The program efcex is a filter program which takes in one or
more CEX files (defaults to standard input) and outputs an expanded
and filtered file on standard output. The input, if it is in the
DockIt output format, has a single molecule object for each ligand
which was docked. The molecule objects have a number of coordinate
sets attached to them, each with score properties. The expand action
of efcex will take each molecule object and expand it out to
multiple molecule objects, each with a single set of coordinates and
score properties. This version is somewhat simpler to deal with
later, although most tools are capable of handling either format.
In any case, the main action of efcex is to only put out those
ligands and conformations which match the filter file (specified using
the -f switch). The filter file can be in one of two formats.
The first format contains lines of the form:
ligandname [confnumber [confnumber]... ]
That is, each line will contain a ligandname (taken from the name property of the molecule object unless specified by -n flag) and,
optionally, one or more integer conformation numbers separated by
spaces. If no ligand numbers are specified, then all conformations of
the ligand are output. More than one line can refer to the same
ligandname and each can have one or more conformation numbers.
However, if the last line which refers to a given ligandname has no
conformation numbers, then all the conformations for the ligand are
output, regardless of what was specified in earlier lines. The
conformation numbers can be in any order.
The second format, which is more ofter used with magnet, contains lines
with the format:
ligandname_number data data data ...
where the first column contains a ligand name and conformation (pose) number connected by the underscore character. This identifier is generated by the SEA action term getid(1). This column is followed by any number of data columns generated by SEA printf actions. This form
of input file is processed by efcex by using the -1 flag.
Use only the first column of the list file to specify filtered ligands.
Skip the first line of the list file. Used when column labels are placed in the first line.
- -x coord_property
Specifies the name of the property in the CEX input stream which contains the 3D coordinates. The default is the standard coordinates property (which conventionally has the CEX tag XYZ).
- -n name_property
Specifies the name of the property in the CEX input stream to be used for the ligand name. The default is the standard name property (which conventionally has the CEX tag NAM).
- -f listfile
Specify the file which contains a list of ligands and pose numbers to retain in output. See the description of the format, above.