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# Release Notes¶

## ROCS 3.2.1¶

September 2015

### New Features¶

• The default ROCS output format is now gzipped OEBinary, oeb.gz, in order to save disk space.
• ROCS will treat database list file entries that do not include a path as though they are relative to the list file location, rather than relative to the working directory. The hlmerge application will do the same with entries in lists of hit lists.

### Bug Fixes¶

• ROCS will no longer crash if an empty shape query is given.
• ROCS now writes a warning and skips any database molecule that have either missing xyz coordinates or are clearly 2 dimensional (z coordinates are all zero and dimension set to 2).
• ROCS now issues a warning and halts if -subrocs is true and the query is a grid. Grids are not supported for SubROCS.
• ROCS now issues a warning and halts if a query grid contains negative values. Grids with negative values are not supported in ROCS.
• Rocs_report will halt if it does not detect a query. Previously, an incorrect query mol was shown in the report when there was no query in the ROCS output file and -refmol was not specified.
• ROCS now writes files ending in _ref.grd, _ref.sq, _errors.sdf, _eon_input.oeb.gz to the directory defined when the -outputdir parameter is specified, along with all the other output files.
• ROCS now works with gzipped grid queries.
• ROCS now issues a warning to clarify that the -optchem parameter is ignored when -opt is false and -scoreonly is false.
• Setting the ROCS parameter -opt to false now turns off optimization directly. Previously, the parameter -scoreonly did this when set to true.
• The ROCS parameter -eon_input_size can now be set to 0, to indicate that no hit list is to be maintained and results are to be streamed, as previous documentation had indicated. Setting the parameter to 0 is required if -besthits and -maxhits are both 0.
• ROCS will terminate if a color force field specified by -chemff is not identical to that defined in a shape query file.
• The ROCS parameter -tanimoto_cutoff is is now restricted to the range 0.0 to 1.0.
• Subtan SD tags are removed if -subtan is false.
• The rocs_report application parameter -maxpages now properly counts the title page.
• The input file to the checkcff and makerocsdb applications is now checked to ensure it is 3-dimensional.

Note

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.

## ROCS 3.2.0¶

September 2013

### New Features¶

• The default hitlist format has been changed from sdf to oeb for increased functionality and decreased filesize. The output format is adjustable with the -oformat parameter.
• The -subrocs option has been added. The -subrocs starting points include 4 positions at every heavy atom in addition to the default inertial alignments.
• The rocs_report application has been added for making pdf reports from a hitlist.
• Now SD tags are prefixed with ROCS_. The tags are now optional with the sdTags parameter.
• vROCS now supports the manual merging of selected color atoms, to create a new color atom at their centroid.
• An improved molecule sketcher in vROCS now highlights unspecified stereochemistry in atoms and bonds when they occur in query structures, and requires the user to correct any unspecified stereochemistry before proceeding with a query.
• Numerous minor enhancements have been made to the user interface.

### Bug Fixes¶

• Multiconformer molecules from OMEGA could be split into multiple molecule when the OMEGA output was written to .sdf instead of .oeb and had invertible stereocenters. Now ROCS will keep these .sdf multiconformer molecules together.
• Color atoms are now removed from ROCS hitlists for all output formats. Color atoms can be added to hitlists using the checkcff utility.
• Fixing bug for when eon_input_size is larger than -best, now it increase -best when needed.
• Now when ROCS hits are being streamed with -besthits 0, then eon_input molecules will be as well.
• Fixed a bug where sometimes .sdf files would get warts applied twice.
• Cleaned up missing entries or zeroes for Subtan and the conf index in the report file.
• Fixed a bug where report file entries could be duplicated with the -scoreonly flag.
• Fixed a bug where -report one could cause problems writing status files.
• Failure cases have been cleaned up. Incorrect and incompatible command line flags will cause ROCS to exit quickly and cleanly.
• Fixed a bug in vROCS in which files saved with a filename ending in ”.sq.gz” would have an additional ”.sq” appended to the end of the name.
• Fixed a problem where ROCS database files (.rocsdb) were not being read properly by vROCS.

### Other changes¶

• PVM (parallel virtual machine) is no longer supported. OpenMPI version 1.6 is supported on all platforms. The -mpi_np and -mpi_hostfile flags are now used to run ROCS in MPI mode. These new flags replace the oempirun script.
• This will be the last release to support SuSe 10.

## ROCS 3.1.2¶

June 2011

### Bug Fixes¶

• Fixed a bug where EON input files were not generated correctly when using multiple queries.
• Fixed a bug where the query was written to the EON input file too many times.
• Fixed a bug concerning validation runs failing in vROCS.
• Fixed a bug where application could crash on exit when using the -maxhits option
• Fixed a bug concerning output of color atoms to non-OEB format. Now precalculated color will only pass through if the output format is OEB.
• Now ROCS will not write EON_input if the ROCS input is a shape query. Only real molecules can be used as ROCS input when writing EON_input.

## ROCS 3.1.1¶

February 2011

### New Features¶

• Added new platform: RedHat 6 x64

### Bug Fixes¶

• Fixed a bug running user-provided command line options in vROCS.
• Fixed a bug of reporting erroneous error messages.
• Fixed a problem concerning DLL dependencies on Windows.

## ROCS 3.1.0¶

November 2010

### New Features¶

• Added new platforms: Ubuntu 10 x64 and Sled 11 x64.
• ROCS now works with named pipes created using mkfifo on non-Windows platforms.
• The hlmerge application was not opening lists unless the file had an extension of ”.list”. Now hlmerge will attempt to open any non-molecule file as a list.

### Bug Fixes¶

• Fixed a bug related to saving screenshots on Linux.
• Fixed a bug related to adding color atoms to a query.
• Fixed a bug related to the contour slider losing focus.
• Fixed a bug related to two contours overlapped by default causing display artifacts.
• Removed spurious warnings for “-auto” and “-rqedbmols”.
• Fixed a bug in chunker that was causing the output file to be empty.
• Fixed a bug where the “-reportfile” option was being ignored.
• Fixed a bug where the “-maxconfs” option was being ignored.
• Fixed a bug in the coloring of aldehydes.
• Fixed a bug where multiple processor jobs would print “Slave started on host Host”. The message now prints the proper hostname for the process.
• Fixed a bug where using “-stats best” was causing an empty report file.

## ROCS 3.0.0¶

November 2009

### New Features¶

• ROCS now comes with a new graphical application, vROCS, for setting up and testing queries. There are new sections in the manual that describe vROCS and new tutorials that walk you through using it. Please note that while vROCS makes creating complex queries much more manageable, it is not required. The rocs command line app will continue to be the core of ROCS. vROCS is not available on AIX or Solaris
• vROCS saves queries as Shape Query (.sq) files. Running ROCS from the command line will not accept Shape Query files as well as all the previously supported file formats.
• ROCS now supports MPI as well as PVM for distributed job management. This new feature is built on top of Open MPI and doesn’t require any additional installs on cluster machines. Please have a look at the openmpi section. OpenMPI is not supported on Microsoft Windows, AIX or Solaris

### Bug Fixes¶

• Fixed a bug that could cause a crash when piping molecules into ROCS via stdin.
• Updated documentation to show that XYZ (.xyz) files are also suitable as ROCS queries.
• Fixed a bug when using .list files, the progress bar was not reset.

## ROCS 2.4.2¶

September 2009

### Bug Fixes¶

• Fixed a bug that caused a crash on Windows when trying to load an external CFF file. (Case 3413)
• Fixed the additional utilities so that they only require a “rocs” license and not an “oechem” license. (Cases 3350, 3435, 3440)
• Removed some extraneous command line arguments from “checkcff” (Case 3392)

## ROCS 2.4.1¶

May 2009

### New Features¶

• As of this release, the new default score for ranking is the TanimotoCombo, the sum of Shape Tanimoto and the new Color Tanimoto. Version 1.7 of the Shape Toolkit introduced new color scores based on Tanimoto. This version of ROCS incorporates all the new scores including Color Tanimoto and the resulting Color Tversky scores. Additionally all the Tversky scores are now named relative to either the Ref(erence) or Fit molecule, instead of the former query and dbase labels. This move is designed to standardize the names used in ROCS and the Shape Toolkit.
• In order to facilitate all the new scores, the Report file columns have been renamed and re-ordered.
• ROCS no longer counts the input file prior to starting the calculation. Progress is now based on file size not number of molecules processed. This alleviates a problem with very long start-up times for extremely large database files.
• This release adds ROCS to the set of applications that now use a common script in openeye/bin to determine the appropriate architecture and run the appropriate binary.
• On Windows, there is now an installer that installs the documentation and sets up a command prompt to facilitate running the ROCS command line.

### Bug Fixes¶

• Fixed a bug that caused a crash when trying to write an empty hitlist.

## ROCS 2.3.1¶

August 2007

### Bug fixes¶

• Fixed a bug reading .rocsdb files.
• Fixed a subtle bug that caused -report one to only work if -reportfile is also used. Using -report one will now create a single report file named based on the -prefix given.
• Removed an annoying but benign warning about the now deprecated and removed -allcolor flag.
• Fixed a bug where the -eon_maxconfs flag expected a value greater than 1. Now any value greater than zero is valid.

## ROCS 2.3.0¶

August 2007

### Enhancements¶

• 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.

## ROCS 2.2¶

March 2006

### 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:

• title just like previous behavior, added index to end of title
• sdtag Conf idx is placed in SD tag <ConfIndex>
• both combination of previous two places
• none conformer indices are not marked on output.

Note

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

-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 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.

### 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.