MDT is simply a Python extension module, and as such can be used in combination with other Python modules, such as MODELLER or the Python standard library.
Running pre-built binaries¶
The easiest way to use MDT is to install the pre-built binary RPM for your
variety of Linux (this will first require you to install the Modeller RPM).
Then you should simply be able to run an MDT script
foo.py just like
any regular Python script with a command similar to:
In the Sali lab, MDT is built as part of the nightly build system at the same time as MODELLER. Thus you can set up your system to run MDT scripts by running:
module load modeller
Using with Anaconda Python¶
There is an MDT package available for Anaconda Python for Mac and Linux. To install it, simply run:
conda install -c salilab mdt
Using a Homebrew package¶
If you are using a Mac with homebrew you can get MDT by running in a terminal window:
brew tap salilab/salilab; brew install mdt
If you don’t already have Modeller installed, you can get it by running brew install modeller before you install MDT.
Add –with-python3 to the end of each brew install command if you also want to use Python 3.
Compilation from source code¶
The MDT source code can be downloaded from GitHub.
Install dependent packages needed for MDT: MODELLER, glib, SWIG, pkg-config, and HDF5:
- MODELLER 9.13 or later is required.
- glib 2.4 or later is required. It is available as pre-built packages for most modern Linux distributions; there is also a MacPorts package for Mac users.
- SWIG 1.3.39 or later is required.
- Unfortunately HDF5 only works if you use the exact same version that is used by MODELLER. See the MODELLER ChangeLog for the version to use.
To compile, run scons in the same directory (and optionally scons test)
to build (and test) MDT. This will produce a script
which can be used to run an MDT Python script
bin/mdtpy.sh python foo.py
If you didn’t use the RPM or Debian package to install Modeller then you
will need to tell MDT where it can find Modeller. To do this, create a file
config.py, and in it set the modeller Python variable to
the directory where you have MODELLER installed (on a Mac, this would look
like modeller=”/Library/modeller-XXX” where XXX is the Modeller version).
If you installed any of the prerequisites in non-standard locations (i.e.
not /usr/include for glib and HDF5, and not /usr/bin for pkg-config
or SWIG) you will also need to tell scons where to find them. Add similar
config.py to set path for pkg-config and SWIG
and includepath for glib and HDF5 (e.g. path=”/opt/local/bin”
and includepath=”/opt/local/include” on a Mac).
If you want to install MDT, run scons install. You can additionally specify
a prefix option (or set it in
config.py) to install in a different
directory. For example, scons prefix=/foo install will install MDT in
Example MDT script¶
Generally speaking, to use MDT, you should
- Create a
- Read any necessary additional files into the library, such as the definitions of chemical bonds (see Chemical bonds for an example), or atom tuples.
- Define one or more features, which are classes in the
- Create one or more
Tableobjects, using a selection of the features you added to the Library, to hold the frequency tables themselves.
- Collect statistics into the table using methods such as
- Post process (e.g.
plot the data, or
write the table to a file.
A simple example, which simply collects the distribution of residue types in a PDB file, is shown below:
import modeller import mdt import mdt.features # Setup of Modeller and MDT system env = modeller.environ() mlib = mdt.Library(env) # Creation of feature types restyp = mdt.features.ResidueType(mlib) # Create a 1D table of residue type table = mdt.Table(mlib, features=restyp) # Read in a PDB file and make an alignment of just this one structure mdl = modeller.model(env, file='5fd1') aln = modeller.alignment(env) aln.append_model(mdl, align_codes='5fd1', atom_files='5fd1') # Collect MDT statistics for this alignment table.add_alignment(aln) # Print out the MDT by treating it as a Python list print "Distribution of residue types:" print [bin for bin in table]
For more applied examples, see Sample studies with MDT.