Rosetta allows us to generate output in several ways, most of them include 'regular' or compressed pdb files. (silent files, pdb_gz, etc) The newly added feature of outputting results to a database allows users to interact with Rosetta's output in a much more convenient way, eliminating most of the needs for clumsy scripts, file corruption, etc.. The current implementation permits 2 formats of databases - mysql and sqlite.

Creating a Rosetta run with a Database output

In order to use the database output feature you have to include 2 basic flags: (for mysql you will also need the following flags - mysql::host, mysql::user, mysql::password, mysql::port) For the purpose of this tutorial , I will concentrate on sqlite3 which suites best our needs and is much simpler to use)

-out:use_database - indicating you are interested in a database output format

-inout:dbms:database_name - the database filename

-inout:database_mode - default is sqlite3 so we won’t touch that.

Using these command line flags is fairly simple, for example:

$ROSETTA_BIN/<protocol>.linuxgccrelease -s 1SFI_cyc.pdb 
-database $ROSETTA_DB -ex1 -ex2 -use_input_sc -nstruct  1 -out:use_database -inout:dbms:database\_name results.db

Getting structures out of the database

How to get results of the database to a pdb file(s)?

Getting all the decoys out of the database

In order to get all the structures out of the database , you can use the score_jd2 flag with the following options:

-inout:dbms:database_name file.db -in:use_database -out:pdb

Getting specific decoys out of the database

If you want to acquire only a subset of structures (for example, the ones that have total_score<0) you just input a query to sqlite3: (verify you have it installed first...)

sqlite3 results.db < query.txt

The query file should look like (remove comments /* */ when run):

.output structures.txt  /*set the output to file mode*/
select tag from structures;  /*the query, should output tag names only!*/

Next, just feed the query output to the -in:file:tags tag, could be in the following way:

$ROSETTA_BIN/score_jd2.linuxgccrelease -inout:dbms:database\_name results.db 
-in:use_database -out:pdb -in:file:tags `cat structures.txt` -database $ROSETTA_DB

Moving old results to a database file

Again , we'll use the score_jd2 application to rescore a set of pdb files and directing the output to a database:

score_jd2.linuxgccrelease -s decoy_* -database $ROSETTA_DB -out:use_database -inout:dbms:database\_name results.db

Useful queries

TODO ...


Simple sqlite examples

See Also