On Windows it is advisable to use the 64-bit ROCS executable during memory-intensive tasks (for example, combining -mcquery with -subrocs) to avoid a crash due to insufficient memory.
Use of the color force field is now on by default. With this, the default score to rank the hitlist has been changed to combo. The following new default flag values:
-chemff ImplicitMillsDean -optchem -rankby combo
ROCS now has multiple methods of showing job progress. In addition to the dots of previous versions, ROCS now has a progress bar by default that show percent completion of the dbase file. Note that means that when ROCS starts, it will count the number of molecules in the dbase and then use that value to measure percent completion. This also allows log file messages to be tagged to the index into the dbase file for each molecule as it is scored. See the description for the new flag -progress for info on the other options.
Since color is now on by default, a new flag -shapeonly has been added to turn on the shape only features of previous versions for ROCS. This is only a convenience flag that just sets the following:
-chemff none -optchem false -rankby tanimoto
Since ROCS is routinely used to preparation of input files for EON, a new set of flags have been added that aid in creation of a specific EON input file, different from the standard ROCS hits file. Please see the section about describing these options:
-eon_input -eon_maxconfs -eon_input_size -eon_input_file
Added a new status file (rocs.pvmlog by default), that shows PVM master and slave statistics, during PVM runs. The actual filename can be modified with the new -pvmlog switch.
Deprecated in the last release, the -allcolor flag has now been removed.
Added ability to read rotor-offset-compressed OEB files as written from OMEGA 2.0 and later.
Added new -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.
-scoreonly flag to allow scoring of pre-aligned positions. Using this one flag is the equivalent of the following settings:
-opt false -besthits 0 -maxhits 0 -scdbase
New -conflabel flag to control where conformer indices are placed in output files. Previous versions added the conformer index at the end of the molecule title following an underscore. The new flag has 4 possible values:
sdtag is only useful if the output file is SDF or OEB.
Several new flags have been added to allow more complete control of the different files ROCS can output. The added flags include:
-logfile Instead of writing to stderr, all logging information goes into a file provided by this switch can be filename or full/relative path
-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.
-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
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.
In order to facilitate using ROCS as part of a larger workflow, the -dbase flag can now be used to force ROCS to read its dbase molecules from stdin. If a file extension (i.e. .sdf, .mol2.gz, etc.), is used as the -dbase filename, ROCS will attempt to read dbase molecules from stdin in the format described by that file extension. For example, if the following is used:
then ROCS will read the dbase molecules from stdin in SDF format.
Note that this option will only work for a single molecule query. If more than one query is provided along with a -dbase flag attempting to read from stdin, ROCS will issue an error and stop.
Changed the way untitled ref and fit molecules are named so that in hits files, they can be distinguished and so that untitled names are different than conformer index names.
-allcolor flag has been deprecated and will be removed from a future version of ROCS.
Added new -out flag to checkcff to output molecules to an OEB file with color atoms attached. This file can be loaded into VIDA and the atoms labeled with “Name” to show the location and type of all added color atoms.