Subsections

4.2 Usage

Makefraglib can be used from the command-line to generate ring templates for use with omega starting from only a collection of molecules. The output file from makefraglib can then be passed directly into Omega using the -setfraglib or -addfraglib flag. Although fragment libraries may be concatenated using the Unix 'cat' command, this is not strictly necessary as multiple fragment libraries may be specified as one argument to the flag.

4.2.1 Command-Line Interface

A listing of all command line options for makefraglib along with a brief description can be obtained by executing makefraglib with the command line option -help all.

prompt> makefraglib --help all

Complete parameter list
    -pvmconf : A text file specifying a PVM configuration

    File Options
      -in : Input filename
      -log : Override prefix used to name output files
      -out : Output filename
      -param : makefraglib control parameter file
      -prefix : Prefix to use to name output files.
      -skip : Existing fragment library to avoid duplicating
      -verbose : Verbose output

    3D Construction Parameters
      -buildff : Force field to use for initial structure refinement
      -ewindow : Energy window covered by final conformers
      -fromCT : Generate structures from connection-table only.
      -rms : Minimum RMS between final conformers
      -startfact : Factor for determining number of random starts

    PVM
      -pvmdebug : Generate an enormous volume of PVM debug information
      -pvmpass : Number of molecules to pass to a slave at one time

4.2.2 Parameters

-buildff: This flag sets the force field used for constructing fragments that are assembled to build an initial model of the input structure. Consult the description of Force Fields (Section 3.2) for an explanation of appropriate arguments for this flag. [default = mmff94s_NoEstat]
-ewindow: The -ewindow flag sets the energy window used as an accept or reject criteria for conformers of ring systems. Any conformer that has a calculated strain energy less than the sum of the energy window and the energy of the global minimum conformer will be accepted. Conformers with strain energies above this threshold are rejected. [default = 10.0]
-in: File containing one or more molecular connection tables to be processed by Omega. File format types are discussed in section 3.1.2.
-log: This argument to this flag specifies the name of the log file. The level of detail for logfile information can be altered using the -verbose (see -verbose) flag. Output can be directed to the terminal instead of a file by giving a hyphen '-' as the argument to the flag instead of a filename. Generation of an output log may be disabled by providing 'nul' or 'null' as an argument. [default = prefix.log]
-out: File to write conformers generated by Omega. File formats are discussed in section 3.1.2. OEBinary is the recommended output format.
-param: The argument for this flag is the name of a file containing control parameters. The control parameter file acts to either replace or augment the command line interface. All parameters necessary for program execution may be provided in the control parameter file, although any command given explicitly on the command line will supercede options found in the parameter file. makefraglib generates a new parameter file containing the full set of execution parameters upon every execution. The name of the parameter file written by makefraglib is created by combining the prefix base name (see -prefix) with the '.parm' extension.
-prefix: The argument for this flag defines the prefix to be used for various information and data files generated by makefraglib. Most important among these is the 'makefraglib.parm' file which includes a copy of all the parameters used in the Omega run. The prefix is also used to generate a default log file name if not explicitly specified with the -log (see -log) flag. [default = makefraglib].
-skip: The argument that follows the skip flag is a file created previously with makefraglib. This enables makefraglib to avoid re-creating fragments for which conformers have already been created. Three dimensional structures will only be generated for unique fragments found in the input molecule file.
-startfact: The floating point argument to the -startfact flag indirectly controls the level of sampling attempted to determine fragment conformation. The equation used to determine the number of random coordinate starting points is number of samples = (10 + ( $\sum$ (nrb==3) - $\sum$ (nrb==4))*startfact). $\sum$ (nrb==3) is the sum of the number of atoms in the molecule that have exactly three ring bonds. $\sum$ (nrb==4) is the sum of the number of atoms in the molecule that have exactly 4 ring bonds. In general, the default level of sampling will far exceed the level necessary to reproduce all reasonably low energy conformations of a ring system. [default = 20.0]
-verbose: This is a boolean flag that controls the level of detail written to the log file. By default Omega will only write minimal information to the log file. Molecule titles and warning messages constitute the bulk of logging at the default level. Verbose logging will cause more information to be written to the log file in order to follow behavior during program execution. [default = false]

4.2.3 Example executions

The following section shows several common command-line executions of makefraglib. Each example is followed by an explanation of what the program will do.

prompt> makefraglib -in drugs.smi -out fraglib.oeb

All of the molecules in drugs.smi will be processed. The set of all unique fragments (according to Omega fragmentation rules) from all of the molecules in drugs.smi will be collected.

prompt> makefraglib -in vendor.smi -out new_fraglib.oeb -skip
fraglib.oeb -ewindow 5.0

Conformers will be generated for all of the unique fragments found in the file vendor.smi that are not present in fraglib.oeb. An energy window of 5 Kcal above the global minimum conformer will be used to accept or reject conformations of flexible ring systems.

				OMEGA C++ Toolkit

				OMEGA C++ Toolkit