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Hello, whenever I try to use vsflow I have the following error:

Start: 02/09/2024, 12:58:15
Running in parallel mode on 2 threads
Downloading database pdb ...
Instrucción ilegal (`core' generado)

"Illegal instruction (core dumped)" in english

It is independent of the instruction given or how many cores I use.

Could anyone help me, please?
Thanks!
G

when I run vsflow in the miniconda, it shows: 'vsflow' not an internal or external command, nor is it a executable program or batch file

Hi!

When setting up VSFlow in a new environment using both the environment.yml and later again with the manual set-up, I ran into this issue:

ImportError: cannot import name 'Standardizer' from 'rdkit.Chem.MolStandardize'

The latest version from RDKit 2024.03.1 does not seem have Standardizer anymore.
The previous version does, but the environment.yml file automatically installs the 2024 version for me.
I am not sure if I am the only one who encountered it, but manually installing the previous version solves the problem.

Maybe something to look into, in case more people encounter this :)

Hello,

When I try to run the shape-based search using a test dataset, I keep having this error:

When I prepare my database, I used this command:
vsflow preparedb -i test.smi -o test -s -c -np 6

And the command to run the shape-based search is this:
vsflow shape -i 111.smi -d test.vsdb -o test_3Dsim -np 30

I'm not sure why this happens, and attached the test files I used for my task. Because I can not attach smi file, I converted them to txt file and attached them here. Really appreciate it if you could help me with this!
111.txt
test.txt

Best,
Bo

Hi,
I am wondering how Vsflow can be used to generate sdf file from a SMILES strings file (csv, or text file). It seems that preparadb supports database format only, not sdf,

Thanks

hi,

Traceback (most recent call last):
File "vsflow", line 6, in
run.main()
File "C:\Users.....\VSFlow-master\vslib\run.py", line 1560, in main
args.func(args)
File "C:\Users.....\VSFlow-master\vslib\run.py", line 1380, in prep_db
prepare.gen_confs(mols, args.nconfs, seed, args.rms_thresh, "mol", nthreads)
File "C:\Users....\VSFlow-master\vslib\prepare.py", line 207, in gen_confs
Chem.EmbedMultipleConfs(mol_H, numConfs=nconfs, params=params)
RuntimeError: Invariant Violation
expected match not found
Violation occurred on line 1062 in file Code\GraphMol\DistGeomHelpers\Embedder.cpp
Failed Expression: strippedMatch.size() == 1
RDKIT: 2022.03.2
BOOST: 1_74

attached please find and see the errors while I'm running vsflow preparedb command line.
could you please help check what problems they are? and how to fix it. thanks

Hi,

When I use the following line:
vsflow preparedb -d chembl -o chembl_ecfp4 -f ecfp -np 6

it crashes right away with this error:
Start: 04/12/2023, 11:48:13
Running in parallel mode on 6 threads
Downloading database chembl ...
Traceback (most recent call last):
File "/home/andrea/anaconda3/envs/vsflow/bin/vsflow", line 6, in
run.main()
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/site-packages/vslib/run.py", line 1560, in main
args.func(args)
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/site-packages/vslib/run.py", line 1167, in prep_db
mols = read.req_chembl(args.nproc, pool)
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/site-packages/vslib/read.py", line 18, in req_chembl
r = urlopen("https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_28/chembl_28_chemreps.txt.gz",
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/urllib/request.py", line 214, in urlopen
return opener.open(url, data, timeout)
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/urllib/request.py", line 523, in open
response = meth(req, response)
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/urllib/request.py", line 632, in http_response
response = self.parent.error(
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/urllib/request.py", line 561, in error
return self._call_chain(*args)
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/urllib/request.py", line 494, in _call_chain
result = func(*args)
File "/home/andrea/anaconda3/envs/vsflow/lib/python3.9/urllib/request.py", line 641, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 404: Not Found

Instead if i remove the -np flag it seems to go through with no errors.

I've also tested it with the pdb database instead of chemble with and without -np and it works fine. So could it be an issue with the chemble database servers?

Thanks a lot,
Andrea