MDT prepares a raw frequency table, given information from MODELLER alignments and/or PDB files. More precisely, MDT uses a sample of sequences, structures, and/or alignments to construct a table N(a,b,c,...,d) for features a, b, c, ..., d. The sample for generating the frequencies N is obtained depending on the type of features a, b, c, ..., d. The sample can contain individual proteins, pairs of proteins, pairs of residues in proteins, pairs of aligned residues, pairs of aligned pairs of residues, chemical bonds, angles, dihedral angles, and pairs of tuples of atoms. Some features work with triple alignments, too. All the needed features a, b, c, ..., d are calculated automatically from the sequences, alignments, and/or PDB files. The feature bins are defined by the user when each feature is created.
To build MDT, simply type scons in this directory. To run it, use
scons install to install it (you may need to set command line options to
install files in the correct locations - see scons -h) and then run MDT
scripts just like any other Python script. Alternatively, you can use the
bin/mdtpy.sh script to run MDT directly from the build directory. Simply
run it before your regular Python invocation
(e.g. "bin/mdtpy.sh python foo.py")
MDT is Copyright 1989-2021 Andrej Sali, and available under the terms of version 2 of the GNU General Public License as published by the Free Software Foundation.