.. _biologics_directory_structure:

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