e3fp

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ERROR|Error generating fingerprints for . Traceback (most recent call last):

2

Hi, I am trying to generate fingerprintvectors 3d following this github "https://github.com/iwatobipen/3dfp/blob/master/sample_script.ipynb" and I get the next error.  could you help me please? Thanks Pablo

PARODBE

Replacing python_utilities.parallel

1

[`python_utilities.parallel`](https://github.com/sethaxen/python_utilities/blob/master/python_utilities/parallel.py) has always been a bit of a hack to have a unified API for 4 parallelization approaches: serial, distributed, multithreaded, and message passing. It would be better to call...

sethaxen

Why you can not generate fingerprints with multiples x3?

1

Hi, When you try to generate fingerprint3d and pass to rdkit, with fold().to_rdkit(). you only can generate bits of 1024 x2,x4,6, it would be interesting can generate another multiples. How...

PARODBE

`e3fp` for diatomic molecules

1

Thanks for making this nice tool for the community. I got problems with computing the e3fp fingerprints for diatomic molecules, such as H2, O2 and CO. Here is the corresponding...

FanwangM

problem with smart_open ?

2

I tried generating conformers by python $E3FP/conformer/generate.py -s temp.smi -o ~/outdir -n 3 where temp.smi is simply Brc4cccc(Nc2ncnc3cc1ccccc1cc23)c4 CHEMBL63786 I encountered the following error. 2020-10-22 21:19:30,180|INFO|Input type: Detected SMILES file(s)...

slchan3

Database I/O and conformer/fingerprint storage

3

I'd like to use e3fp fingerprints on a very large database of molecules (~millions, possibly billions). I was wondering if you had any benchmarks on speed and conformer/fingerprint storage sizes....

aparente-nurix

Add timeout feature during conformer generation

2

Dear professors: When I used the function fprints_from_smiles in e3fp, it cost much time to find the conformers if there were none. For example, I wanted to get the fingerprint...

wujinkui

Fingerprint generation runs and fails on [Cl-].[K+] (and possibly similar molecules)

4

Fingerprint generation (using `generate.py` in serial mode) for [Cl-].[K+] raises the following catastrophic error: ``` 2017-05-16 14:51:41,242|INFO|Generating fingerprints for CHEMBL1200731. 2017-05-16 14:51:41,242|ERROR|Error generating fingerprints for CHEMBL1200731. Traceback (most recent call...

8li

`e3fp` is now a package that can be installed with `setup.py` or `pip`, so it no longer makes sense for `e3fp/conformer/generate.py` and `e3fp/fingerprint/generate.py` to be runnable scripts, as in the...

sethaxen

Add unit tests

1

Because the possibility of breaking something and not knowing it is very real and very scary.

sethaxen