First of all, thank you for the free availability of your software to all the scientific community.
I have just built the docker image in a linux host machine x86_64 under Ubuntu 22.04. The checking command "python run_DXGB.py --help" is OK, but a test running "python run_DXGB.py --runfeatures --datadir ../Test_2al5 --pdbid 2al5 --average" fails showing several error lines as you can find below. Reading another related issue, I could realized that vina4dv binary is the issue source, so is there any fix for that?
Thank you so much in advance for your reply.
pdb index: 2al5
file directory: /app/Test_2al5
feature will be calculated:all
output filename : score.csv
1 molecule converted
Ligand for conformation stability:2al5_ligand.mol2
Ligand for Vina, SASA, BA, ION:2al5_ligand_rename.pdb
Protein without water molecules:2al5_protein.pdb
Protein with water molecules:2al5_protein_all.pdb
Finish Input Preparation
No Consideration of Water
No Optimized Ligand
C
Please verify that both the operating system and the processor support Intel(R) X87, CMOV, MMX, FXSAVE, SSE, SSE2, SSE3, SSSE3, SSE4_1, SSE4_2 and POPCNT instructions.
Traceback (most recent call last):
File "run_DXGB.py", line 103, in
main()
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/click/core.py", line 764, in call
return self.main(args, kwargs)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/click/core.py", line 555, in invoke
return callback(args, **kwargs)
File "run_DXGB.py", line 43, in main
run_features(datadir, pdbid, water_type = water, opt_type = opt, rewrite = rewrite, feature_type = featuretype)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/DXGB-0.1.0-py3.7.egg/DXGB/run_features.py", line 599, in run_features
feature_calculation_ligand(datadir, pdbid, inlig_pdb, inlig_rdkit, inpro_pro, water_type, opt_type, rewrite, feature_type)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/DXGB-0.1.0-py3.7.egg/DXGB/run_features.py", line 522, in feature_calculation_ligand
run_Vina_features(datadir, i, fn, inpro, inlig)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/DXGB-0.1.0-py3.7.egg/DXGB/run_features.py", line 364, in run_Vina_features
featureVina(outfile, fn, inpro, inlig, datadir)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/DXGB-0.1.0-py3.7.egg/DXGB/cal_vina58.py", line 58, in featureVina
vinalist = runVina(fn,protpdbqt,ligpdbqt)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/DXGB-0.1.0-py3.7.egg/DXGB/cal_vina58.py", line 15, in runVina
for lines in fileinput.input("score_v1.txt"):
File "/opt/conda/envs/DXGB/lib/python3.7/fileinput.py", line 252, in next
line = self._readline()
File "/opt/conda/envs/DXGB/lib/python3.7/fileinput.py", line 364, in _readline
self._file = open(self._filename, self._mode)
FileNotFoundError: [Errno 2] No such file or directory: 'score_v1.txt'
First of all, thank you for the free availability of your software to all the scientific community. I have just built the docker image in a linux host machine x86_64 under Ubuntu 22.04. The checking command "python run_DXGB.py --help" is OK, but a test running "python run_DXGB.py --runfeatures --datadir ../Test_2al5 --pdbid 2al5 --average" fails showing several error lines as you can find below. Reading another related issue, I could realized that vina4dv binary is the issue source, so is there any fix for that? Thank you so much in advance for your reply.
pdb index: 2al5 file directory: /app/Test_2al5 feature will be calculated:all output filename : score.csv 1 molecule converted Ligand for conformation stability:2al5_ligand.mol2 Ligand for Vina, SASA, BA, ION:2al5_ligand_rename.pdb Protein without water molecules:2al5_protein.pdb Protein with water molecules:2al5_protein_all.pdb Finish Input Preparation No Consideration of Water No Optimized Ligand C
Please verify that both the operating system and the processor support Intel(R) X87, CMOV, MMX, FXSAVE, SSE, SSE2, SSE3, SSSE3, SSE4_1, SSE4_2 and POPCNT instructions.
Traceback (most recent call last): File "run_DXGB.py", line 103, in
main()
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/click/core.py", line 764, in call
return self.main(args, kwargs)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/click/core.py", line 555, in invoke
return callback(args, **kwargs)
File "run_DXGB.py", line 43, in main
run_features(datadir, pdbid, water_type = water, opt_type = opt, rewrite = rewrite, feature_type = featuretype)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/DXGB-0.1.0-py3.7.egg/DXGB/run_features.py", line 599, in run_features
feature_calculation_ligand(datadir, pdbid, inlig_pdb, inlig_rdkit, inpro_pro, water_type, opt_type, rewrite, feature_type)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/DXGB-0.1.0-py3.7.egg/DXGB/run_features.py", line 522, in feature_calculation_ligand
run_Vina_features(datadir, i, fn, inpro, inlig)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/DXGB-0.1.0-py3.7.egg/DXGB/run_features.py", line 364, in run_Vina_features
featureVina(outfile, fn, inpro, inlig, datadir)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/DXGB-0.1.0-py3.7.egg/DXGB/cal_vina58.py", line 58, in featureVina
vinalist = runVina(fn,protpdbqt,ligpdbqt)
File "/opt/conda/envs/DXGB/lib/python3.7/site-packages/DXGB-0.1.0-py3.7.egg/DXGB/cal_vina58.py", line 15, in runVina
for lines in fileinput.input("score_v1.txt"):
File "/opt/conda/envs/DXGB/lib/python3.7/fileinput.py", line 252, in next
line = self._readline()
File "/opt/conda/envs/DXGB/lib/python3.7/fileinput.py", line 364, in _readline
self._file = open(self._filename, self._mode)
FileNotFoundError: [Errno 2] No such file or directory: 'score_v1.txt'