rdchiral

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Dear @connorcoley, Your team's paper on [Merging enzymatic and synthetic chemistry with computational synthesis planning](https://www.nature.com/articles/s41467-022-35422-y) is absolutely excellent! As I'm not an expert in chemoinformatics, your work helps people like...

0m1n0

bugfix stereochemistry of conjugated bonds

6

Hi, this is the promised bugfix for #39. The problem was that depending on the atom numbering the direction (up/down) of a double bond system might change for the whole...

hesther

The explicit definition of "spectator" and its impact on RDChiral

8

Hi, I work in the bioinformatics field and I found your tool very interesting. I saw that a reaction can be written as: - `reactant>>product` - `reactant>spectator>product` In biology and...

0m1n0

Is there any way to disable logs?

1

I'm using Jupyter Notebook with Multiprocessing Pool method to extract templates from reactions. But the log like this keep coming out and finally forced my jupyter notebook to be shut...

wmhcqw

rdkit cpp version 'Package not found error'

3

Hello! I was setting up the rdchiral C++ version on my local machine recently and found that invocation to install the C++ version through conda was failing with a package...

pgg1610

Wrong outcome of RunReaction depending on atom numbering

5

Hi, I just noticed that the outcome of RunReaction depends on the atom ordering of the input molecule for some edge cases. For example, applying the template `'[C:1]/[C:2](-[C;D1;H3:3])=[C:4]/[CH2;D2;+0:5]-[OH;D1;+0:6]>>[C:1]/[C:2](-[C;D1;H3:3])=[C:4]/[CH;D2;+0:5]=[O;H0;D1;+0:6]' ` (a...

hesther

The program is stuck and no error is reported when I extract template.

1

### When i extract template from the following reactants and products, Rdchiral is stuck ,does not terminateand and does not report any error: 'reactants': 'CC(C)(C)C(=O)[O:1][C@@H:2]1[C@H:3]([O:4][C@@H]([C@H:5]([C@@H:6]1[O:7]C(=O)C(C)(C)C)OC(=O)C(C)(C)C)COC(=O)C(C)(C)C)[c:8]1[cH:9][cH:10][c:11]([s:12]1)[C@H:13]1[O:14][C@@H:15]([C@H:16]([C@@H:17]([C@@H:18]1[O:19]C(=O)C(C)(C)C)[O:20]C(=O)C(C)(C)C)[O:21][C:22](=[O:23])C(C)(C)C)[CH2:24][O:25]C(=O)C(C)(C)C', 'products': '[OH:23][CH2:22][C@H:26]1[O:27][C@@H:5]([C@H:6]([C@H:2]([C@@H:3]1[OH:4])[OH:1])[OH:7])[c:9]1[cH:8][s:12][c:11]([cH:10]1)[C@H:13]1[O:14][C@@H:15]([C@H:16]([C@@H:17]([C@@H:18]1[OH:19])[OH:20])[OH:21])[CH2:24][OH:25]' 'reactants': 'CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](COC(c1ccccc1)(c1ccccc1)c1ccccc1)NC(=O)[C@H](COC(C)(C)C)N[C:1](=[O:2])[CH2:3][NH:4][C:5](=[O:6])[O:7][C:8]([CH3:9])([CH3:10])[CH3:11])C(=O)N[C@@H](COC(C)(C)C)C(=O)N1CCC[C@H]1C(=O)N[C@@H](CCC(=O)OC(C)(C)C)C(=O)N[C@@H](Cc1cn(cn1)C(=O)OC(C)(C)C)C(=O)N[C@@H](CCC(=O)NC(c1ccccc1)(c1ccccc1)c1ccccc1)C(=O)N[C@@H](CCCNC(=N)NS(=O)(=O)c1c(c2CCC(Oc2c(c1C)C)(C)C)C)C(=O)N[C@H](C(=O)N[C@@H](CCC(=O)NC(c1ccccc1)(c1ccccc1)c1ccccc1)C(=O)N[C@@H](CCC(=O)NC(c1ccccc1)(c1ccccc1)c1ccccc1)C(=O)N[C@@H](CCCNC(=N)NS(=O)(=O)c1c(c2CCC(Oc2c(c1C)C)(C)C)C)C(=O)N[C@@H](CCCCNC(=O)OC(C)(C)C)C(=O)N[C@@H](CCC(=O)OC(C)(C)C)C(=O)N[C@@H](COC(C)(C)C)C(=O)N[C@@H](CCCCNC(=O)OC(C)(C)C)C(=O)N[C@@H](CCCCNC(=O)OC(C)(C)C)C(=O)N1CCC[C@H]1C(=O)N1CCC[C@H]1C(=O)N[C@@H](C)C(=O)N[C@@H](CCCCNC(=O)OC(C)(C)C)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCC(=O)NC(c1ccccc1)(c1ccccc1)c1ccccc1)C(=O)N1CCC[C@H]1C(=O)N[C@@H](CCCNC(=N)NS(=O)(=O)c1c(c2CCC(Oc2c(c1C)C)(C)C)C)C(=O)O)C(C)C', 'products':...

milktea-lab

extract_from_reaction error

2

When i extract template from my reaction: single product and single reactant, but i got a template with more than one products and reactants. input: 'reactants': '[N:1]#[C:2][CH2:3][N:4]1[CH2:5][CH2:6][CH:7]([CH2:8][CH2:9]1)[CH2:10][CH2:11][O:12][c:13]1[cH:14][cH:15][cH:16][cH:17][c:18]1[F:19]', 'products': '[NH2:1][CH2:2][CH2:3][N:4]1[CH2:5][CH2:6][CH:7]([CH2:8][CH2:9]1)[CH2:10][CH2:11][O:12][c:13]1[cH:14][cH:15][c:16]([cH:17][cH:18]1)[F:19]' the...

milktea-lab

Seems that github updated the protocol some time in 2022, so this part of the README should be deprecated (?) `$ pip install -e "git://github.com/connorcoley/rdchiral.git#egg=rdchiral" Obtaining rdchiral from git+git://github.com/connorcoley/rdchiral.git#egg=rdchiral Cloning...

zhengkaitu

Explicit hydrogens

1

We've encountered a case where we want to run a reaction with explicit hydrogens. From what I can see, the default behavior of rdchiral is to strip them at the...

kjelljorner