Install

#!/usr/bin/env bash

USAGE="""
Usage: 

    Install <install path>

    For example, 

        Install /usr/local

    will install the executables into /usr/local/bin.
"""

if [[ -z "${1}" ]] ; then
	echo "Must supply location for installation."
	echo "${USAGE}"
	exit 1
fi

if [ ! -d "${1}/bin" ] ; then 
	mkdir ${1}/bin || echo "Cannot make directory ${1}/bin." && exit 1
fi

cp  0.configure/setup_AD_Directory \
    1.prepare_antibody/align_antibody/align  \
    1.prepare_antibody/generate_antibody_pdbqt  \
    2.prepare_glycan/generate_glycan_pdbqt \
    2.prepare_glycan/get_flexible_bond_info \
    3.prepare_docking_directories/prepare_AD_docking_directory \
    4.run_docking/run_AD_docking \
    4.run_docking/start_all_docking_jobs \
    5.analyze_results/clustering \
    5.analyze_results/plot_results \
    5.analyze_results/reorderpdb \
    5.analyze_results/write_output \
    6.check_status/get_AD_docking_status \
    6.check_status/Check_Status \
    AD_Evaluate  \
    AD_Get_Status  \
    AD_Run_AD  \
    AD_Setup  \
    AD_Validate \
    AD_Analyze \
    ${1}/bin