navan
/
Curie-Web
mirror of https://github.com/navanchauhan/Curie-Web.git
1
0
Fork 0
Code Issues Projects Releases Wiki Activity

added title,date to pdf

This commit is contained in:
Navan Chauhan 2020-10-03 19:11:04 +05:30
parent e300d53d0d
commit 6fe0c3114b
4 changed files with 11 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
app/scripts/add-pictures.py
View File

@ -1,4 +1,4 @@
print("## Figures", end="\n\n") print("# Figures", end="\n\n")
print("![Back View](output-back.png){width=100%}", 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("![Front View](output-front.png){width=100%}", end="\n\n")

10
app/scripts/get_dock_score.py
View File

@ -1,5 +1,5 @@
#!/usr/bin/python3 #!/usr/bin/python3
from datetime import datetime
import argparse import argparse
parser = argparse.ArgumentParser(description="Get Docking Score") parser = argparse.ArgumentParser(description="Get Docking Score")
@ -21,7 +21,11 @@ ligand = args.ligand
from os.path import basename from os.path import basename
print("# " + str(basename(protein)).replace(".pdbqt","") + "-" + str(basename(ligand)).replace("_out.pdbqt",""), end="\n\n") print("% Molecular Docking of " + str(basename(ligand)).replace("_out.pdbqt","") + " with " +str(basename(protein)).replace(".pdbqt",""))
print("%")
print("% " + str(datetime.now().strftime("%b %d, %Y")))
print("![Structure of %s](compound.svg)"%(str(basename(ligand)).replace("_out.pdbqt","")),end="\n\n")
from tabulate import tabulate from tabulate import tabulate
@ -41,6 +45,6 @@ for line in lines:
if ta != []: if ta != []:
results.append(ta) results.append(ta)
print("## Docking Scores",end="\n\n") print("# Docking Score",end="\n\n")
print(tabulate(results,headers=["No.","Affinity","rmsd l.b","rmsd u.b"])) print(tabulate(results,headers=["No.","Affinity","rmsd l.b","rmsd u.b"]))
print("",end="\n\n") print("",end="\n\n")

2
app/scripts/main.sh
View File

@ -142,6 +142,8 @@ fi
if [[ $interactions == "true" ]]; then if [[ $interactions == "true" ]]; then
file=$(echo "$ligandPath" | cut -f 1 -d '.') file=$(echo "$ligandPath" | cut -f 1 -d '.')
python3 ./get-best.py -p $proteinPath -l "$(echo $file)_out.pdbqt" python3 ./get-best.py -p $proteinPath -l "$(echo $file)_out.pdbqt"
echo "Generating SVG of Compound"
obabel $ligandPath -O compound.svg
echo "Running PLIP" echo "Running PLIP"
plip -f best.pdb -qpxy plip -f best.pdb -qpxy
echo "Getting Dock Score" echo "Getting Dock Score"

2
app/scripts/makeReport.py
View File

@ -49,7 +49,7 @@ name = doc.report.pdbid.cdata
# print(("# " + (name.replace("_"," ")).replace("PROTEIN","")), end="\n\n") # print(("# " + (name.replace("_"," ")).replace("PROTEIN","")), end="\n\n")
fallback = 0 fallback = 0
print("## Visualisation", end="\n\n") print("# Visualisation", end="\n\n")
print(f"![]({image})", end="\n\n") print(f"![]({image})", end="\n\n")
natural_ligands = [] natural_ligands = []