MDT change history

MDT 5.4 05-25-2017

  • Development is now open and hosted at GitHub.
  • Experimental cmake build support.
  • Installation packages now available for Homebrew (“brew tap salilab/salilab; brew install mdt”) and Anaconda Python (“conda install -c salilab mdt”).

MDT 5.3 05-19-2015

  • A new function write_statpot() can generate a Modeller statistical potential file given a suitable input table.
  • A new feature Cluster allows clustering of two features into a single one.
  • A new feature AtomTable takes as input a table of precalculated per-atom values, and can be used to implement user-defined features or to use externally-calculated properties.
  • To save space, the data for the MDT table itself can be compressed when writing to an HDF5 file with Table.write_hdf5().
  • Certain library information (such as the mapping from feature values to bin indices, and atom or tuple class information) and information about the last scan is now written into MDT files in HDF5 format by Table.write_hdf5().
  • The maximum value of bond_span_range can now be -1, to allow atom pairs that have no path of bonds between them. This is helpful to include inter-chain interactions, for example.

MDT 5.2 10-29-2012

  • A new method Table.get_array_view() allows the raw MDT table data to be modified using NumPy functions.
  • Disulfide bonds can now be considered in the calculation of atom bond separation, by the AtomBondSeparation feature and the Table.add_alignment() method.
  • Atoms in atom tuples can now be restricted to match only in certain residue types.

MDT 5.1 09-29-2011

  • All atom features, with the exception of AtomType, are now considered undefined if the atom coordinates are equal to the Modeller undefined value (-999.0).
  • Support for bond separation, with a new AtomBondSeparation feature and a bond_span_range argument to Table.add_alignment().
  • Support Python 3 (requires Modeller 9.10 or later).
  • “scons test” now reports the Python coverage (and also C coverage, if using gcc and adding “coverage=true” to the scons command line).
  • The Table constructor now takes an optional ‘shape’ argument, which acts identically to that accepted by Table.reshape().

MDT 5.0 03-31-2011

  • First open source (GPLv2) release.
  • Duplicated Modeller Fortran code removed; MDT now uses Modeller itself for handling of protein structures and alignments.
  • Added scans over atom pairs, atom tuples, atom tuple pairs, and chemical bonds.
  • Complete documentation, examples, and unit tests added.
  • TOP scripting interface replaced with Python.
  • Support storing MDT tables in binary form, using the HDF5 format and library.

MDT 4.0 April 2002

  • Reorganize directory structure.

MDT 3.1 March 2002

  • Allow for a structure to be assessed against an existing MDT table.