#!/bin/sh

# here your own locations should be assigned 
# -----------------------------------------------------------------------------------
# assign local directories 

# anywhere installed, for example, 
pipsa_distr_dir=/home/yourname/pipsa/
# the directory below is a subdirectory only for distribution example, 
# in your own cases - can be any (writable for you)
pipsa_wrk_dir=/home/yourname/pipsa/exa/PHR/
export pipsa_distr_dir
export pipsa_wrk_dir

# assign local executables 

path_to_grid_bin=/software/grid22a_linux/
path_to_uhbd_exe=/software/uhbd/uhbd065_G77
path_to_apbs_exe=/software/apbs/bin/i686-pc-linux/apbs
path_to_phylip_bin=/software/phylip/
export path_to_uhbd_exe
export path_to_grid_bin
export path_to_apbs_exe
export path_to_phylip_bin

# The rest is independent of local assignments 
# -----------------------------------------------------------------------------------


# 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