ReleaseNotes0190

Oliver Beckstein edited this page Dec 1, 2018 · 1 revision

Releases 0.19.0, 0.19.1, and 0.19.2 happened in quick succession so see also

Release 0.19.0

CHANGELOG

Enhancements

  • Added bond/angle/dihedral reading in PARM7 TOPParser (PR #2052)
  • Replaced multiple apply (_apply_distmat, _apply_kdtree) methods in distance based selections with lib.distances.capped_distance for automatic selection of distance evaluation method. (PR #2035)
  • Modified analysis.rdf.InterRDF to use lib.distances.capped_distance to handle rdf calculations for large systems. (PR #2013)
  • Added return_distances argument in lib.distances.capped_distances to evaluate and return distances only when required. Modified the optimization rules in lib.distances._determine_method for faster computations. (PR #2041)
  • Added method search_tree in lib.pkdtree to find all the pairs between two kdtrees. (PR #2041)
  • Added a wrapper of lib.nsgrid in lib.distances.self_capped_distance and lib.distances.capped_distance to automatically chose the fastest method for distance based calculations. (PR #2008)
  • Added Grid search functionality in lib.nsgrid for faster distance based calculations. (PR #2008)
  • Modified around selections to work with KDTree and periodic boundary conditions. Should reduce memory usage (#974 PR #2022)
  • Modified topology.guessers.guess_bonds to automatically select the fastest method for guessing bonds using lib.distance.self_capped_distance (PR # 2006)
  • Added lib.distances.self_capped_distance to internally select the optimized method for distance evaluations of coordinates with itself. (PR # 2006)
  • Added augment functionality to create relevant images of particles in the vicinity of central cell to handle periodic boundary conditions (PR #1977)
  • Added lib.distances.capped_distance function to quickly calculate all distances up to a given maximum distance (PR #1941)
  • Added a rotation coordinate transformation (PR #1937)
  • Added a box centering trajectory transformation (PR #1946)
  • Added a on-the-fly trajectory transformations API and a coordinate translation function (Issue #786)
  • Added various duecredit stubs
  • Import time reduced by a factor two (PR #1881)
  • Added compound kwarg to center, centroid, center_of_geometry, center_of_mass (PR #1903)
  • Added rdf.InterRDF_s to calculate site-specific pair distribution functions (PR #1815)
  • Increased performance of (repeated) calls to AtomGroup.pack_into_box() (PR #1922)
  • Added boolean property *Group.isunique (PR #1922)
  • Added *Group.copy() methods returning an identical copy of the respective group (PR #1922)
  • Use a faster function to deduplicate indices (PR #1951)
  • Calculations in *Group.center() are performed in double precision (#PR1936)
  • Functions in lib.distances accept coordinate arrays of arbitrary dtype (PR #1936)
  • Added pbc kwarg to Bond/Angle/Dihedral/Improper object value method, default True. (Issue #1938)
  • ChainReader can correctly handle continuous trajectories split into multiple files, generated with gromacs -noappend (PR #1728)
  • MDAnalysis.lib.mdamath now supports triclinic boxes and rewrote in Cython (PR #1965)
  • AtomGroup.write can write a trajectory of selected frames (Issue #1037)
  • Added MDAnalysis.analysis.dihedrals with Dihedral, Ramachandran, and Janin classes to analysis module (PR #1997, PR #2033)
  • Added the analysis.data module for reference data used in analysis (PR #2033)
  • Added augment functionality to create relevant images of particles
  • Most functions in MDanalysis.lib.distances previously only accepting arrays of coordinates now also accept single coordinates as input (PR #2048, Issues #1262 #1938)
  • Performance improvements to make_whole (PR #1965)
  • Performance improvements to fragment finding (PR #2028)
  • Added user-defined boxes in density code (PR #2005)
  • MemoryReader now can accept velocities and forces (PR #2080)
  • Universe.transfer_to_memory now copies dimensions, velocities and forces (where possible) (Issue #1041 PR #2080)

Fixes

  • Rewind in the SingleFrameReader now reads the frame from the file (Issue #1929)
  • Fixed order of indices in Angle/Dihedral/Improper repr
  • coordinates.memory.MemoryReader now takes np.ndarray only (Issue #1685)
  • Silenced warning when duecredit is not installed (Issue #1872)
  • Fixed HBondAnalysis not considering PBC for distances (Issue #1878)
  • Adding new TopologyAttrs with values defined always coerces this into a numpy array (Issue #1876)
  • Groups passed to select_atoms() are now type checked (Issue #1852)
  • Fixed inconsistent handling of groups with/without duplicates in pack_into_box() (Issue #1911)
  • Fixed format of MODEL number in PDB file writing (Issue #1950)
  • PDBWriter now properly sets start value
  • Introduced compatibility for pdb files hybrid36 format encoding (Issue #1897)
  • Zero length TopologyGroup now return proper shape array via to_indices (Issue #1974)
  • Added periodic boundary box support to the Tinker file reader (Issue #2001)
  • Modifying coordinates by assignation is consistently persistent when using the memory reader (Issue #2018)
  • Allow import of WaterBridgeAnalysis from analysis.hbonds (#2064)
  • Fixed SphericalLayer and SphericalZone selections with pbc=True. Previously these shifted all atoms to inside the primary unit cell when calculating the center of the reference group (Issue #1795)
  • PCA analysis now uses start frame as reference frame rather than 0th frame (PR #2055)
  • Fixed trajectory iteration from a MDAnalysis.Universe.empty (#2076)
  • Fixed copies MemoryReader not linking to the underlying coordinate array on initial Timestep (Issue #2081 PR #2080)

Changes

  • TopologyAttrs are now statically typed (Issue #1876)
  • updated meta data for new PyPi (#1837)
  • AtomGroup.atoms, ResidueGroup.residues, and SegmentGroup.segments now return themselves instead of a new object to increase performance (PR #1922)
  • *Group.unique now returns a new object only if the respective group contains duplicates. Otherwise, the group itself is returned. Repeated access of *Group.unique will always return the same object unless the group is updated or modified. (PR #1922)
  • SurvivalProbability does not dilute SP anymore when the reference frame (t0) cannot find any molecules in the first place. (PR #1995)
  • The TPR parser reads SETTLE constraints as bonds. (Issue #1949)
  • Indexing a trajectory with a slice or an array now returns an iterable (Issue #1894)
  • Removed unused function MDAnalysis.lb.mdamath.one_to_many_pointers() (issue #2010)
  • Box input for functions in MDAnalysis.lib.distances is now consistently enforced to be of the form [lx, ly, lz, alpha, beta, gamma] as required by the docs (Issue #2046, PR #2048)
  • Added periodic keyword to select_atoms (#759)
  • PCA.transform now requires that PCA.run() has already been called otherwise a ValueError is raised (PR #2055)
  • The quiet keyword has been removed and replaced with verbose (Issue #1975 PR #2055)
  • MDAnalysis.Universe.empty now creates a MemoryReader trajectory (#2076 #2077)

Deprecations

  • start/stop/step are deprecated in the initialization of Analysis classes. These parameters should instead be given to the run() method of the class. (Issue #1463 #1979 PR #2055)
  • Almost all "save()", "save_results()", "save_table()" methods in analysis classes were deprecated and will be removed in 1.0 (Issue #1972 and #1745)
  • Deprecated use of core.flags. For use_pbc, the pbc keyword should be used, use_KDTree_routines is obsolete as all distance calculations select the fastest method, all other uses of flags are deprecated. (#782)

Testsuite

  • skip tests for duecredit when duecredit is not installed (#1906)
  • updated meta data for PyPi and updated README and INSTALL

Authors

tylerjereddy, richardjgowers, palnabarun, orbeckst, kain88-de, zemanj, VOD555, davidercruz, jbarnoud, ayushsuhane, hfmull, micaela-matta, sebastien.buchoux, arm61, p-j-smith, IAlibay

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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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