diff options
Diffstat (limited to 'app/dock-single.py')
| -rw-r--r-- | app/dock-single.py | 31 |
1 files changed, 26 insertions, 5 deletions
diff --git a/app/dock-single.py b/app/dock-single.py index e9ef9b2..3526985 100644 --- a/app/dock-single.py +++ b/app/dock-single.py @@ -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()
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