Magnet Programs

magnet rules.sea protein.cex [ligands.cex...]

The main program in the Magnet suite. Magnet processes or filters the ligand file(s) according to the SEA rules file. The output goes to standard output stream (stdout) and can be redirected to a file or pipe in the normal Unix manner. If not ligand input files are given, the input is taken from the standard input stream.

efcex [-1] [-skiplabels] [-x coord_property] [-n name_property] [-f filterfilename] [ligands.cex...]

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]... ]
ligandname etc.

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 ...
etc...

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.

-1: Use only the first column of the list file to specify filtered ligands.
-skiplabels: 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.

babelcx

babelcx is a modified version of the babel program for converting molecular structure formats. The source is provided in babelcx.tar.gz. It has been modified to read and write CEX format. Use -icex or -ocex to read or write CEX files. This program might be of particular use in converting various connection table formats (like MDL Mol files or Tripos Sybyl Mol2 files) in CEX input files for ligands. Note that babelcx is a general purpose conversion program and it is not set up to deal with general data fields in the various file formats that it works on. For example, babelcx does not save the various CEX properties (like multiple docked conformations, scores and rms values) into other molecular structure formats. Of particular note, babelcx only outputs the first conformation found for each ligand in a CEX file. The program efcex can be used to expand a multiconformer CEX file into a CEX file which has only one conformation per molecule (duplicating the molecules as necessary). Such a file can be converted correctly via babelcx.

pdb2cex <input_pdb_file > output_cex_file cex2pdb < input_cex_file > output_pdb_file

These two programs convert between CEX and PDB (Protein Data Bank) format files.

	Magnet Documentation Magnet Programs Overview Programs		`magnet` `rules.sea` `protein.cex` [`ligands.cex`...] The main program in the Magnet suite. Magnet processes or filters the ligand file(s) according to the SEA rules file. The output goes to standard output stream (stdout) and can be redirected to a file or pipe in the normal Unix manner. If not ligand input files are given, the input is taken from the standard input stream. `efcex` [-1] [-skiplabels] [-x `coord_property`] [-n `name_property`] [-f `filterfilename`] [`ligands.cex`...] 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]... ] ligandname etc. 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 ... etc... 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. -1 Use only the first column of the list file to specify filtered ligands. -skiplabels 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. `babelcx` babelcx is a modified version of the babel program for converting molecular structure formats. The source is provided in babelcx.tar.gz. It has been modified to read and write CEX format. Use -icex or -ocex to read or write CEX files. This program might be of particular use in converting various connection table formats (like MDL Mol files or Tripos Sybyl Mol2 files) in CEX input files for ligands. Note that babelcx is a general purpose conversion program and it is not set up to deal with general data fields in the various file formats that it works on. For example, babelcx does not save the various CEX properties (like multiple docked conformations, scores and rms values) into other molecular structure formats. Of particular note, babelcx only outputs the first conformation found for each ligand in a CEX file. The program efcex can be used to expand a multiconformer CEX file into a CEX file which has only one conformation per molecule (duplicating the molecules as necessary). Such a file can be converted correctly via babelcx. `pdb2cex` <`input_pdb_file` > `output_cex_file` `cex2pdb` < `input_cex_file` > `output_pdb_file` These two programs convert between CEX and PDB (Protein Data Bank) format files.