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#!/bin/bash
echo "$(pwd)"
currentVersion="0.9"
protein="false"
ligand="false"
docking="false"
visualisations="false"
interactions="false"
proteinPath=""
ligandPath=""
pdfPath=""
smile=""
name="report"
config=""
usage()
{
cat <<EOF
Curie-CLI
Description: OwO.
Usage: curie [flags] or curie [-a] [arg] [-s] [arg]
-d Perform Docking using AutoDock Vina
-p Visualisations using PyMOL
-i Protein-Ligand Interactions using PLIP
-s SMILES Code for Ligand
-n Name for ligand if using the -s option
-r Specify Receptor file path (PDBQT Format Only!)
-l Specify Ligand file path (PDBQT Format Only!)
-c Specify AutoDock Vina Configuration File (TXT Format Only!)
-h Show the help
-v Get the tool version
Examples:
./main.sh -v
./main.sh -v
EOF
}
while getopts "r:l:s:n:c:vhdip" opt; do
case "$opt" in
\?) echo "Invalid option: -$OPTARG" >&2
exit 1
;;
h) usage
exit 0
;;
v) echo "Version $currentVersion"
exit 0
;;
u)
getConfiguredClient || exit 1
checkInternet || exit 1
update
exit 0
;;
d)
docking="true"
;;
i)
interactions="true"
;;
p)
visualisations="true"
;;
s)
smile="$OPTARG"
;;
n)
name="$OPTARG"
;;
r)
proteinPath="$OPTARG"
;;
l)
ligandPath="$OPTARG"
;;
c)
config="$OPTARG"
;;
a)
artist="true"
if [[ "$(echo "$@" | grep -Eo "\-s")" == "-s" ]];then song="true";fi # wont go through both options if arg spaced and not quoted this solves that issue (dont need this but once had bug on system where it was necessary)
if [[ "$(echo "$@" | grep -Eo "\-f")" == "-f" ]];then filePath=$(echo "$@" | grep -Eo "\-f [ a-z A-Z / 0-9 . \ ]*[ -]?" | sed s/-f//g | sed s/-//g | sed s/^" "//g);fi
;;
#s)
# song="true"
# if [[ "$(echo "$@" | grep -Eo "\-a")" == "-a" ]];then artist="true";fi # wont go through both options if arg spaced and not quoted this solves that issue (dont need this but once had bug on system where it was necessary)
# if [[ "$(echo "$@" | grep -Eo "\-f")" == "-f" ]];then filePath=$(echo "$@" | grep -Eo "\-f [ a-z A-Z / 0-9 . \ ]*[ -]?" | sed s/-f//g | sed s/-//g | sed s/^" "//g);fi
# ;;
:) echo "Option -$OPTARG requires an argument." >&2
exit 1
;;
esac
done
if [[ $# == "0" ]]; then
usage ## if calling the tool with no flags and args chances are you want to return usage
exit 0
elif [[ $# == "1" ]]; then
if [[ $1 == "update" ]]; then
getConfiguredClient || exit 1
checkInternet || exit 1
update || exit 1
exit 0
elif [[ $1 == "help" ]]; then
usage
exit 0
fi
fi
if [[ $docking == "true" ]]; then
if [[ $proteinPath != "" ]]; then
if [[ $smile != "" ]] || [[ $ligandPath != "" ]]; then
if [[ $config == "" ]]; then
echo "Configuration File Not Specified!"
exit 1
else
dockingCheck="true"
fi
else
echo "WTF Only Protein!"
exit 1
fi
fi
fi
if [[ $smile != "" ]]; then
if [[ $name == "" ]]; then
name="ligand"
obabel -:"$smile" --gen3d -opdbqt -O$name.pdbqt
ligandPath="$name.pdbqt"
fi
fi
if [[ $dockingCheck == "true" ]]; then
echo ""
vina --receptor $proteinPath --ligand $ligandPath --config $config
fi
if [[ $interactions == "true" ]]; then
file=$(echo "$ligandPath" | cut -f 1 -d '.')
python3 ./get-best.py -p $proteinPath -l "$(echo $file)_out.pdbqt"
echo "Running PLIP"
plip -f best.pdb -qpxy
echo "Getting Dock Score"
python3 ./get_dock_score.py -l "$(echo $file)_out.pdbqt" -p $proteinPath > report.md
echo "Making partial report"
python3 ./makeReport.py --input . >> report.md
if [[ $visualisations == "true" ]]; then
echo "Creating Visualisations"
python3 ./quick-ligand-protein.py -p $proteinPath -l "$(echo $file)_out.pdbqt"
python3 ./add-pictures.py >> report.md
fi
echo "Generating PDF"
pandoc -V geometry:margin=1in report.md --pdf-engine=xelatex -o $name.pdf
fi
#echo "$proteinPath and $ligandPath and $docking and $interactions and $visualisations"
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