SILCS-Biologics Directory Structure

silcs-biologics creates the below directories in $WORKDIR. By default, $WORKDIR is the directory in which silcs-biologics was run. Otherwise, $WORKDIR is determined by the parameter passed to silcs-biologics through the command line option workdir=.

Step 1 SILCS FragMap results will be in 1_fragmap.$job_id/,

                                      |>>> 1_setup
                      |>>> $prot1 >>> |>>> 2a_run_gcmd
                      |               |>>> 2b_gen_maps
                      |               |>>> silcs_fragmaps_$prot1
1_fragmap.$job_id >>> |>>> $prot2 ...
                      |>>> $prot3 ...

Step 2 SILCS-PPI results will be in 1_ppi.$job_id/,

                                         |>>> maps1
                  |>>> $prot1_$prot1 >>> |>>> maps2
                  |                      |>>> 3_ppi
2_ppi.$job_id >>> |>>> $prot1_$prot2 ...
                  |>>> $prot1_$prot3 ...
                  |>>> $prot2_$prot1 ...
                  |>>> $prot2_$prot2 ...
                  |>>> $prot2_$prot3 ...
                  |>>> $prot3_$prot1 ...
                  |>>> $prot3_$prot2 ...
                  |>>> $prot3_$prot3 ...

Step 3 SILCS-Hotspots excipient docking results will be in 3_excipients.$job_id/,

                          |>>> mols
                          |>>> $prot1 >>> 4_hotspots >>> ***
3_excipients.$job_id >>>  |>>> $prot2 ...
                          |>>> $prot3 ...

and Step 4 reporting will be in 4_report.$job_id,

4_report.$job_id