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.