Subsections

A.3 ROCS 2.2

March 2006

A.3.1 Enhancements

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:
- -conflabel title just like previous behavior, added index to end of title
- -conflabel sdtag Conf idx is placed in SD tag <ConfIndex>
- -conflabel both combination of previous two places
- -conflabel none conformer indices are not marked on output.
Note that "sdtag" is only useful if the output file is SDF or OEB.
Several new flags have been added to allow more complete constrol 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:
```
   -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.
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:
```
   -dbase .sdf
```
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 and error and stop.
Changed the way untitled ref and fit molecules are named so that in hits files, they can be distiguished 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 Vida2 and the atoms labeled with "Name" to show the location and type of all added color atoms.

A.3.2 Bug fixes

Added check for untitled reference (query) molecules. If no title is found, a title similar to "untitled-ref-N" is applied. This address a bug in EON caused by blank titles in ROCS queries, resulting in broken SD tags in the input to EON.
Fixed a bug that caused molecules of high-symmetry to be skipped. If a molecule's moments of inertia were all equal, it would be skipped. If the molecule was the reference, no hits would be found.
Fixed a bug in random starts.