MDT change history
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.