Andrew Dalke

**Describe the bug** I used `off_coverage.py` to cross-compare the OpenFF Molecule objects created by OpenEyeToolkitWrapper with those created by RDKitToolkitWrapper, using `oe_mol.is_isomorphic_with(rd_mol)`. The failure cases were only those with a...

bond_order==0 in CHEBI:52729

1

**Describe the bug** The RDKitToolkitWrapper can parse [CHEBI:52729](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:52729) into a Molecule object but cannot convert that Molecule back into an RDMol because there are bonds with a bond type of...

DrugBank_6182, RDKit, and OpenEye atom stereochemistry assumptions

2

**Describe the bug** DrugBank_6182, when read by RDKitToolkitWrapper, creates a Molecule that when passed to OpenEyeToolkitWrapper's `to_openeye()` raises the exception "Programming error: OpenEye atom stereochemistry assumptions failed". This may seem...

Following on https://github.com/openforcefield/openff-toolkit/issues/1008 , I processed 45,043 records from ChEBI to identify all those records where OEChem *bond* stereochemistry assumptions fail, *when read by RDKitToolkitWrapper and converted to an OpenEye...

merge common toolkit tests

2

The openff/toolkit/tests/test_toolkits.py has a number of tests which should be equivalent across all toolkits (except for some I/O values, like the specific details of SMILES canonicalization). This test code is...

Replace use of tar file with zip file

1

The test suite uses the tar.gz files AlkEthOH_tripos.tar.gz and FreeSolv.tar.gz . Test configuration requires reading those files to figure out what names are present. Test runs require unpacking the contents...

reduce use of test_toolkits.get_mini_drug_bank()

1

I will be working on the toolkit wrapper API. I want to reduce the time needed to run the tests to make it easier to run the test suite after...

disallow closures after branches

3

I think that closures should not be allowed after ')' terms. To start, I think there's a bug in how the deepsmiles implementation handles this case. Consider `COPNBCl))=3`. I expected...

Shift closure values

2

The closure values "0" and "1" will never be seen in the current DeepSMILES. C0 is meaningless, and C1 has a loop to itself. Proposal 1: Shift the closure numbers...

dot disconnection combined with branches and closures

2

I think that the dot disconnection "." should reset the system state so that closures and branches cannot cross it. Here's an example of using a branch to cross a...