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This section has a series of example Omega command-line executions. Each example is followed by a brief description of its behavior.
prompt> omega2 drugs.smi drugs.oeb.gz prompt> omega2 -in drugs.smi -out drugs.oeb.gz
These two commands will yield identical results. These execute Omega with the
default parameters. The file drugs.smi is opened in SMILES format for
input, and the output is written to the file drugs.oeb.gz in gzipped
OEBinary format.
prompt> omega2 -in drugs.smi -out drugs.oeb.gz -param myparameters
This command is the same as the one above except for the -param flag.
It executes Omega with the parameters found in the myparameters
file. The file drugs.smi is opened in SMILES format for input, and
the output is written to the file drugs.oeb.gz in gzipped OEBinary
format.
prompt> omega2 -param myparameters drugs.smi drugs.oeb.gz prompt> omega2 drugs.smi drugs.oeb.gz -param myparameters
Thre first of these two commands will yield exactly the same results as the
example above. drugs.smi will be mapped to the -in flag and
drugs.oeb.gz will be mapped to the -out flag begin the second to
last and last command-line arguments respectively. Unfortunately, the second
of these two commands, will fail to parse because the implicit input and output
arguments are not the final two arguments in the list.
prompt> omega2 -in drugs.smi -out drugs.oeb.gz -param myparameters -maxconfs 600
Again, this is a very similar command. It executes Omega using the
parameters in the myparameters file, except the -maxconfs
parameter is over-ridden with the 600 from the command line. The
command-line -maxconfs parameter would take precedence over the
value in the parameter file independent of the order of flags on the
command line.
prompt> DBQuery "barbiturate" | omega2 -in .sdf -out .oeb.gz | vida2 .oeb.gz
This execution assums that a process called "DBQuery" can be called with
the parameter "barbiturate" and return a stream of molecules in MDL's .sdf
format. This output is piped into Omega, which interprets the format
correctly and generates multiconformer molecules using the default
parameters. Omega writes the output to std::cout in gzipped
OEBinary format, which is read by OpenEye's Vida2 molecular
viewer.
prompt> omega2 -in drugs.mol2 -out drugs.oeb.gz -fromCT true
The -fromCT true flag will cause Omega to ignore the input
conformations in the drugs.mol2 file. An initial conformation will
be generated by a distance-bounds algorithm from the connection-table of
the molecules in the input file. Be aware that the default value of
-fromCT is true, however it is listed explicitly here for emphasis.
prompt> omega2 -in drugs.smi -out drugs.oeb.gz -log null
The -log flag normally allows specification of the log file's name.
However, nul and null are reserved names which indicate that
no log file will be written.
prompt> omega2 -in drugs.smi -out drugs.oeb.gz -log null
When the -log parameter is set to nul or null, no
logging will be written (this includes failure modes).
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