ReleaseNotes0160

MDAnalysis v0.16.0 release!

• release date: 04/10/17

CHANGELOG

Enhancements

• Added 'filename' attribute to 'MemoryReader'
• GRO reader conforms to the reader API standard(#1196)
• Improved __str__ and __repr__ of 'GroupBase' class in MDAnalysis.core.groups (addresses Issue #1223)
• Added dynamic selections (addresses Issues #175 and #1074).
• Added 'MemoryReader' class to allow manipulation of trajectory data in-memory, which can provide substantial speed-ups to certain calculations.
• Universe creation now takes an 'in_memory' option, which will transfer the corresponding trajectory to memory. Likewise a new 'Universe.transfer_to_memory()' method makes it possible to make this transfer after construction of the universe
• Added 'in_memory' option to 'rms_fit_trj', which makes it possible to do in-place (in-memory) alignment of trajectories.
• All classes derived from 'AnalysisBase' now display a ProgressMeter with 'quiet=False'
• The 'run' method from all 'AnalysisBase' derived classes return the class itself.
• Added boolean flag at lib.distances.USED_OPENMP to reveal if OpenMP was used in compilation (Issue #883)
• Added Principal Component Analysis module for linear dimensionality reduction.
• Added Auxiliary module for reading additional timeseries data alongside trajectories (Issue #785)
• Added AnalysisFromFunction & analysis_class, see (Issue #946 and PR #950)
• Established the MDAnalysis.analysis.legacy module for unmaintained analysis code (Issue #743)
• Added ProgressMeter to 'transfer_to_memory' function, to show progress of loading trajectory to memory (Issue #1028 and PR #1055).
• Selecting atoms by resid now respects icodes if they were present. Ie select_atoms('resid 163A') works! (Issue #839 PR #1066)
• Added ability to read MMTF format files (#907 PR #1069)
• Added MDAnalysis.fetch_mmtf function to download from PDB and create Universe (#810 PR #1082)
• Added coordinates.null.NullWriter, which behaves like a Writer but ignores all input; useful for suppressing output.
• Added random access support to GMSReader and TRJReader (#1081)
• Added atomgroup.center(weights, pbc) method to calculate the center of a group given weights
• Universe anchors (for unpickling) now use a uuid (rather than filename) to distinguish themselves by default. Can still use anchor_name kwarg to control the anchor name manually. (PR #1125)
• Added groupby method to Group objects. (PR #1112)
• Added singleframe attribute to Writer API to exclude from known Writers for a single frame (Issue #1199 PR #1201)
• Correct the display error of HydrogenBondAnalysis when start is not 0 or step is not one.
• Groups (atomgroup, residuegroup, and segmentgroup) have more operators, included set operators (Issue #726)
• Universes built with Merge now use the MemoryReader (Issue #1251)
• speed improvement for analysis.gnm.closeContactGNMAnalysis(..., weights="size") by about 5x (partially Issue #1191)

Fixes

• Trajectory slicing made completely Pythonic (Issue #918 PR #1195)
• Argument validation of dist_mat_to_vec is fixed (#597 PR #1183)
• Give correct error when the topology file format is not recognized (Issue #982)
• Give correct error when file doesn't exist/ has bad permissions (Issue #981)
• Improvement of analysis/waterdynamics module (Issue #935)
• Removed MDAnalysis.analysis.PDBToBinaryTraj (Issue #1035)
• MDAnalysis.analysis.distances.between() is no longer broken
• GROWriter resids now truncated properly (Issue #886)
• reading/writing lambda value in trr files (Issue #859)
• fix iter/next redundancy (Issue #869)
• SingleFrameReader now raises StopIteration instead of IOError on calling next (Issue #869)
• Display of Deprecation warnings doesn't affect other modules anymore (Issue #754)
• Changed nframes to n_frames in analysis modules for consistency (Issue #890)
• fixed incompatibility with newer matplotlib in analysis.hole
• Fixed modules that improperly documented and/or used frame slicing defaults (#914)
• Fixed same interRDF can be run twice (Issue #924)
• Support for TPR files produced by Gromacs-2016 (Issue #932)
• Fixed parsing PDB files with CONECT records to TER entries (Issue #936)
• Fixed parsing PDB files with single entry in CONECT record (Issue #937)
• Progress meters are now displayed as expected on jupyter notebooks (Issue #927)
• Reset trajectory to 0 after sliced iteration (Issue #1031)
• Fixed rotaxis returning NaN if a=b (Issue #1045)
• Fixed align_principal_axis onto a principal axes (Issue #1045)
• Fixed NCDFWriter wrote velocities instead of forces if convert_units=False was set: now correctly writes forces (PR #1113)
• Fixed warn about missing cython package in dev builds
• Fix align.rotation_matrix checks array shape equality (Issue #1152)
• Fixed strange error when writing a PDB with 0 atoms (Issue #1083 PR #1103)
• Fixed selections using operators backwards ('prop 10 > mass') and sensitivity about whitespace around these (PR #1156 Issue #1011 #1009)
• Fixed PSA analysis is now using AlignTraj
• Fixed Principal Axes to order from highest to lowest eigenval (Issue #1162)
• Fixed analysis.density with soluteselection and notwithin_coordinates_factory when using KDTree (Issue #1211)
• GRO files with greater than 99,999 residues now read correctly (Issue #728)

Changes

• Started unifying the API of analysis classes (named internally "Bauhaus" style; see Issue #719)
• Added protected variable _frame_index to to keep track of frame iteration number in AnalysisBase
• Added new AlignTraj class for alignment. (Issue #845)
• Added new diffusionmap module for dimension reduction (Issue #857)
• Added new PCA module for dimension reduction (PR #896)
• Qcprot now takes N x 3 arrays instead of 3 x N arrays. This gives about a 40% speed up. (PR #930)
• The ProgressMeter class now has a dynamic keyword argument. It is now recommended to provide format strings using the new python format syntax, the old %-based syntax is still available but will be deprecated. (PR #944)
• Analysis.rms.RMSD now confirms to standard analysis API (Issue #893)
• Fragments in Universe.fragment are now sorted by the index of their first atom. (Issue 1007)
• atoms.tranform/translate/rotate/rotateby return original atomgroup (Issue #1010)
• atoms.translate/rotateby don't accept AtomGroup tuples as parameters anymore (Issue #1025)
• atoms.rotate can be given center of rotation (Issue #1022)
• XTCFile and TRRFile only raise IOError now on error.
• Deprecate usage of MDAnalysis.core.AtomGroup
• get_writer_for() returns NullWriter when filename=None instead of raising TypeError and filename is now a required arg instead of kwarg
• moved coordinates.base.ChainReader to coordinates.chain.ChainReader
• renamed private method ChainReader.get_flname() to ChainReader._get_filename()
• totaltime now considers the first frame to be at time 0 (Issue #1137)
• analysis.rms.RMSF now conforms to standard analysis API (PR #1136)
• analysis.rms/align function keyword mass_weighted is replaced by generic weights='mass'. This new keyword allows to pass it an arbitrary weights array as well. (PR #1136)
• Renamed various base classes for clarity. Iobase -> IOBase, Reader -> ReaderBase, SingleFrameReader -> SingleFrameReaderBase, Writer -> WriterBase, TopologyReader -> TopologyReaderBase, SelectionWriter -> SelectionWriterBase (Issue #921)
• Selection writers do not have a 'wa' mode anymore, but they have a 'close' method (Issue #1244)
• Remove deprecated PrimitivePDB* classes
• Remove deprecated delta keyword for ChainReader
• Remove deprecated permissive_pdb_reader flag
• Removed superfluous and confusing keywords start and end for resid selection in analysis.helanal.helanal_main() and analysis.helanal.helanal_trajectory()
• weights="size" parameter in analysis.gnm.closeContactGNMAnalysis to replace MassWeight=True
• bump minimum numpy version to 1.10.4

Deprecations

• Use of rms_fit_trj deprecated in favor of AlignTraj class (Issue #845)
• Moved analysis.x3dna to the analysis.legacy module (Issue #906)
• The keyword argument quiet is deprecated in favor of verbose throughout the library (Issue #903)
• MassWeight=True parameter in analysis.gnm.closeContactGNMAnalysis deprecated in favor of weights="size".

Authors

kain88-de, fiona-naughton, richardjgowers, tyler.je.reddy, jdetle, euhruska, orbeckst, rbrtdlg, jbarnoud, wouterboomsma, shanmbic, dotsdl, manuel.nuno.melo, utkbansal, vedantrathore, shobhitagarwal1612, xiki-tempula