Hello all,
While reading the source code for ASKCOS (
https://github.com/connorcoley/ASKCOS/blob/master/makeit/utilities/io/draw.py)
I noticed this code snippet (line 216 on the GitHub):
reactants, agents, products = [mols_from_smiles_list(x) for x in
[mols.split('.') for mols in rxn_string.split('>')]]
When the above code is applied on a SMILES reaction string, the result
unpacks the reactants, agents, and products mol objects into the respected
variables, with pretty good accuracy. The function 'mols_from_smiles'
essentially just applies Chem.MolFromSmiles over a list of smiles.
I think this code snippet is really cool but I cannot find any
documentation on how this is working. Searching this mailing list I came
across the thread (https://sourceforge.net/p/rdkit/mailman/message/36316849/)
where this operation of labeling reactants, agents, and products seems to
be determined by the threshold_unmapped_reactant_atoms explained in the
quoted text from the message (linked above)
Here's what's going on: By default the cartridge code does an extra step
> after reading a reaction from SMILES/SMARTS: it looks at all the reactants
> and moves any that don't have a sufficient fraction of mapped atoms to the
> agents. We do this by default because the reactions that we found "in the
> wild" often have agents, solvents, etc. mixed in with the reactants. The
> key parameter used there is threshold_unmapped_reactant_atoms, which
> defaults to 0.2.
The only further reading I can find is from Greg's paper (
https://pubs.acs.org/doi/10.1021/ci5006614). I have two main questions:
1. Where in the code is this atom mapping being applied? I cannot tell when
this method is being applied or where the meta data is being saved.
Applying the code snippet above to a SMILES reaction string results in a
list of rdkit.Chem.rdchem.Mol objects. I cannot seem to find any static
method or attributes specifying if it's a reactant, agent, or product when
inspecting a mol object using help in a python terminal.
2. How can I change the value of the
variables threshold_unmapped_reactant_atoms
and move_unmmapped_reactants_to_agents? I am using rdkit version 2019.03.4
in an Anaconda environment. I want to experiment changing the mapping
threshold.
Very Respectfully,
Benjamin
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