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.
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
How to get results of the database to a pdb file(s)?
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
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!*/ .exit
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
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