Increased Speed by 50%
This commit is contained in:
Navan Chauhan
parent
c00e771b4d
commit
5ad24bfceb
|
|
@ -209,6 +209,23 @@ def email(zipArchive):
|
|||
s.quit()
|
||||
|
||||
|
||||
def CopyContentOfFolder(sauce,destination):
|
||||
src_files = os.listdir(sauce)
|
||||
for file_name in src_files:
|
||||
full_file_name = os.path.join(sauce, file_name)
|
||||
if os.path.isfile(full_file_name):
|
||||
copy(full_file_name, destination)
|
||||
|
||||
def RemoveAllFilesMatching(directory,pattern):
|
||||
print(directory+"/*"+pattern)
|
||||
FileList = glob.glob(directory+"/*"+pattern)
|
||||
for FilePath in FileList:
|
||||
try:
|
||||
print(FilePath)
|
||||
os.remove(FilePath)
|
||||
except:
|
||||
print("Error in removing misc file")
|
||||
|
||||
inPDB = records[2]
|
||||
jobID = records[0]
|
||||
toaddr = records[1]
|
||||
|
|
@ -218,16 +235,17 @@ date = records[6]
|
|||
#pdb_file_name = pdbpath.split('/')[-1]
|
||||
#pdbpath="./6lu7.pdb"
|
||||
|
||||
import os
|
||||
import os,glob
|
||||
cd = os.getcwd()
|
||||
f = os.path.join(cd,"static/uploads")
|
||||
scripts = os.path.join(cd,"scripts")
|
||||
reportDirectory = os.path.join(f,"reports")
|
||||
modelDirectory = os.path.join(f,"3DModels")
|
||||
#t = os.path.join(f,"receptor",target)
|
||||
#r = os.path.join(f,"ligands",ligand)
|
||||
#c = os.path.join(f,"configs",config)
|
||||
import tempfile
|
||||
from shutil import make_archive, copyfile
|
||||
from shutil import make_archive, copyfile,copy
|
||||
import time
|
||||
|
||||
with tempfile.TemporaryDirectory() as directory:
|
||||
|
|
@ -247,7 +265,11 @@ with tempfile.TemporaryDirectory() as directory:
|
|||
os.system('obabel -:"%s" --gen3d -opdbqt -O%s.pdbqt' % (records[3],records[4]))
|
||||
print("Ligand:",records[4])
|
||||
print(str(records[4]+".pdbqt"))
|
||||
os.system("docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) navanchauhan/curie-cli -r %s -l %s -c config.txt -dpi" % (pdbqt,str(records[4]+".pdbqt")))
|
||||
CopyContentOfFolder(scripts,directory)
|
||||
os.system("./main.sh -r %s -l %s -c config.txt -dpi" % (pdbqt,str(records[4]+".pdbqt")))
|
||||
#os.system("docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) navanchauhan/curie-cli -r %s -l %s -c config.txt -dpi" % (pdbqt,str(records[4]+".pdbqt")))
|
||||
RemoveAllFilesMatching(directory,".py")
|
||||
RemoveAllFilesMatching(directory,".sh")
|
||||
z = "Curie_Web_Result_"+str(jobID)
|
||||
zi = os.path.join(f,z)
|
||||
make_archive(zi, 'zip', directory)
|
||||
|
|
@ -256,6 +278,7 @@ with tempfile.TemporaryDirectory() as directory:
|
|||
os.system("collada2gltf -i model.dae -o model.gltf")
|
||||
copyfile("model.gltf",os.path.join(modelDirectory,(str(jobID)+".gltf")))
|
||||
arch = os.popen("uname -m").read()
|
||||
print("Generating 3D Model")
|
||||
if "x86" in arch:
|
||||
os.system("docker run -it --rm -v $(pwd):/usr/app leon/usd-from-gltf:latest model.gltf model.usdz")
|
||||
elif "aarch64" in arch:
|
||||
|
|
@ -264,8 +287,6 @@ with tempfile.TemporaryDirectory() as directory:
|
|||
copyfile("model.usdz",os.path.join(modelDirectory,(str(jobID)+".usdz")))
|
||||
except:
|
||||
print("Could not generate USDZ file")
|
||||
#copy(("Curie_Web_Result_"+str(jobID)),f)
|
||||
email(zi)
|
||||
#print((str(zi) + ".zip"))
|
||||
mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
|
||||
mycon.commit()
|
||||
|
|
@ -68,6 +68,23 @@ def get3DModel(protein,ligand):
|
|||
cmd.save("model.dae")
|
||||
session.stop()
|
||||
|
||||
def CopyContentOfFolder(sauce,destination):
|
||||
src_files = os.listdir(sauce)
|
||||
for file_name in src_files:
|
||||
full_file_name = os.path.join(sauce, file_name)
|
||||
if os.path.isfile(full_file_name):
|
||||
copy(full_file_name, destination)
|
||||
|
||||
def RemoveAllFilesMatching(directory,pattern):
|
||||
print(directory+"/*"+pattern)
|
||||
FileList = glob.glob(directory+"/*"+pattern)
|
||||
for FilePath in FileList:
|
||||
try:
|
||||
print(FilePath)
|
||||
os.remove(FilePath)
|
||||
except:
|
||||
print("Error in removing misc file")
|
||||
|
||||
receptor_name = "protein.pdbqt"
|
||||
ligand_name = "ligand.pdbqt"
|
||||
description = "Curie Web Task"
|
||||
|
|
@ -87,41 +104,43 @@ date = r[8]
|
|||
if r[9] is not None:
|
||||
description = r[9]
|
||||
|
||||
import os
|
||||
import os,glob
|
||||
cd = os.getcwd()
|
||||
f = os.path.join(cd,"static/uploads")
|
||||
reportDirectory = os.path.join(f,"reports")
|
||||
scripts = os.path.join(cd,"scripts")
|
||||
modelDirectory = os.path.join(f,"3DModels")
|
||||
#t = os.path.join(f,"receptor",target)
|
||||
#r = os.path.join(f,"ligands",ligand)
|
||||
#c = os.path.join(f,"configs",config)
|
||||
print(f)
|
||||
import tempfile
|
||||
from shutil import make_archive, copyfile
|
||||
from shutil import make_archive, copyfile,copy
|
||||
|
||||
with tempfile.TemporaryDirectory() as directory:
|
||||
print('The created temporary directory is %s' % directory)
|
||||
os.chdir(directory)
|
||||
# copy(t,os.getcwd())
|
||||
# copy(r,os.getcwd())
|
||||
# copy(c, os.getcwd())
|
||||
with open(receptor_name,"wb") as file:
|
||||
file.write(targetB)
|
||||
with open(ligand_name,"wb") as file:
|
||||
file.write(ligandB)
|
||||
with open("config.txt","wb") as file:
|
||||
file.write(configB)
|
||||
os.system("docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) navanchauhan/curie-cli -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name))
|
||||
#copy("report.pdf",f)
|
||||
# Legacy Docker Curie-Cli Run
|
||||
#os.system("docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) navanchauhan/curie-cli -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name))
|
||||
CopyContentOfFolder(scripts,directory)
|
||||
os.system("./main.sh -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name))
|
||||
RemoveAllFilesMatching(directory,".py")
|
||||
RemoveAllFilesMatching(directory,".sh")
|
||||
z = "Curie_Web_Result_"+str(jobID)
|
||||
zi = os.path.join(f,z)
|
||||
make_archive(zi, 'zip', directory)
|
||||
#copy(("Curie_Web_Result_"+str(jobID)),f)
|
||||
copyfile("report.pdf",os.path.join(reportDirectory,(str(jobID)+".pdf")))
|
||||
get3DModel(receptor_name,ligand_name.replace(".pdbqt","_out.pdbqt"))
|
||||
os.system("collada2gltf -i model.dae -o model.gltf")
|
||||
copyfile("model.gltf",os.path.join(modelDirectory,(str(jobID)+".gltf")))
|
||||
arch = os.popen("uname -m").read()
|
||||
print("Generating 3D Model")
|
||||
if "x86" in arch:
|
||||
os.system("docker run -it --rm -v $(pwd):/usr/app leon/usd-from-gltf:latest model.gltf model.usdz")
|
||||
elif "aarch64" in arch:
|
||||
|
|
@ -131,6 +150,5 @@ with tempfile.TemporaryDirectory() as directory:
|
|||
except:
|
||||
print("Could not generate USDZ file")
|
||||
email(zi)
|
||||
#print((str(zi) + ".zip"))
|
||||
mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
|
||||
mycon.commit()
|
||||
|
|
|
|||
|
|
@ -0,0 +1,6 @@
|
|||
print("## Figures", end="\n\n")
|
||||
|
||||
print("{width=100%}", end="\n\n")
|
||||
print("{width=100%}", end="\n\n")
|
||||
print("{width=100%}", end="\n\n")
|
||||
print("{width=100%}", end="\n\n")
|
||||
|
|
@ -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")
|
||||
|
|
@ -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")
|
||||
|
|
@ -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"
|
||||
|
|
@ -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"", 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")
|
||||
|
||||
|
||||
|
|
@ -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.")
|
||||
Loading…
Reference in New Issue