Subsections
A description of the command line interface can be obtained by executing ROCS
with the -help option.
prompt> ROCS --help
will generate the following output:
Help functions:
ROCS --help simple : Get a list of simple parameters
ROCS --help all : Get a complete list of parameters
ROCS --help <parameter> : Get detailed help on a parameter
ROCS --help html : Create an html help file for this program
-query (-ref)- File containing molecules or a single grid to use a
shape query.
For molecule queries, available formats include:
| File type |
Extension |
| SDF |
.sdf .mol .sdf.gz .mol.gz |
| MOL2 |
.mol2 .mol2.gz |
| PDB |
.pdb .ent .pdb.gz .ent.gz |
| MacroModel |
.mmod .mmod.gz |
| OEBinary v2 |
.oeb .oeb.gz |
| Old OEBinary |
.bin |
For grid queries, available formats (and file extensions) include:
| Grid File type |
Extension |
| Grasp |
.phi |
| OpenEye |
.grd |
| ASCII Grid |
.agd |
| CCP4 |
.map .ccp4 |
| X-PLOR |
.xplor .xplmap |
-dbase (-fit)- File containing one or more 3D molecules to
overlay against query from above. This flag supports all the same molecules
file formats (not grids) as
-query plus the ROCS DB format
(.rocsdb) and the list file (.lst or .list) as described in
Section 2.2.1.
-param- Defines the control parameter file. This file can
contain a collection of parameters which can be used instead of writing each
parameter to the command-line. In addition, the parameter file written by
any ROCS run (see
-prefix below), can be used with the -param
flag in subsequent ROCS executions. Any command given explicitly on the
command line will supercede any command found in a file specified with the
-param parameter.
-mcquery- Combine contiguous conformers in
-query
file into single multi-conformer query molecule, following the same rules
for combining sequential conformers in the -dbase file. By
default, this is false and each connection table in the -query
file is treated as a separate query. [default = false]
-scdbase- Don't combine contiguous conformers in
-dbase file into single multi-conformer query molecule. Note: For .bin and .oeb files that store a
multi-conformer molecule, this switch has no effect. [default = false]
-prefix- Prefix used to name output files. Using
-prefix
FOO will create a hits structure file named like FOO_hits_1.sdf
and a report file, FOO_1.rpt, where ``_1'' will be replaced
by a sequential number corresponding to the index of the query in the
-query file. Addtionally, a parameter file containing all options for
the current run will be written to FOO.parm. This parameter
file can be used with the -param switch. [default = rocs]
-besthits N- Search entire dbase file and keep a hitlist, sorted
by score given by
-rankby switch. Size of hitlist is determined by
integer value N. Note that all members of the hitlist must pass the
-cutoff, if given, so the final size can be smaller than the N
requested. This switch is ignored if -maxhits is given. Note, that if
this is set to zero (0) and -maxhits is also zero (0), then no
hitlist will be maintained and all results will be streamed directly to
the respective output files. [default = 500]
-cutoff F- Cutoff (F) to determine whether a specific
overlay should be considered good enough for hitlist inclusion. This
is a floating point value and the actual parameter used for the
scoring is as defined by the
-rankby switch. [default = -1.0]
-rankby- Score to use for ranking the hitlist. Legal values
include: tanimoto, tverskyd, tverskyq, scaledcolor, combo and
overlap. [default = combo]
-maxconfs N- Maximum number of overlays returned for each
comparison of a dbase molecule with a query molecule. This defaults to 1.
As an example, if the query has
n conformers and a given dbase
molecule has m conformers, then a total of nxm overlays
will be performed. By default, the single best one (1) will be returned
(if it passes any -cutoff given). Choosing an alternate value for
-maxconfs will cause up to the top N of these overlays to be
returned and merged into the hitlist. In the hitlist, these conformers will
not be associated with each other. Throughout a run, some can drop off the
hitlist while others remain. [default = 1]
-maxhits M- Maximum number of hits to return. This option
causes ROCS to finish as soon as M molecules are in the hitlist. Useful
for a quick check of a query to see what hits it is finding; this
option overrides any value for
-besthits. [default = 0]
-conflabel- Where to put conformer index labels.
-outputquery- Put the query structures at the top of the
output structure file. This is very useful for keeping the query structure
in the same file as the hits, so that for instance, you only need to load
one file into VIDA to browse the results. For a grid query, a copy of the
grid will be written to PREFIX_ref.grd, where PREFIX is defined by the
-prefix commandline option.
[default = true]
-nostructs- Don't write a structure file. There are times when
all you really want are the numerical results from ROCS. If you don't want
or need an output structure file, you can prevent its creation with this
switch. [default = false]
-hitsfile- Instead of writing to PREFIX_hits_n.sdf
(for example) where PREFIX
is provided by the -prefix commandline flag, write all hit structures to
the file provided with this flag. Can be a filename or full/relative path.
Also, if the name provided is actually an molecule file format extension
(i.e. .sdf, .mol2.gz, .oeb, etc.), ROCS will write to stdout using the
format derived from the file extension. For example if the following is
used:
-hitsfile .sdf
then ROCS will write all the hits out to stdout in SDF format.
Note that this option will only work for a single molecule query. If more
than one query is provided along with the -hitsfile option, ROCS will
issue an error and stop.
-oformat- Format for the output structure file(s). This
option gives a file extension to be used for all output structure
files. The format for the file is determined from the
extension. Valid values include all the molecule file formats listed
in the table above for
-query files except old
OEbinary (.bin). [default = sdf]
-reportfile- Instead of writing to PREFIX_n.rpt where
PREFIX is provided by the -prefix commandline flag, write all report
information (stats) to the file provided with this flag. Can be
filename or full/relative path. Note that if more than one query
molecule is provided, this flag will not work unless the "-report
one" flag is also provided to put all report info into one report
file.
-report- Controls report file generation. The default, ``each'',
writes a separate report file for each query in the
-query file. If
``one'' is chosen, stats for multiple queries in the same query file
will be placed in a single report file. This is useful for computing a NxN
comparison of a file as both the dbase and query. Finally, to prevent
ROCS from writing report files, use ``none''. [default = each]
-stats- Determines which stats get placed into report files.
Values include ``hits'' (the default), ``best'' and ``all''. The default
is to include just the stats for the compounds in the hitlist. If ``best'' is
chosen, the report file will include stats for the best overlay(s) for
every dbase molecule. The number of best overlay score is determined by the
value of
-maxconfs. Finally, if ``all'' is given, stats for every
single overlay will be placed in the report file. Be careful. For a
multi-conformer query against a large dbase file, ``all'' can generate a
HUGE amount of data. [default = hits]
-logfile FILE- Filename for log file. Overrides log filename
created from
-prefix.
-progress- Method for showing job progress on the command line.
Choices include:
percent - show a percent complete progress bar (DEFAULT)
log - echo the log message for each molecule
dots - show dots as in ROCS 2.2
none - print nothing to console
-verbose- Add extra verbosity to log file.
-tanimoto_cutoff- Flag that can be used to limit output hits to
only those with some minimum shape score. This can be used regardless of which
score is chosen (-rankby) for ranking the hitlist. For example, using
-rankby combo -cutoff 1.2 -tanimoto_cutoff 0.6
any molecule with shape tanimoto 
0.6 will not be
retained. Additionally, the constraint on combo to be at least 1.2
implies that scaledcolor must also be > 0.6 so that the sum can be
greater than 1.2.
-randomstarts N- Specifies number (N) of random starting
positions to try instead of inertial frame overlay as described in the
theory section. Since inertial frame alignment involves 4 (or 8 in the case
of highly symmetric molecules) starting positions, setting
-randomstarts to a value much larger will result in much slower run
times.
-subtan- Also calculate sub-Tanimoto score. See Section
2.5 for a complete description of how sub-Tanimoto is calculated.
-shapeonly- As of ROCS 2.3, a color force field is used by
default and optimization against shape and color is the default overlap method.
As an easy way to run ROCS with just shape overlap, this flag is the
equivalent of setting:
-chemff none
-optchem false
-rankby tanimoto
-scoreonly- Perform scoring calculation only on input molecules.
Sets the following flags:
-opt false
-optchem false
-besthits 0
-maxhits 0
-scdbase
-opt- Turn optimizer on if true, off if false. Not normally used
by itself, but with other flags via the
-scoreonly flag.
[Default = true]
-chemff- Color-force-field name. Either the name of one
of the built-in color force fields (ImplicitMillsDean or
ExplicitMillsDean) or the name of a user-defined color force field
file. The format of this file is given in section 2.6.
[default = ImplicitMillsDean]
-optchem- Use color force field forces and gradients as part of
overlay optimization. [default = true]
-eon_input- Create an input file suitable for input to
EON. This file will contain one or more conformers, aligned by ROCS,
and output to an OEB file. The query will also be written to the
beginning of the file so that this file is the only input required
to feed into EON. By default, this file will contain up to 3
conformers of the top 1000 ROCS molecules. The number of conformers
per molecule can be controlled with
-eon_maxconfs while the
total number of molecules can be controlled with
-eon_input_size. By default, the file will be named
PREFIX_eon_input_N.oeb.gz, but the actual name can be controlled
via the -eon_input_file flag. [default = false]
-eon_maxconfs- Number of conformers per molecule to be
written to the EON input file. Has no effect unless
-eon_input is true. [default = 3]
-eon_input_size- Number of top molecules to keep and
write to the EON input file. If a value of 0 is given, all ROCS
input molecules will be aligned and written to the EON input
file. [default = 1000]
-eon_input_file- Actual filename for creating an EON
input file. Overrides the value created from
-prefix. Must be
an OEB file.
-pvmconf FILE- Causes ROCS to run in PVM mode using the
hosts defined in FILE. A complete description of PVM setup is beyond
the scope of this section, but more information can be found in
Section 3.3.
-pvmlog FILE- Actual filename for writing PVM log and
status info during the run. This overrides the default
PREFIX.pvmlog.
-pvmpass N- Determines number of molecules passed to each slave
in a given message. Can be a useful tuning parameter, but for the most part
this should be left at the default. The legal range is 1-100. [default = 5]
