ReleaseNotes0110

Release 0.11.0 is a major update for MDAnalysis. It contains a number of backwards-incompatible API changes, i.e. existing code is likely to break. Additionally, some old functionality has been deprecated and will be removed for the 1.0.0 release.

The MDAnalysis 0.11 unifying release user guide should help you with porting your code. We have also included a tool ten2eleven as part of the package that automates some of the API changes in your existing code, as described in Migrating MDAnalysis code with ten2eleven.

CHANGELOG

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 (Issue #376):
  • numberOfAtoms() → n_atoms
  • numberOfResidues() → n_residues
  • numberOfSegments() → n_segments
• Changed trajectory reader numframes → n_frames (Issue #376)
• Changed Timestep.numatoms → 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 neighboring 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. MDAnalysis.KDTree still exists in this version to load the NeighborSearch module but is deprecated and will be removed in 1.0. (Issue #383)
• Moved MDAnalysis.core.transformations → MDAnalysis.lib.transformations (Issue #287)
• Moved MDAnalysis.core.util → MDAnalysis.lib.util (Issue #287)
• Moved MDAnalysis.core.log → MDAnalysis.lib.log (Issue #287)
• Moved MDAnalysis.core.units → MDAnalysis.units (Issue #287)
• Moved MDAnalysis.core.distances → MDAnalysis.lib.distances (Issue #287)
• Moved MDAnalysis.core.parallel → 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 → MDAnalysis.lib.distances.calc_dihedrals (Issue #373)
• TopologyGroup.selectBonds renamed → select_bonds (Issue #389)
• deprecated camelCase AtomGroup methods in favour of underscore_style (Issue #389)
• deprecated 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_<property> now plural for consistency with property names (Issue #385)
• DCDReader no longer supports the "skip" keyword. Use slicing on reader iteration to achieve same effect. (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
• MDAnalysis.lib.log.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)

Authors

tyler.je.reddy, richardjgowers, alejob, orbeckst, dotsdl, manuel.nuno.melo, cyanezstange, khuston, ivirshup, kain88-de, gormanstock