From 5ad24bfceb8a22a4940c6d076ea3befc928ab1cd Mon Sep 17 00:00:00 2001
From: Navan Chauhan <navanchauhan@gmail.com>
Date: Tue, 22 Sep 2020 13:28:48 +0530
Subject: Increased Speed by 50%

---
 app/scripts/main.sh | 160 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 160 insertions(+)
 create mode 100755 app/scripts/main.sh

(limited to 'app/scripts/main.sh')

diff --git a/app/scripts/main.sh b/app/scripts/main.sh
new file mode 100755
index 0000000..b1c789c
--- /dev/null
+++ b/app/scripts/main.sh
@@ -0,0 +1,160 @@
+#!/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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