#!/bin/sh

# assign local directories 

pipsa_distr_dir=/home/gabdourf/pipsa/
pipsa_wrk_dir=/home/gabdourf/pipsa/exa/PHR/
export pipsa_distr_dir
export pipsa_wrk_dir


# assign local executables 

path_to_grid_bin=/sw/mcm/app/grid/grid22a_linux/
path_to_uhbd_exe=/sw/mcm/app/uhbd/uhbd_linux_pp/uhbd065_G77
path_to_apbs_exe=/sw/mcm/app/apbs/dist-0.3.1.linux/bin/i686-pc-linux/apbs
path_to_phylip_bin=/sw/mcm/app/phylip/bin.linux/
export path_to_uhbd_exe
export path_to_grid_bin
export path_to_apbs_exe
export path_to_phylip_bin


# Run analytical electrostatic similarity calculations

$pipsa_distr_dir/scr/do_pipsa_analyt_sim $pipsa_distr_dir/ $pipsa_wrk_dir/pdbs/

# UHBD electrostatic similarity calculations

$pipsa_distr_dir/scr/do_pipsa_UHBD_prep $pipsa_distr_dir/ $pipsa_wrk_dir/
$pipsa_distr_dir/scr/do_pipsa_UHBD_grids $pipsa_distr_dir/ $pipsa_wrk_dir/uhbd/ $path_to_uhbd_exe
$pipsa_distr_dir/scr/do_pipsa_sim $pipsa_distr_dir/ $pipsa_wrk_dir/uhbd/
# results in the directory $pipsa_wrk_dir/uhbd/

# APBS electrostatic similarity calculations

$pipsa_distr_dir/scr/do_pipsa_APBS_prep $pipsa_distr_dir/ $pipsa_wrk_dir/
$pipsa_distr_dir/scr/do_pipsa_APBS_grids $pipsa_distr_dir/ $pipsa_wrk_dir/apbs/ $path_to_apbs_exe
$pipsa_distr_dir/scr/do_pipsa_sim $pipsa_distr_dir/ $pipsa_wrk_dir/apbs/

# GRID probe PO4 interaction field similarity calculations

$pipsa_distr_dir/scr/do_pipsa_GRID_prep $pipsa_distr_dir/ $pipsa_wrk_dir/
$pipsa_distr_dir/scr/do_pipsa_GRID_grids $pipsa_distr_dir/ $pipsa_wrk_dir/grid/ $path_to_grid_bin/
$pipsa_distr_dir/scr/do_pipsa_sim $pipsa_distr_dir/ $pipsa_wrk_dir/grid/


# All phylogenic tree calculations

$pipsa_distr_dir/scr/do_pipsa_phylip $pipsa_distr_dir/ $pipsa_wrk_dir/pdbs/ $path_to_phylip_bin
$pipsa_distr_dir/scr/do_pipsa_phylip $pipsa_distr_dir/ $pipsa_wrk_dir/uhbd/ $path_to_phylip_bin
$pipsa_distr_dir/scr/do_pipsa_phylip $pipsa_distr_dir/ $pipsa_wrk_dir/apbs/ $path_to_phylip_bin
$pipsa_distr_dir/scr/do_pipsa_phylip $pipsa_distr_dir/ $pipsa_wrk_dir/grid/ $path_to_phylip_bin


# Save and remove grid files (because they are too large for distribution)

cd $pipsa_wrk_dir/../
tar cvf PHR_grids_linux.tar PHR/*/names PHR/*/*.grd PHR/pdbs/*.pdb PHR/pdbs/pdbnames
\rm -f PHR/*/*.grd

# Test Whatif calculations. 
# We already have UHBD readable pdb files in pdbs/ subdirectory.
# This part will produce them in whatif/ subdirectory. 

path_to_whatif_exe=path_to_whatif_exe=/sw/mcm/app/Whatif.Linux/whatif
export path_to_whatif_exe
$pipsa_distr_dir/scr/do_pipsa_WHATIF $pipsa_distr_dir/ $pipsa_wrk_dir/ $path_to_whatif_exe

