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