cmiles

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Explicit valence issue with rdkit

5

Hi folks, please have a look at the following code snippet: ``` import qcportal as ptl import cmiles qc_client = ptl.FractalClient("https://api.qcarchive.molssi.org:443/") ds = qc_client.get_collection('OptimizationDataset', "FDA Optimization Dataset 1") qcrecord =...

wutobias

Problem when loading TorsionDrive qcmol from QCA

4

Hi folks, please have a look at the following code: ``` import qcportal as ptl import cmiles print(ptl.__version__) print(cmiles.__version__) qc_client = ptl.FractalClient("https://api.qcarchive.molssi.org:443/") ds = qc_client.get_collection('TorsionDriveDataset', "OpenFF Substituted Phenyl Set 1")...

wutobias

CI has been failing for a few days, probably related to a recent OpenEye release. Tests pass with 2020.1.1 but fail with 2020.2.0 (`pytest -n auto && pytest -v --lf...

mattwthompson

A stripped-down version of what I did in #44: 1. Update the toolkit: `conda update rdkit -c conda-forge` 2. Run this script to re-generate the reference files `cd cmiles/tests/reference/ ;...

mattwthompson

This is a "master" issue for tracking various ideas relating to a future refactor: * What shall be included * What shall not be included * Relationship with the toolkit...

mattwthompson

Arguably trivial but it would be nice to handle the wrong input separately from checking that toolkit(s) are installed. Here I accidentally pass in an OpenFF `Molecule` and confused myself...

mattwthompson

Hydrogens move and stereochemistry flip when reading qcschema molecule

1

@vtlim pointed out that the `cmiles` SMILES changed for this molecule. ``` client = ptl.FractalClient() ds = client.get_collection('OptimizationDataset', 'OpenFF Full Optimization Benchmark 1') entry = ds.get_entry(name='CO/N=C/1\C[N@](C[C@H]1C[NH3+])c2c(cc3c(=O)c(cn(c3n2)C4CC4)C(=O)[O-])F-3') record = ds.get_record('CO/N=C/1\C[N@](C[C@H]1C[NH3+])c2c(cc3c(=O)c(cn(c3n2)C4CC4)C(=O)[O-])F-3', specification='default')...

ChayaSt

## Description When loading a qcschema molecule with N that has an explicit valence of 4, rdkit will fail unless the formal charge is changed for the offending N. ##...

ChayaSt

cmiles.utils.to_canonical_label failure

2

The following code raises an exception: ```python >>> import cmiles >>> cmiles.utils.to_canonical_label("[H:13][c:1]1[c:3]([n:8][c:5]([n:10][c:6]1[N:12]([H:19])[c:7]2[c:2]([c:4]([n:9][n:11]2[H:18])[H:16])[H:14])[H:17])[H:15]", (9, 5, 11, 5)) Traceback (most recent call last): File "", line 1, in File "/Users/choderaj/miniconda/lib/python3.7/site-packages/cmiles/utils.py", line 193,...

jchodera

It looks like there's no direct way to generate CMILES ids for an `OEMol`. Instead, we have to go through the SMILES (which loses information about atom ordering) or QCSchema...

jchodera