non-flatness check

[chmnk]

Addresses this issue #53

Adds a non-flatness check for non-flat 5- and 6-membered rings with the following SMARTS patterns

    "nonaromatic_5_membered_rings": "[C,O,S,N&!a]~1[C,O,S,N&!a][C,O,S,N&!a][C,O,S,N&!a][C,O,S,N&!a]1",
    "nonaromatic_6_membered_rings": "[C,O,S,N&!a]~1[C,O,S,N&!a][C,O,S,N&!a][C,O,S,N&!a][C,O,S,N&!a][C,O,S,N&!a]1",
    "nonaromatic_6_membered_rings_db03_0": "[C&!a]~1[C&!a][C,O,S,N&!a]~[C,O,S,N&!a][C&!a][C&!a]1",
    "nonaromatic_6_membered_rings_db03_1": "[C&!a]~1[C&!a][C&!a]~[C&!a][C,O,S,N&!a][C&!a]1",
    "nonaromatic_6_membered_rings_db02_0": "[C&!a]~1[C&!a][C&!a][C,O,S,N&!a]~[C,O,S,N&!a][C&!a]1",
    "nonaromatic_6_membered_rings_db02_1": "[C&!a]~1[C&!a][C,O,S,N&!a][C&!a]~[C&!a][C&!a]1",

[maabuu]

Could you merge the latest main branch into the PR?

The tests failed due to a deprecated version of actions/upload-artifact. The main branch is now on the latest version.

[maabuu]

The SMARTS do not seem completely correct yet. Could the &!a be dropped?
smarts.plus shows the second and third SMARTS as:

[maabuu]

If I understand SMARTS correctly, capital letters match only aliphatic atoms and hence we can drop the &!a. How about these?

    "nonaromatic_5_membered_rings": "[C,O,S,N]~1[C,O,S,N][C,O,S,N][C,O,S,N][C,O,S,N]1",
    "nonaromatic_6_membered_rings": "[C,O,S,N]~1[C,O,S,N][C,O,S,N][C,O,S,N][C,O,S,N][C,O,S,N]1",
    "nonaromatic_6_membered_rings_db03_0": "[C]~1[C][C,O,S,N]~[C,O,S,N][C][C]1",
    "nonaromatic_6_membered_rings_db03_1": "[C]~1[C][C]~[C][C,O,S,N][C]1",
    "nonaromatic_6_membered_rings_db02_0": "[C]~1[C][C][C,O,S,N]~[C,O,S,N][C]1",
    "nonaromatic_6_membered_rings_db02_1": "[C]~1[C][C,O,S,N][C]~[C][C]1",

[chmnk]

capital letters match only aliphatic atoms

Good to know, I didn't check it. Updated the PR

[maabuu]

Looks good to me.

[maabuu]

Thank you very much for your contribution.