From 4be08f7bdd77991e9e453c1cda863c3f20c338d5 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Thu, 2 Jul 2020 20:48:33 +0530 Subject: initial commit --- scripts/convert-smile.sh | 38 +++++ scripts/dock-and-score.sh | 51 +++++++ scripts/get-best.py | 43 ++++++ scripts/main.sh | 152 +++++++++++++++++++ scripts/makeReport.py | 315 ++++++++++++++++++++++++++++++++++++++++ scripts/quick-ligand-protein.py | 99 +++++++++++++ scripts/report.sh | 67 +++++++++ scripts/test.sh | 63 ++++++++ 8 files changed, 828 insertions(+) create mode 100644 scripts/convert-smile.sh create mode 100644 scripts/dock-and-score.sh create mode 100644 scripts/get-best.py create mode 100755 scripts/main.sh create mode 100644 scripts/makeReport.py create mode 100644 scripts/quick-ligand-protein.py create mode 100644 scripts/report.sh create mode 100644 scripts/test.sh (limited to 'scripts') diff --git a/scripts/convert-smile.sh b/scripts/convert-smile.sh new file mode 100644 index 0000000..a86f675 --- /dev/null +++ b/scripts/convert-smile.sh @@ -0,0 +1,38 @@ +if [ -z "$1" ] + then + echo "CSV path not provided! 😠" + exit +fi +input="$1" + +echo "Reading ligands from $input" + +total=$(wc -l $input | awk '{print $1}') +file=1 +while IFS= read -r line +do + mails=$(echo $line | tr "," "\n") + i=0 + code="" + echo "Structure $file of $total" + for a in $mails; do + i=$((i+1)) + if ((i == 1)) + then + code=$(echo "$a") + fi + if ((i == 2)) + then + echo "===========================================" + echo "Generating Structure for $a" + fi + if ((i == 3)) + then + echo "obabel -:"$a" --gen3d -opdbqt -O$code.pdbqt" + obabel -:"$a" --gen3d -opdbqt -O$code.pdbqt + echo "===========================================" + fi + mv $code.pdbqt ligands/ + done + file=$((file+1)) +done < "$input" diff --git a/scripts/dock-and-score.sh b/scripts/dock-and-score.sh new file mode 100644 index 0000000..c71baef --- /dev/null +++ b/scripts/dock-and-score.sh @@ -0,0 +1,51 @@ +if [ -z "$1" ] + then + echo "CSV path not provided! 😠" + exit +fi +input="$1" +echo "Reading ligands from $input" + +targets=() + +for file in ./configs/* +do + targets+=($file) +done + +total=$(wc -l $input | awk '{print $1}') +file=1 +while IFS= read -r line +do + mails=$(echo $line | tr "," "\n") + i=0 + code="" + echo "Structure $file of $total" + for a in $mails; do + i=$((i+1)) + if ((i == 1)) + then + echo $a + for target in ${targets[@]}; do + echo "Docking $(basename $target .txt) and $a" + vina --config $target --ligand ligands/$a.pdbqt + sentence=$(awk '{if(NR==2) print $0}' ./ligands/$(echo $a)_out.pdbqt) + mkdir -p ./Reports/$(basename $target .txt)/$(echo $a)/ + mkdir ./$(basename $target .txt)/ + cp ligands/$(echo $a)_out.pdbqt ./$(basename $target .txt)/ + mv ligands/$(echo $a)_out.pdbqt ./Reports/$(basename $target .txt)/$(echo $a)/$(echo $a).pdbqt + f=1 + for word in $sentence; do + if ((f == 4)) + then + echo "$(echo $a),$word" >> $(basename $target .txt).csv + fi + f=$((f+1)) + done + done + fi + done + file=$((file+1)) +done < "$input" + + diff --git a/scripts/get-best.py b/scripts/get-best.py new file mode 100644 index 0000000..748251e --- /dev/null +++ b/scripts/get-best.py @@ -0,0 +1,43 @@ +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) + + +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/scripts/main.sh b/scripts/main.sh new file mode 100755 index 0000000..612f626 --- /dev/null +++ b/scripts/main.sh @@ -0,0 +1,152 @@ +#!/bin/bash +echo "$(pwd)" +currentVersion="0.9" +protein="false" +ligand="false" +docking="false" +visualisations="false" +interactions="false" +proteinPath="" +ligandPath="" +pdfPath="" +smile="" +name="" +config="" + +usage() +{ + cat <&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 [[ $visualisations == "true" ]]; then + file=$(echo "$ligandPath" | cut -f 1 -d '.') + python3 /src/scripts/quick-ligand-protein.py -p $proteinPath -l "$(echo $file)_out.pdbqt" +fi + +if [[ $interactions == "true" ]]; then + python3 /src/scripts/get-best.py -p $proteinPath -l "$(echo $file)_out.pdbqt" + python3 /src/plip/plipcmd.py -f best.pdb -qpxy + python3 /src/scripts/makeReport.py --input . > report.md + pandoc -V geometry:margin=1in report.md --pdf-engine=xelatex -o $name.pdf +fi + +echo "$proteinPath and $ligandPath and $docking and $interactions and $visualisations" \ No newline at end of file diff --git a/scripts/makeReport.py b/scripts/makeReport.py new file mode 100644 index 0000000..dcf3576 --- /dev/null +++ b/scripts/makeReport.py @@ -0,0 +1,315 @@ +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") + +print("## Visualisation", end="\n\n") +print(f'![]({image})', end="\n\n") + +print("## Interactions", end="\n\n") + +fallback = 0 +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 = [] + l.append(i) + l.append(x.resnr.cdata) + l.append(x.restype.cdata) + l.append(x.dist.cdata) + l.append(x.ligcarbonidx.cdata) + l.append(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 = [] + l.append(i) + l.append(x.resnr.cdata) + l.append(x.restype.cdata) + l.append(x.dist_h_a.cdata) + l.append(x.dist_d_a.cdata) + l.append(x.don_angle.cdata) + l.append(x.protisdon.cdata) + l.append(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 = [] + l.append(i) + l.append(x.resnr.cdata) + l.append(x.restype.cdata) + l.append(x.dist.cdata) + l.append(x.protispos.cdata) + l.append(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 = [] + l.append(i) + l.append(x.resnr.cdata) + l.append(x.restype.cdata) + l.append(x.dist.cdata) + l.append(x.offset.cdata) + l.append(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 = [] + l.append(i) + l.append(x.resnr.cdata) + l.append(x.restype.cdata) + l.append(x.dist.cdata) + l.append(x.ligcarbonidx.cdata) + l.append(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 = [] + l.append(i) + l.append(x.resnr.cdata) + l.append(x.restype.cdata) + l.append(x.dist_h_a.cdata) + l.append(x.dist_d_a.cdata) + l.append(x.don_angle.cdata) + l.append(x.protisdon.cdata) + l.append(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 = [] + l.append(i) + l.append(x.resnr.cdata) + l.append(x.restype.cdata) + l.append(x.dist.cdata) + l.append(x.protispos.cdata) + l.append(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 = [] + l.append(i) + l.append(x.resnr.cdata) + l.append(x.restype.cdata) + l.append(x.dist.cdata) + l.append(x.offset.cdata) + l.append(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") + +print("## Figures", end="\n\n") + +print(f'![](output-back.png)', end="\n\n") +print(f'![](output-front.png)', end="\n\n") +print(f'![](closeup-back.png)', end="\n\n") +print(f'![](closeup-front.png)', end="\n\n") diff --git a/scripts/quick-ligand-protein.py b/scripts/quick-ligand-protein.py new file mode 100644 index 0000000..f2409ef --- /dev/null +++ b/scripts/quick-ligand-protein.py @@ -0,0 +1,99 @@ +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) +loadMol(ligand,m2) +changeColor(m1,"grey60") +changeColor(m2,ligandColor) +orientEtZoom() +showSurface(m1) +surfaceTransparency(0.6) + +generatePictures() + +endTime = time.time() +print("Finished Execution in " + str(round((endTime - startTime),2)) + " seconds.") \ No newline at end of file diff --git a/scripts/report.sh b/scripts/report.sh new file mode 100644 index 0000000..98437a3 --- /dev/null +++ b/scripts/report.sh @@ -0,0 +1,67 @@ +pwd=$(pwd) + +if [ -z "$1" ] + then + echo "CSV path not provided! 😠" + exit +fi +input="$1" + +ligands=() + +while IFS= read -r line +do + mails=$(echo $line | tr "," "\n") + i=0 + code="" + for a in $mails; do + i=$((i+1)) + if ((i == 1)) + then + code=$(echo "$a") + fi + if ((i == 2)) + then + #ligands+=("./ligands/$a.pdbqt") + ligands+=("$a") + fi + done +done < "$input" + + +proteins=() +#for file in ./configs/* +#do +# proteins+=("$(basename $file .txt)") +#done + +proteins+=("6VXX") + +#ligands=() +#for file in ./ligands/* +#do +# ligands+=("$(basename $file .pdbqt)") +#done + +for protein in ${proteins[@]}; do + for ligand in ${ligands[@]}; do + ###cd $pwd/Reports/$protein/$ligand/ + ###docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) pharmai/plip:latest -f $ligand.pdb -qpxy + echo "Saving Protein-Ligand Complex $ligand" + python3.7 ./scripts/get-best.py -p ./targets/$protein.pdbqt -l ./Reports/$protein/$ligand/$ligand.pdbqt + fname=$(echo ${protein}_${ligand}.pdb) + mv best.pdb ./Reports/$protein/$ligand/$fname + cd $pwd/Reports/$protein/$ligand/ + echo "Processing in PLIP" + docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) pharmai/plip:latest -f $fname -qpxy + cd $pwd + echo "Generating Images" + #python3.7 ./scripts/quick-ligand-protein.py -p ./targets/$protein.pdbqt -l ./Reports/$protein/$ligand/$ligand.pdbqt + #mv closeup-front.png closeup-back.png output-back.png output-front.png ./Reports/$protein/$ligand/ + echo "Generating PDF Report" + python3.7 ./scripts/makeReport.py --input ./Reports/$protein/$ligand/ > ./Reports/$protein/$ligand/report.md + cd $pwd/Reports/$protein/$ligand/ + pandoc -V geometry:margin=1in report.md --pdf-engine=xelatex -o $ligand.pdf + cd $pwd + done +done \ No newline at end of file diff --git a/scripts/test.sh b/scripts/test.sh new file mode 100644 index 0000000..3d5bf8f --- /dev/null +++ b/scripts/test.sh @@ -0,0 +1,63 @@ +#declare -a ligands=() +#for file in ./ligands/* +#do +# echo $file +# ligands+=("$(basename $file .pdbqt)") +#done +# +#for i in "${ligands[@]}"; do echo "$i"; done + +if [ -z "$1" ] + then + echo "CSV path not provided! 😠" + exit +fi +input="$1" + +ligands=() + +while IFS= read -r line +do + mails=$(echo $line | tr "," "\n") + i=0 + code="" + for a in $mails; do + i=$((i+1)) + if ((i == 1)) + then + code=$(echo "$a") + fi + if ((i == 2)) + then + #ligands+=("./ligands/$a.pdbqt") + ligands+=("$a") + fi + done +done < "$input" + +targets=() + +for file in ./configs/* +do + targets+=($file) +done + +for a in ${ligands[@]}; do + for target in ${targets[@]}; do + echo "Docking $(basename $target .txt) and $a" + vina --config $target --ligand ligands/$a.pdbqt + sentence=$(awk '{if(NR==2) print $0}' ./ligands/$(echo $a)_out.pdbqt) + mkdir -p ./Reports/$(basename $target .txt)/$(echo $a)/ + mkdir ./$(basename $target .txt)/ + cp ligands/$(echo $a)_out.pdbqt ./$(basename $target .txt)/ + mv ligands/$(echo $a)_out.pdbqt ./Reports/$(basename $target .txt)/$(echo $a)/$(echo $a).pdbqt + f=1 + for word in $sentence; do + if ((f == 4)) + then + echo "$(echo $a),$word" >> $(basename $target .txt).csv + fi + f=$((f+1)) + done + done +done \ No newline at end of file -- cgit v1.2.3