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Canonicalization requires an input molecule whose double bonds will not give rise to DIME. There should be a function that selects atoms such that the resulting molecule is incapable of DIME.
A thu…
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I am processing a large set of compounds, provided as SMILES strings, and the first thing I do is to check if the SMILES are sanitizable/readable by RDKit. I did that by simply using `Chem.MolFromSmil…
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i currently simply use `.dropna(subset=["SMILES"])`. But this is the most naive way of doing it. Not sure if there is one "higher quality" point we should preferentially retain
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Historically we used `qcelemental.models.Molecule.extras` for storing e.g. `canonical_isomeric_explicit_hydrogen_mapped_smiles`, but we may wish to start using `qcelemental.models.Molecule.identifier`…
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### Bug Description
There are two separate but related issues that I observed. First, an RMG website user mentioned that using RMG kinetics search for nitro-substituted benzenes causes the kinetics s…
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Hi,
I am trying to get atoms' property (e.g bonds, atomic_mass), but the error shows 'Atom' object has no attribute 'bonds'
import skchem
import rdkit.Chem
mol = skchem.Mol.from_smiles('CC(…
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In composer some of my users will change an atom to a lower case "o" thinking its an oxygen atom "O", and the smiles get screwed up. Is there some way to prevent lower case letters as input for atom …
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## Due Date
*To be completed by:* 2018-04-25
## Description
@jrmerwin As discussed, forming a deep learning tutorial on how to predict a chemical property when using its composition in a SMILE …
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Created protein vectors saved in a list by the getligprotvec.py in order to protein names in smiles_sample.txt. For big files it creates a readability problem. A dictionary might help for this issue s…
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**Describe the bug**
I've come across a couple of cases where the library change handler SMARTS matching code hangs when attempting to match a full molecule SMILES.
This is likely because there …