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Branch: develop
Commits on Feb 29, 2016
  1. Test and docstring cleanup

    jandom authored and kain88-de committed Feb 24, 2016
    - numpy style docs,
    - renamed a few methods,
    - @staticmethod annotation in tests
  2. Deprecate the old ContactAnalysis1 class

    jandom authored and kain88-de committed Feb 15, 2016
    - checked if tests pass
  3. Re-link to gro.bz2 files in setup.py

    jandom authored and kain88-de committed Feb 14, 2016
  4. Clean-up docs, bzip conf files

    jandom authored and kain88-de committed Feb 12, 2016
  5. Single class that supports both cutoff and best-hummer contacts

    jandom authored and kain88-de committed Feb 12, 2016
    - scipy.sparse will cause an ImportException
    - updated tests (appear to be passing...)
  6. Fixed imports (iii)

    jandom authored and kain88-de committed Feb 11, 2016
  7. Fixed module imports (ii)

    jandom authored and kain88-de committed Feb 11, 2016
  8. Fixed module import

    jandom authored and kain88-de committed Feb 11, 2016
  9. Correct typo in tests

    jandom authored and kain88-de committed Feb 11, 2016
  10. Contact analysis: move the example to cookbook

    jandom authored and kain88-de committed Feb 11, 2016
    - remove accidentally included CoordinateNeighborSearch,
    - single test class in test_contacts.py, remove test_contacts_best.py,
  11. Arguments refactored, numpy-style docs

    jandom authored and kain88-de committed Feb 10, 2016
  12. Revert to changes to contacts.py

    jandom authored and kain88-de committed Feb 10, 2016
    - removed a dependancy on pandas, update tests
  13. Improved, Best-like contact analysis (Issue #702)

    jandom authored and kain88-de committed Feb 9, 2016
    A worked example with GpA dimer in a bilayer
    
    Added tests to the BestHummerContacts calculation
    
    Tests for fraction of native contacts (Q)
Commits on Apr 27, 2015
  1. Partially resolves #222

    jandom committed Apr 27, 2015
    - still no tests, likely still broken for more complex cases
Commits on Apr 20, 2014
  1. New feature: support PDB altloc records (Issue 170)

    jandom committed Apr 16, 2014
    - read and write PDB's containing altlocs (tested),
    - support for 'altloc' atomsel, see docs,
    
    Tests are based on a simple PDB with some altloc records
    - check sum atom counts for the 'altloc' selection string,
    - check bonds, when guessing bonds from PDB,
    - check if output written has same number of atoms as original.
Commits on Apr 19, 2014
  1. New feature: capping proteins

    jandom committed Apr 19, 2014
    An example script is added showing how MDAnalysis can be used to modify a
    simple peptide and add terminal caps to it. The peptide is AAQAA3 and the
    caps are ACE and NMA.
    
    Tests descriptions:
    - check if cap resids were changed correctly,
    - check number of atoms after capping (compare to maestro output),
    - check if box dimensions were changed.
  2. New feature: MOL2 format support

    jandom committed Apr 19, 2014
    MOL2 molecular structure format, developed by Trips,
    is used to store structures of small molecules and proteins.
    
    Mol2 files can have multiple blocks, with different number of atoms,
    much like MAE files. This is not supported. Similarly to PDB reader,
    only multi-molecule mol2 files with the same number of atoms are supported.
    
    - Basic unit testing, tests for corrupt mol2 files. Added support for atom selections,
    - Added example to the Mol2 reader docs,
    - Mol2Parser is a class,
    - Parser errors are just exceptions.
Commits on Oct 31, 2013
  1. New feature: merge AtomGroups together giving a new Universe

    jandom committed Oct 31, 2013
    - Merge two or more AtomGroups into a new Universe,
    
        use MDAnalysis.Merge(gr1, gr2, ...)
    
    - possible to use a single AtomGroup, if atoms were
      re-ordered for example,
    - support for an empty universe, u = Universe(),
    
    - add basic test class,
    - add other tests, make sure that merge doesn't messup the origin
      universes from which the input AtomGroups come,
    - test write out of merged pdb file,
    - CHANGELOG modified
  2. Added VdW radius for phosphorus

    jandom committed Oct 31, 2013
    - corrected the fix for the presence of an atom radius
Commits on May 26, 2013
  1. Fixed Issue 144 PrimitivePDBWriter bug

    jandom committed May 26, 2013
    - AtomGroup rotate() method modified positions stored in
      the AtomGroup object.universe.trajectory.ts._pos,
    - AtomGroup write() method was using the coordinates copied
      to instantiate the AtomGroup, stored in object.ts._pos,
    - To correct that, in the write() method use
      object.universe.trajectory.ts._pos,
Commits on May 11, 2013
  1. Closing fixes to Issue 23: guessing bonds

    jandom committed May 11, 2013
    - Moved vdwradii to topology.core and remove the factor of
      10 multiplication (converting to Angstroms)
    - Use self_distance_array and appropriate indexing, rather than
      computing a full distance-matrix
  2. Extending the bond-guessing

    jandom committed May 11, 2013
    - PrimitivePDBParser can now tolerate TER records in PDBs, in the
      context of bonds,
    - The bonds can be written out to a PDB, either only the ones
      originally defined in CONECT records, or all (including those
      guessed internally in MDAnalysis)
Commits on Feb 20, 2013
Commits on Feb 7, 2013
  1. DMSReader for topology and coordinates

    jandom authored and orbeckst committed Feb 3, 2013
    - added CHANGELOG and __init__.py trivia,
    - python 2.5 compatibility
  2. DMSReader for topology and coordinates

    jandom authored and orbeckst committed Jan 21, 2013
    - only read support, via sqlite3,
    - reads coordinates, velocities and bonds only,
    - added sanity tests (number of atoms and bonds),
    - added atomselection tests (name, resname, segid).
Commits on Feb 3, 2013
  1. DMSReader for topology and coordinates

    jandom committed Feb 3, 2013
    - added CHANGELOG and __init__.py trivia,
    - python 2.5 compatibility
Commits on Jan 21, 2013
  1. DMSReader for topology and coordinates

    jandom committed Jan 21, 2013
    - only read support, via sqlite3,
    - reads coordinates, velocities and bonds only,
    - added sanity tests (number of atoms and bonds),
    - added atomselection tests (name, resname, segid).
Commits on Dec 1, 2012
  1. Issue 23: generate bond list when using a PDB instead of a PSF

    jandom committed Dec 1, 2012
    - bonds are guessed basing on distances between atom pairs,
    - VdW radii of atoms are taken from GROMACS vdwradii.dat file,
    - fudge factor is changed from 0.6 (VMD) to 0.7 to make it all
      work (VMD likely has a slightly different VdW radii table),
    - added a basic sanity check based on the pdb/psf pair available
      in the test suite.
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