Bugs item #3310779, was opened at 2011-06-02 19:35
Message generated for change (Tracker Item Submitted) made by baoilleach
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Noel O'Boyle (baoilleach)
Assigned to: Nobody/Anonymous (nobody)
Summary: Handling of Implicit H in Smarts
Initial Comment:
>From Andrew Dalke on list:
One of RDKit MACCS key definitions is
[!#6;!#1]~[!#6;!#1;!H0]
I'm working on my test suite for those definitions, as mentioned in my previous
email.
Here's a test case
>>> mol = pybel.readstring("smi", "[U]S(C)C")
>>> matcher = pybel.Smarts("[!#6;H0]")
>>> matcher.findall(mol)
[(1,), (2,)]
>>> matcher = pybel.Smarts("[!#6;!#1]~[!#6;!#1;!H0]")
>>> matcher.findall(mol)
[]
>>>
RDKit, OEChem, and Daylight say that that pattern matches that structure.
That's because all three programs say that the "S" has an implicit hydrogen on
it.
Daylight says that sulfur has valence levels of "S (2,4,6)"
http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
This looks to be a bug in the code which calculates the implicit hydrogen count.
Here's another another case where the implicit h-count is wrong, this time with
P.
Daylight says the valence levels for P in SMILES are (3,5)
Given N=PPCC
The second atom (the first P) has a double bond and a single,
so it's valences are filled. It should have no implicit hydrogens.
However, here's first the RDKit.MACCS pattern which passed, unexpectedly, in
OpenBabel
>>> mol = pybel.readstring("smi", "N=PPCC")
>>> matcher = pybel.Smarts("[!#6;!#1;!H0]~[!#6;!#1;!H0]")
>>> matcher.findall(mol)
[(1, 2), (2, 3)]
>>> Hmatcher = pybel.Smarts("[!H0]")
>>> Hmatcher.findall(mol)
[(1,), (2,), (3,), (4,), (5,)]
>>>
You can see it's because the matcher thinks all of the atoms have at least one
implicit hydrogen.
Compare this to RDKit, which correctly has the P with no implicit hydrogens.
>>> mol = Chem.MolFromSmiles("N=PPCC")
>>> pat = Chem.MolFromSmarts("[!#6;!#1;!H0]~[!#6;!#1;!H0]")
>>> mol.GetSubstructMatches(pat)
()
>>> Hpat = Chem.MolFromSmarts("[!H0]")
>>> mol.GetSubstructMatches(Hpat)
((0,), (2,), (3,), (4,))
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