.. _filters:

DCA Filtering Syntax
====================

Sometimes it may be necessary to filter and modify DCA contacts.

To specify filters on the command line the following syntax is used::

    filter:<arg>:<arg>:<arg>:...

The number of arguments depends on the filter being used.

Multiple filters may be chained by separating them with ``,``.

The following filters are implemented:

``none``
--------

The ``none`` filter works as a dummy filter and does nothing. It takes no
options.

``threshold``
-------------

The ``threshold`` filter looks up DCA contacts in a target PDB file,
calculates their distances, and discards or includes them depending on
the threshold setting.

The syntax is the following::

    threshold:<n>:<cst>:<mode>:<moodel>

Arguments:

* ``n``: threshold (< 0: keep below, > 0: keep above)
* ``cst``: prediction / constraints selection to look up PDB file
* ``mode``, ``model``: model selection mode (see `README <README.rst>` for details)

Example::

    threshold:8.0:100dca_FADE_-100_26_20_-2_2:cluster:1,threshold:-6.0:100dca_FADE_-100_26_20_-2_2:cluster:1

This uses the first cluster of the ``100dca_FADE_-100_26_20_-2_2`` predicton
as target PDB file. All DCA contacts whose distance is between 6Å and 8Å in
the target PDB are kept.