Non-stereo Encoding Problem with Explicit Hydrogens

[tylerperyea]

In certain cases, explicit hydrogens seem to cause trouble for the atom-labelling layer of the hash. In these cases, it seems that the smiles generated by the standardizer produces a different hash than the input molfile itself.

Consider the following poorly layed-out structure:

[molfile below]

Direct generation of hash from this Std_SMILES:

[H][C@@]12CC3=C(C(O)=C(OC)C(C)=C3)[C@@]([H])(N1C)[C@@]4([H])N([C@H]2O)[C@@]5([H])COC(=O)[C@]8(CS[C@]4([H])C6=C5C7=C(OCO7)C(C)=C6OC(C)=O)NCCC9=C8C=C(OC)C(O)=C9

And this hash:

DCLRH149F-FGAV2BD6PA-FA8DSLTXL4L-FALJX635AFC5

However, when that same smiles is fed into the standardizer, I get:

DCLRH149F-FFMPLZ16VC-FC1Y2MQMGXU-FCUZ42LBF8VB

If the explicit hydrogens are removed entirely:

The output hash is now compatible with the smiles.

DCLRH149F-FFMPLZ16VC-FC1Y2MQMGXU-FCU1SY5C8458

Molfile for explicit hydrogen version:

  Ketcher 12201304332D 1   1.00000     0.00000     0

 59 67  0     1  0            999 V2000
   -2.2321   -1.8660    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7321   -1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5981   -0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.4641    1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.4641   -1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

[caodac]

This example isn't so much about explicit H's but more about their parities. To fix this we need to be able to define a canonical set of parity flags for the specified stereocenters. This is far from a trivial fix.

[tylerperyea]

It can't just be parity though, because this messes up the atom label layer, not just the stereo layer. If it only had a problem with stereo, that'd be less concerning.

[caodac]

This particular example should now work properly from the recent commit 9b38dbd.