AD_Validate

#!/usr/bin/env bash

## Validate the contents of the working directory for Automated Antibody Docking

UGAGE="""
Usage:

        ADValidate <working directory>
	
	The working directory should contain these things:

	    - The antibody PDB file 
	    - The glycan PDB file
	    - An initial configuration file
	    - If Use_Docker=True, there should also be a docker config file

	Return:

	    - The format is negotiable.
	    - Indication of success or failure and more info written to a log file.

        Notes:

	    - The two PDB files do not have name restrictions. 
	    - Their names should be in the configuration file.
"""

if [ -z "${1}" ] ; then
	echo "A working directory must be specified."
	echo "${USAGE}"
	exit 1
fi
if [ ! -d "${1}" ] ; then
        echo "The supplied name is not a directory."
	echo "The supplied name is: "
	echo "        ${1}  "
        echo "${USAGE}"
        exit 1
fi


#echo "About to call setup"
COMMAND="AD_Setup ${1}"
#echo "The command for calling AD_Setup is $COMMAND"
eval ${COMMAND} 
result=$?
if [ ${result} != "0" ] ; then
	echo "There was a problem setting up the working directory." 
	exit 1
fi


if [ ! -e "${1}/ad2config" ] ; then
        echo "The supplied directory does not contain an ad2config file."
	echo "The supplied name is: "
	echo "        ${1}  "
        echo "${USAGE}"
        exit 1
fi
export WORKDIR="${1}"
#echo "Workdir in validate is ${WORKDIR}"
export AD2CONFIG="${WORKDIR}/ad2config"
source "${AD2CONFIG}"
if [ -z "Antibody_File_Name" ] ; then
        echo "The ad2config file does not contain the name of the antibody file."
	echo "${USAGE}"
	exit 1
fi
if [ -z "Glycan_File_Name" ] ; then
        echo "The ad2config file does not contain the name of the glycan file."
	echo "${USAGE}"
	exit 1
fi

if [ "${Use_Docker}" == "True" ] ; then
#	if [ ! -e "${1}/ad2dockerconfig" ] ; then
#		echo "Use_Docker is set to True, but no ad2dockerconfig file is found."
#                echo "${USAGE}"
#                exit 1
#	fi
#	source "${1}/ad2dockerconfig"
	if [ -z "${Image}" ] ; then
		echo "Use_Docker is set to True, but no Image name is specified."
                echo "${USAGE}"
                exit 1
	fi
fi