Increased Speed by 50%

6 files changed, 836 insertions, 0 deletions

diff --git a/app/scripts/add-pictures.py b/app/scripts/add-pictures.py
new file mode 100644
index 0000000..95079f0
--- /dev/null
+++ b/app/scripts/add-pictures.py
@@ -0,0 +1,6 @@
+print("## Figures", end="\n\n")
+
+print("![Back View](output-back.png){width=100%}", end="\n\n")
+print("![Front View](output-front.png){width=100%}", end="\n\n")
+print("![Close Up View of the Back](closeup-back.png){width=100%}", end="\n\n")
+print("![Close Up View of the Front](closeup-front.png){width=100%}", end="\n\n")
\ No newline at end of file
diff --git a/app/scripts/get-best.py b/app/scripts/get-best.py
new file mode 100644
index 0000000..b5f69a8
--- /dev/null
+++ b/app/scripts/get-best.py
@@ -0,0 +1,45 @@
+#!/usr/bin/python3
+import argparse
+import pymol2
+import re
+
+#################
+# Configuration #
+#################
+
+version = "1.0"
+desc_text = "PyMol Quick Visualtion " + version
+
+parser = argparse.ArgumentParser(description=desc_text)
+parser.add_argument("-p","--protein",help="Path to protein file")
+parser.add_argument("-l","--ligand",help="Path to ligand_out file")
+
+args = parser.parse_args()
+
+def li(s):
+    #log.info(s)
+    None
+
+
+if args.protein == None:
+    print("Error: Please specify protein file")
+    exit(1)
+if args.ligand == None:
+    print("Error: Please specify ligand file")
+    exit(1)
+
+print("Getting Best ligand from",args.protein,args.ligand)
+
+protein = args.protein
+ligand = args.ligand
+
+session = pymol2.PyMOL()
+session.start()
+cmd = session.cmd
+cmd.load(protein,'pro')
+cmd.load(ligand,'lig')
+cmd.split_states('lig')
+
+#fname = re.sub(r'^.*?/', '', protein.replace(".pdbqt","")) + "-" + re.sub(r'^.*?/', '', ligand.replace(".pdbqt","")) + ".pdb" 
+
+cmd.save("best.pdb","pro lig_0001")
diff --git a/app/scripts/get_dock_score.py b/app/scripts/get_dock_score.py
new file mode 100644
index 0000000..c8b87d5
--- /dev/null
+++ b/app/scripts/get_dock_score.py
@@ -0,0 +1,46 @@
+#!/usr/bin/python3
+
+import argparse
+
+parser = argparse.ArgumentParser(description="Get Docking Score")
+parser.add_argument("-p","--protein",help="Path to protein file")
+parser.add_argument("-l","--ligand",help="Path to ligand_out file")
+
+args = parser.parse_args()
+
+if args.protein == None:
+    print("Error: Please specify protein file")
+    exit(1)
+if args.ligand == None:
+    print("Error: Please specify ligand file")
+    exit(1)
+
+
+protein = args.protein
+ligand = args.ligand
+
+from os.path import basename
+
+print("# " + str(basename(protein)).replace(".pdbqt","") + "-" + str(basename(ligand)).replace("_out.pdbqt",""), end="\n\n")
+
+from tabulate import tabulate
+
+file = open(ligand, "r")
+lines = file.readlines()
+results = []
+i = 1
+for line in lines:
+    ta = []
+    if line.find('REMARK VINA') == 0 and line.split()[3] != "":
+        l = line.split()
+        ta.append(i)
+        ta.append(l[3])
+        ta.append(l[4])
+        ta.append(l[5])
+        i += 1
+    if ta != []:
+        results.append(ta)
+
+print("## Docking Scores",end="\n\n")
+print(tabulate(results,headers=["No.","Affinity","rmsd l.b","rmsd u.b"]))
+print("",end="\n\n")
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"
diff --git a/app/scripts/makeReport.py b/app/scripts/makeReport.py
new file mode 100644
index 0000000..4f693ac
--- /dev/null
+++ b/app/scripts/makeReport.py
@@ -0,0 +1,458 @@
+#!/usr/bin/python3
+import argparse
+
+parser = argparse.ArgumentParser(description="Make Report Helper Script")
+parser.add_argument("-i", "--input", help="Path to report folder")
+
+args = parser.parse_args()
+
+if args.input == None:
+    print("Error: Please specify path")
+    exit(1)
+
+path = args.input
+# path = '/Users/navanchauhan/Desktop/nCOV-19/scripts/pymol/test/'
+
+import untangle
+from tabulate import tabulate
+
+# import sys
+# report = path + "report.md"
+# sys.stdout = open(report, 'w')
+
+from os import listdir
+from os.path import isfile, join
+
+onlyfiles = [f for f in listdir(path) if isfile(join(path, f))]
+image = ""
+for x in onlyfiles:
+    if ".png" in x and "UNL" in x:
+        image = x
+import os
+
+fname = os.path.join(path, "report.xml")
+
+doc = untangle.parse(fname)
+
+hi, hb, wb, sb, ps, pc, hab, mc = 0, 0, 0, 0, 0, 0, 0, 0
+
+indexForUNL = 0
+
+for x in doc.report.bindingsite:
+    if x.identifiers.longname.cdata == "UNL":
+        break
+    else:
+        indexForUNL += 1
+
+
+name = doc.report.pdbid.cdata
+# print(("# " + (name.replace("_"," ")).replace("PROTEIN","")), end="\n\n")
+fallback = 0
+
+print("## Visualisation", end="\n\n")
+print(f"![]({image})", end="\n\n")
+
+natural_ligands = []
+showNaturalLigands = True
+
+try:
+    for x in range(len(doc.report.bindingsite)):
+        if doc.report.bindingsite[x]["has_interactions"] == "True" and x != indexForUNL:
+            natural_ligands.append(x)
+except:
+    fallback == 1
+
+if natural_ligands == []:
+    showNaturalLigands == False
+
+for ligand in natural_ligands:
+    print("### Natural Ligand " + str(ligand+1), end="\n\n")
+    if doc.report.bindingsite[ligand].interactions.hydrophobic_interactions.cdata == "":
+        print("No Hydrophobic Interactions Found", end="\n\n")
+    else:
+        print("#### Hydrophobic Interactions", end="\n\n")
+        tableBody = []
+        tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
+        i = 1
+        for x in doc.report.bindingsite[
+            ligand
+        ].interactions.hydrophobic_interactions.hydrophobic_interaction:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.ligcarbonidx.cdata,
+                x.protcarbonidx.cdata,
+            ]
+            i += 1
+            tableBody.append(l)
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+    if doc.report.bindingsite[ligand].interactions.hydrogen_bonds.cdata == "":
+        print("No Hydrogen Bonds Found", end="\n\n")
+    else:
+        print("## Hydrogen Bonds", end="\n\n")
+        tableBody = []
+        tableHeaders = [
+            "No.",
+            "Res.",
+            "AA",
+            "Dist H-A",
+            "Dist D-A",
+            "Don Angle",
+            "Protisdon?",
+            "Sidechain?",
+            "D. Atom",
+            "A. Atom",
+        ]
+        i = 1
+        for x in doc.report.bindingsite[
+            ligand
+        ].interactions.hydrogen_bonds.hydrogen_bond:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist_h_a.cdata,
+                x.dist_d_a.cdata,
+                x.don_angle.cdata,
+                x.protisdon.cdata,
+                x.sidechain.cdata,
+            ]
+            l.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
+            l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
+            i += 1
+            tableBody.append(l)
+            # print(i, x.resnr.cdata, x.restype.cdata, x.dist_h_a.cdata, x.dist_d_a.cdata, x.don_angle.cdata, x.protisdon.cdata, x.sidechain.cdata, (x.donoridx.cdata + "[" + x.donortype.cdata + "]"), (x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+print("## Docked Ligand Interactions", end="\n\n")
+
+try:
+    if (
+        doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata
+        == ""
+    ):
+        print("No Hydrophobic Interactions Found", end="\n\n")
+    else:
+        print("**Hydrophobic Interactions Found**", end="\n\n")
+        hi = 1
+except AttributeError:
+    fallback = 1
+
+if fallback == 0:
+    if (
+        doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata
+        == ""
+    ):
+        print("No Hydrophobic Interactions Found", end="\n\n")
+    else:
+        print("**Hydrophobic Interactions Found**", end="\n\n")
+        hi = 1
+    if doc.report.bindingsite[indexForUNL].interactions.hydrogen_bonds.cdata == "":
+        print("No Hydrogen Bonds Found", end="\n\n")
+    else:
+        print("**Hydrogen Bonds Found**", end="\n\n")
+        hb = 1
+    if doc.report.bindingsite[indexForUNL].interactions.water_bridges.cdata == "":
+        print("No Water Bridges Found", end="\n\n")
+    else:
+        print("**Water Bridges Found**", end="\n\n")
+        wb = 1
+    if doc.report.bindingsite[indexForUNL].interactions.salt_bridges.cdata == "":
+        print("No Salt Bridges Found", end="\n\n")
+    else:
+        print("**Salt Bridges Found**", end="\n\n")
+        sb = 1
+    if doc.report.bindingsite[indexForUNL].interactions.pi_stacks.cdata == "":
+        print("No Pi Stacks Found", end="\n\n")
+    else:
+        print("**Pi Stacks Found**", end="\n\n")
+        ps = 1
+    if (
+        doc.report.bindingsite[indexForUNL].interactions.pi_cation_interactions.cdata
+        == ""
+    ):
+        print("No Pi Cation Interactions Found", end="\n\n")
+    else:
+        print("**Pi Cation Interactions Found**", end="\n\n")
+        pc = 1
+    if doc.report.bindingsite[indexForUNL].interactions.halogen_bonds.cdata == "":
+        print("No Halogen Bonds Found", end="\n\n")
+    else:
+        print("** Halogen Bonds Found**", end="\n\n")
+        hab = 1
+    if doc.report.bindingsite[indexForUNL].interactions.metal_complexes.cdata == "":
+        print("No Metal Complexes Found", end="\n\n")
+    else:
+        print("**Metal Complexes Found**", end="\n\n")
+        mc = 1
+
+if fallback == 1:
+    if doc.report.bindingsite.interactions.hydrophobic_interactions.cdata == "":
+        print("No Hydrophobic Interactions Found", end="\n\n")
+    else:
+        print("**Hydrophobic Interactions Found**", end="\n\n")
+        hi = 1
+    if doc.report.bindingsite.interactions.hydrogen_bonds.cdata == "":
+        print("No Hydrogen Bonds Found", end="\n\n")
+    else:
+        print("**Hydrogen Bonds Found**", end="\n\n")
+        hb = 1
+    if doc.report.bindingsite.interactions.water_bridges.cdata == "":
+        print("No Water Bridges Found", end="\n\n")
+    else:
+        print("**Water Bridges Found**", end="\n\n")
+        wb = 1
+    if doc.report.bindingsite.interactions.salt_bridges.cdata == "":
+        print("No Salt Bridges Found", end="\n\n")
+    else:
+        print("**Salt Bridges Found**", end="\n\n")
+        sb = 1
+    if doc.report.bindingsite.interactions.pi_stacks.cdata == "":
+        print("No Pi Stacks Found", end="\n\n")
+    else:
+        print("**Pi Stacks Found**", end="\n\n")
+        ps = 1
+    if doc.report.bindingsite.interactions.pi_cation_interactions.cdata == "":
+        print("No Pi Cation Interactions Found", end="\n\n")
+    else:
+        print("**Pi Cation Interactions Found**", end="\n\n")
+        pc = 1
+    if doc.report.bindingsite.interactions.halogen_bonds.cdata == "":
+        print("No Halogen Bonds Found", end="\n\n")
+    else:
+        print("** Halogen Bonds Found**", end="\n\n")
+        hab = 1
+    if doc.report.bindingsite.interactions.metal_complexes.cdata == "":
+        print("No Metal Complexes Found", end="\n\n")
+    else:
+        print("**Metal Complexes Found**", end="\n\n")
+        mc = 1
+
+if fallback == 0:
+    if hi == 1:
+        print("## Hydrophobic Interactions", end="\n\n")
+        tableBody = []
+        tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
+        i = 1
+        for x in doc.report.bindingsite[
+            indexForUNL
+        ].interactions.hydrophobic_interactions.hydrophobic_interaction:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.ligcarbonidx.cdata,
+                x.protcarbonidx.cdata,
+            ]
+            i += 1
+            tableBody.append(l)
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+    if hb == 1:
+        print("## Hydrogen Bonds", end="\n\n")
+        tableBody = []
+        tableHeaders = [
+            "No.",
+            "Res.",
+            "AA",
+            "Dist H-A",
+            "Dist D-A",
+            "Don Angle",
+            "Protisdon?",
+            "Sidechain?",
+            "D. Atom",
+            "A. Atom",
+        ]
+        i = 1
+        for x in doc.report.bindingsite[
+            indexForUNL
+        ].interactions.hydrogen_bonds.hydrogen_bond:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist_h_a.cdata,
+                x.dist_d_a.cdata,
+                x.don_angle.cdata,
+                x.protisdon.cdata,
+                x.sidechain.cdata,
+            ]
+            l.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
+            l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
+            i += 1
+            tableBody.append(l)
+            # print(i, x.resnr.cdata, x.restype.cdata, x.dist_h_a.cdata, x.dist_d_a.cdata, x.don_angle.cdata, x.protisdon.cdata, x.sidechain.cdata, (x.donoridx.cdata + "[" + x.donortype.cdata + "]"), (x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+    if sb == 1:
+        print("## Salt Bridges", end="\n\n")
+        tableBody = []
+        tableHeaders = [
+            "Index",
+            "Residue",
+            "AA",
+            "Distance",
+            "Protein positive?",
+            "Ligand Group",
+            "Ligand Atoms",
+        ]
+        i = 1
+        for x in doc.report.bindingsite[
+            indexForUNL
+        ].interactions.salt_bridges.salt_bridge:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.protispos.cdata,
+                x.lig_group.cdata,
+            ]
+            atoms = []
+            for y in x.lig_idx_list.idx:
+                atoms.append(y.cdata)
+            l.append(atoms)
+            i += 1
+            tableBody.append(l)
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+    if pc == 1:
+        print("## Pi Cation Interactions", end="\n\n")
+        tableBody = []
+        tableHeaders = ["Index", "Residue", "AA", "Distance", "Prot charged?", "Atoms"]
+        i = 1
+        for x in doc.report.bindingsite[
+            indexForUNL
+        ].interactions.pi_cation_interactions.pi_cation_interaction:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.offset.cdata,
+                x.protcharged.cdata,
+            ]
+            atoms = []
+            for y in x.lig_idx_list.idx:
+                atoms.append(y.cdata)
+            l.append(atoms)
+            i += 1
+            tableBody.append(l)
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+elif fallback == 1:
+    if hi == 1:
+        print("## Hydrophobic Interactions", end="\n\n")
+        tableBody = []
+        tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
+        i = 1
+        for (
+            x
+        ) in (
+            doc.report.bindingsite.interactions.hydrophobic_interactions.hydrophobic_interaction
+        ):
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.ligcarbonidx.cdata,
+                x.protcarbonidx.cdata,
+            ]
+            i += 1
+            tableBody.append(l)
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+    if hb == 1:
+        print("## Hydrogen Bonds", end="\n\n")
+        tableBody = []
+        tableHeaders = [
+            "No.",
+            "Res.",
+            "AA",
+            "Dist H-A",
+            "Dist D-A",
+            "Don Angle",
+            "Protisdon?",
+            "Sidechain?",
+            "D. Atom",
+            "A. Atom",
+        ]
+        i = 1
+        for x in doc.report.bindingsite.interactions.hydrogen_bonds.hydrogen_bond:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist_h_a.cdata,
+                x.dist_d_a.cdata,
+                x.don_angle.cdata,
+                x.protisdon.cdata,
+                x.sidechain.cdata,
+            ]
+            l.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
+            l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
+            i += 1
+            tableBody.append(l)
+            # print(i, x.resnr.cdata, x.restype.cdata, x.dist_h_a.cdata, x.dist_d_a.cdata, x.don_angle.cdata, x.protisdon.cdata, x.sidechain.cdata, (x.donoridx.cdata + "[" + x.donortype.cdata + "]"), (x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+    if sb == 1:
+        print("## Salt Bridges", end="\n\n")
+        tableBody = []
+        tableHeaders = [
+            "Index",
+            "Residue",
+            "AA",
+            "Distance",
+            "Protein positive?",
+            "Ligand Group",
+            "Ligand Atoms",
+        ]
+        i = 1
+        for x in doc.report.bindingsite.interactions.salt_bridges.salt_bridge:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.protispos.cdata,
+                x.lig_group.cdata,
+            ]
+            atoms = []
+            for y in x.lig_idx_list.idx:
+                atoms.append(y.cdata)
+            l.append(atoms)
+            i += 1
+            tableBody.append(l)
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+    if pc == 1:
+        print("## Pi Cation Interactions", end="\n\n")
+        tableBody = []
+        tableHeaders = ["Index", "Residue", "AA", "Distance", "Prot charged?", "Atoms"]
+        i = 1
+        for (
+            x
+        ) in (
+            doc.report.bindingsite.interactions.pi_cation_interactions.pi_cation_interaction
+        ):
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.offset.cdata,
+                x.protcharged.cdata,
+            ]
+            atoms = []
+            for y in x.lig_idx_list.idx:
+                atoms.append(y.cdata)
+            l.append(atoms)
+            i += 1
+            tableBody.append(l)
+        print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
+
+
diff --git a/app/scripts/quick-ligand-protein.py b/app/scripts/quick-ligand-protein.py
new file mode 100644
index 0000000..6ea16c1
--- /dev/null
+++ b/app/scripts/quick-ligand-protein.py
@@ -0,0 +1,121 @@
+#!/usr/bin/python3
+import argparse
+
+# import logzero
+# import logging
+# from logzero import logger as log
+import pymol2
+import time
+
+import os
+
+print(os.getcwd())
+
+#################
+# Configuration #
+#################
+
+startTime = time.time()
+version = "1.0"
+desc_text = "PyMol Quick Visualtion " + version
+ligandColor = "red"
+# logzero.loglevel(logging.INFO)
+height = 1000
+width = 800
+dpi = 300
+ray = 0
+
+
+m1 = "target"
+m2 = "ligand"
+
+parser = argparse.ArgumentParser(description=desc_text)
+parser.add_argument("-p", "--protein", help="Path to protein file")
+parser.add_argument("-l", "--ligand", help="Path to ligand_out file")
+parser.add_argument("-c", "--color", help="Color for ligand in visualisation")
+
+args = parser.parse_args()
+
+if args.protein == None:
+    print("Error: Please specify protein file")
+    exit(1)
+if args.ligand == None:
+    print("Error: Please specify ligand file")
+    exit(1)
+if args.color == None:
+    print("No color was speciifed, using default settings.")
+
+protein = args.protein
+print("Protein: ", protein)
+ligand = args.ligand
+
+
+def loadMol(filename, name):
+    print("Loading " + filename + " as " + name)
+    cmd.load(filename, name)
+
+
+def changeColor(name, colorName):
+    print("Changed " + name + "'s color to " + colorName)
+    cmd.color(colorName, name)
+
+
+def orientEtZoom():
+    cmd.orient()
+    cmd.zoom()
+
+
+def showSurface(name):
+    cmd.show("surface", name)
+
+
+def surfaceTransparency(amount):
+    print("Changed surface transparency to " + str(amount * 100) + "%")
+    cmd.set("transparency", amount)
+
+
+def generatePNG(filename, height=height, width=width, dpi=dpi, ray=ray):
+    print("Generating " + filename + ".png")
+    cmd.png(filename, height, width, dpi=dpi, ray=ray)
+
+
+def flipHorizontal():
+    cmd.rotate("y", 180)
+
+
+def zoomTo(name):
+    cmd.zoom(name)
+
+
+def generatePictures():
+    generatePNG("output-front")
+    flipHorizontal()
+    generatePNG("output-back")
+    zoomTo(m2)
+    generatePNG("closeup-back")
+    orientEtZoom()
+    flipHorizontal()
+    zoomTo(m2)
+    generatePNG("closeup-front")
+
+
+print("Initialising PyMol")
+session = pymol2.PyMOL()
+print("Starting PyMol Session")
+session.start()
+cmd = session.cmd
+
+loadMol(protein, m1)
+cmd.remove("resn hoh")  # remove water
+loadMol(ligand, m2)
+changeColor(m1, "grey60")
+changeColor(m2, ligandColor)
+cmd.color("blue", "hetatm")  # color heteroatoms
+orientEtZoom()
+showSurface(m1)
+surfaceTransparency(0.6)
+
+generatePictures()
+
+endTime = time.time()
+print("Finished Execution in " + str(round((endTime - startTime), 2)) + " seconds.")