rd_filters

rd_filters copied to clipboard

Hi, Currently, the created .csv contains a single FILTER column when multiple filters are executed in parallel. I suggest to generate a separate FILTER column per each applied filter. I...

boazi68

Mismatching pattern due to RDKit aromaticity model

1

I started to play with different filters and found that many compounds were rejected by some of them and started to investigate the cases. One example is Filter82_pyridinium rule (`[c,n]1[c,n][c,n][c,n][c,n]n(C)1`)...

DrrDom

more unixish behavior

3

Hello, The default behavior should be the filter command (because the other commands should only rarely be used). -i: input file -o: output file, same file format than the input...

UnixJunkie

it would be safer to explicitly require the user to list on the command-line which rule set to use

1

I feel, hiding away in a configuration file which rule set to use is a little dangerous, because this is indirect (some users will not know/realize which rule set is...

UnixJunkie

inelegant exit for smiles file with no names

3

using a *.smi file which contains smiles strings but no names causes an inelegant error. benzene.smi = c1ccccc1 > rd_filters filter --in benzene.smi --prefix foo > using 8 cores >...

MikeBowerReverie

Revamp and simplify code, tests, build; add CI/CD

1

Goals: simplify, allow easier programmatic access, stream to output (rather than building up in memory first), enable Unix pipes, optionally or preferentially stream JSON, allow CSV/JSON/TSV everywhere, remove Pandas and...

dmyersturnbull