gromacs) and
atom types (from CHARMM, Amber, OPLS, GROMOS) and moved
masses and types into new module topology.tables; the type recognition
is still incomplete but can be easily enhanced in tables
* analysis.align: convenience functions rotation_matrix() and alignto()
* TrajectoryReader gained Writer() method which returns an appropriate
TrajectoryWriter instance that can be used for processing this
trajectory (enhancement of the Trajectory API); if no Writer is known
then a NotImplementedError is raised
* doc improvements
Fixes
* installation: removed dependency on Cython; developer should
use setup_developer.py instead of setup.py (Issue 66)
* Fixed a problem with the strict PDBReader: raised exception when the
pdb did not contain a segid
* Support for PDBs with 4 character resnames and segID output when
writing (Issue 63) --- makes the (default) PrimitivePDBReader/Writer
more suitable for NAMD/CHARMM but breaks strict PDB standard. If
you need full PDB reading capabilities, use the strict PDB reader
[i.e. use Universe(..., permissive=False)]
* fixed bug in (experimental) phi and psi selections
* fixed bugs in reading of unit cells (Issue 60, Issue 61, Issue 34)
* universe.trajectory.delta returns the full precision dt value
instead of a value rounded to 4 decimals (Issue 64)
* fixed bug in DCDWriter (XTC->DCD was broken, Issue 59)
02/08/11 orbeckst, denniej0, jandom, tyler.je.reddy, Joshua Adelman
* 0.7.1 release
* online documentation
* AMBER topology and trj capabilities (netcdf not yet available)
* PQR file reading support
* new analysis.contacts.ContactAnalysis1 class that supports a
native contact analysis between arbitrary groups
* new examples (e.g. peptide helix clustering in a membrane)
* fixed Issue 58 (align.rms_fit_trj; fix reported by Joshua Adelman)
* new analysis module 'density': creation and analysis of volume data
* fast RMSD aligner based on Douglas Theobald's QCP method for
calculating the minimum RMSD between two structures and
determining the optimal least-squares rotation matrix;
replaces the slower previous code (implemented by Joshua Adelman from
his pyqcprot package https://github.com/synapticarbors/pyqcprot);
deprecated core.rms_fitting.rms_rotation_matrix() and scheduled for
removal in 0.8
* uses cython instead of pyrex
11/05/10 orbeckst, denniej0, tyler.je.reddy, danny.parton, joseph.goose
* major release 0.7.0
(includes changes that can BREAK BACKWARDS COMPATIBILITY)
* Removed ALL DEPRECATED code:
- AtomGroup.principleAxes (Issue 33)
- DCD.DCDReader.dcd_header() and DCD.DCDWriter.dcd_header()
(use _dcd_header())
- Universe.dcd (and Universe.xtc, Universe.trr...) --- from
now on only Universe.trajectory is supported.
WILL BREAK LEGACY CODE!
- removed the following packages from top-level MDAnalysis
name space:
- AtomGroup, Selection: import them from MDAnalysis.core if
really needed (e.g. 'import MDAnalysis.core.AtomGroup')
- distances, rms_fitting: 'import MDAnalysis.analysis.distances'
or 'import MDAnalysis.analysis.align.rms_fitting' (the
actual modules still live in MDAnalysis.core but they
might get moved in the future and bundled with
transformations)
- 'from MDAnalysis import *' will only get ['Timeseries',
'Universe', 'asUniverse', 'Writer', 'collection']
- removed copy flag from distance_array and self_distance_array:
setting it to False would always give wrong results so there was
no good reason keeping it around
* whitespace is no longer required around parentheses for
selectAtoms strings but the old syntax with white space
still works (Issue 43)
* improved trajectory writing
- MDAnalysis.Writer() factory function that provides an
appropriate writer for the desired file format
- Writer.write() accepts a Timestep, a Universe, or a
arbitrary AtomGroup (e.g. from a selection); this is much
more flexible than Writer.write_next_timestep()
* New attributes for trajectory readers: dt (time between
frames) and totaltime (length of the trajectory)
* Changes to AtomGroup
- Indexing is made consistent with the way lists behave:
1. indexing with integers returns a single Atom
2. slicing always returns a new AtomGroup
3. advanced slicing with a list or array returns a new
AtomGroup (NEW, fixes Issue 36)
- AtomGroup coordinates can be manipulated (translate(),
rotate() and rotateby() methods; when appropriate, these methods
can take AtomGroups or arrays to determine coordinates)
- new attributes 'residues' and 'segments' for AtomGroup to give
access to the list of residue/segment objects of the group
- new exception 'NoDataError'; raised when creation of an empty
AtomGroup is attempted (see also Issue 12)
- consistent representation of the Segment > Residue > Atom
hierarchy: all classes related to AtomGroup have the
attributes 'atoms', 'residues', 'segments' which provide
access to groups of the corresponding objects
* improvements to Residue, ResidueGroup and Segment classes
- documented accessing residues from Segment as
Segment.r<resid>; resid is 1-based -- BREAKS OLD CODE
that relied on this being 0-based
- added SegmentGroup class
- can write from Residue, ResidueGroup and Segment (Issue 46)
- residue name attribute of a Segment now consistently
returns a ResidueGroup (Issue 47) -- MIGHT BREAK OLD CODE
- added documentation and examples in the doc strings
- new special dihedral angle selections defined for Residue
class to simplify analysis of backbone torsions (experimental)
* new contact_matrix method for calculating contacts
(Issue 30); for large (N > ~10000) coordinate arrays
automatically switches to a method using a sparse matrix (slower)
* more example scripts (e.g. for membrane analysis, trajectory writing,
coordinate transformations)
* CRDReader added (fixes Issue 40 ) ... it will work for both
standard and extended formats: NO special flags needed.
* CRDWriter will now write extended crd files: NO special flags needed.
* By default, PDB files are read with the PrimitivePDBReader and not
the Bio.PDB reader anymore because the latter can drop atoms when
they have the same name in a residue (which happens for systems
generated from MD simulations) The PrimitivePDBReader copes just fine
with those cases (but does not handle esoteric PDB features such as
alternative atoms and insertion codes that are not needed for
handling MD simulation data).
- The default behaviour of MDAnalysis can be set through the flag
MDAnalysis.core.flag['permissive_pdb_reader']. The default is True.
- One can always manually select the PDB reader by providing the
permissive keyword to Universe; e.g. Universe(...,permissive=False)
will read the input file with the Bio.PDB reader. This might be
useful when processing true Protein Databank PDB files.
* fixed Issue 51 (distance_array() did not properly check its
input and wrong results could be returned if the input was a
float64 and a float32 array)
09/19/10 orbeckst
* quick-fix release 0.6.4.1
* fixed import issue with python 2.5 (Issue 41)
09/16/10 orbeckst, danny.parton
* release 0.6.4
* GRO writer added
* fixed XTC writer (Issue 38)
* convert box representations (Issue 37)
* primitive PDB parser added (slightly faster and ignores
correctness of resids, atomnames etc but reads CRYST1 into unitcell)
* Universe gained the 'permissive' flag to switch on the
primitive PDB parser/reader
* Simple 'chained reader' which enables a Universe to
transparently read a list of trajectory files (Issue 39).
* Additional methods for AtomGroup: numberOfResidues(), resids(), resnames()
* new bilayer analysis script for membrane composition on a
per-leaflet basis (examples/membrane-composition.py); also
renamed examples/leaflet.py to membrane-leaflets.py
07/08/10 orbeckst, denniej0, danny.parton, philipwfowler
* 0.6.3 release
* minimum requirement is python 2.4 (using with_statement in the
analysis module and we have not tested on 2.3 in a while)
* analysis modules (MDAnalysis.analysis):
- lipid bilayer leaflet detection
- native contact analysis ("q1-q2")
- rms-fitting based on sequence alignment
* write selections for other codes from AtomGroups (VMD, pymol, CHARMM,
Gromacs ndx)
* gro reader (Issue 31)
* better API for loading a topology and a coordinate file in Universe()
* trajectory reader: DCDReader can reverse trajectory with negative
step increment; XTC/TRRReader can do simple (forward) slices by doing
(slow!) sequential iteration
* deprecated principleAxes() and introduced principalAxes() with less
confusing return values (Issue 33).
* fixed wrong unitcell dimensions for XTC/TRR (Issue 34)
* added basic XYZ reader with compression support (Issue 35)
* PDB reader guesses masses (unknown elements are set to 0)
* installation requires Biopython (www.biopython.org)
05/28/10 orbeckst, denniej0
* 0.6.2 release
* removed a number of imports from the top level (such as rms_fitting);
this might break some scripts that still rely on the layout that was
used for 0.5.x (which is now officially declared deprecated)
* defined trajectory API
* deprecated DCD.dcd_header --> DCD._dcd_header
* XTC and TRR compute numframes by iterating through trajectory (slow!)
* introduced units: base units are ps (time) and Angstrom (length); see
core.flags
* XTC and TRR automatically convert between native Gromacs units (ps, nm) and
base units (uses core.flags['convert_gromacs_lengths'] = True)
* more test cases
* *really* FIXED Issue 16 (can easy_install from tar file)
* FIXED a bug in AtomGroup.principalAxes()
* added dependency information to setup.py (numpy and
biopython by default; nose for tests)
04/30/10 orbeckst
* 0.6.1 release
* can build a simple Universe from a PDB file (FIXES Issue 11)
* can read Gromacs XTC and TRR files (FIXES Issue 1) but no
Timeseries or Collections yet for those formats
* removed Universe.load_new_dcd() and Universe.load_new_pdb()
--- use the generic Universe.load_new() (MIGHT BREAK OLD CODE)
* removed deprecated Universe._dcd attribute (MIGHT BREAK OLD CODE)
* FIXED bug in PDB.PDBWriter and CRD.CRDWriter
* use SloppyPDB in order to cope with large PDB files
* core.distances.self_distance_array() is now behaving the
same way as distance_array()
* defined Trajectory API (see MDAnalysis/coordinates/__init__.py)
* renamed _dcdtest to dcdtimeseries (will not affect old code)
* unit tests added (still need more test cases)
03/31/10 orbeckst, denniej0
* 0.6.0 release
* added KDTree and Neighbour searching code from Biopython for
faster distance selections: used for AROUND selections;
POINT is using distance matrix by default as this is
faster. This can be configured with core.flags
* core.flags infrastructure to tweak behaviour at run time
* updated LICENSE file with Biopython License
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED (partial): Issue 18 (Timeseries from a universe.segID
selection, reported by lordnapi)
* FIXED: Issue 19 (Timeseries collections were broken,
reported by Jiyong)
* can write single frames as pdb or crd (AtomGroup gained the
write() method)
* some selections for nucleic acids
* completely reorganized directory structure to make
enhancements easier to incorporate
* FIXED: Issue 19 (Timeseries collections were broken)
* improved installation
- EasyInstall (setuptools) support (FIXED Issue 16)
- better instructions in INSTALL
- slightly better handling of the configuration of the fast
linear algebra libs via the setup.cfg file
08/23/08 naveen, orbeckst
* 0.5.1 release
* primitive PDB writer (only works if coordinates were read from a pdb)
* B-factor property (detailed implementation subject to change)
* periodic flag for PointSelection
* new correl series: orientation vector for 3-site molecules
(to calculate the water dipole moment of SPC or TIP3P)
* distance.distance_array() bug fixed (see doc string)
* updated LICENSE file UIUC Open Source License
01/29/08 orbeckst
* prepared 0.5.0 release. Includes previously disabled
distance code, PDB reader, incomplete XTC reader (code by
Benjamin Hall), and marginally updated documentation &
licenses
11/12/07 naveen
* prepared for release outside lab
To generate a diff of this commit:
cvs -z3 rdiff -u -r1.2 -r1.3 wip/py-mdanalysis/PLIST \
wip/py-mdanalysis/distinfo
cvs -z3 rdiff -u -r1.8 -r1.9 wip/py-mdanalysis/Makefile
To view a diff of this commit:
http://pkgsrc-wip.cvs.sourceforge.net/pkgsrc-wip/wip/py-mdanalysis/PLIST?r1=1.2&r2=1.3
http://pkgsrc-wip.cvs.sourceforge.net/pkgsrc-wip/wip/py-mdanalysis/distinfo?r1=1.2&r2=1.3
http://pkgsrc-wip.cvs.sourceforge.net/pkgsrc-wip/wip/py-mdanalysis/Makefile?r1=1.8&r2=1.9
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
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