On Nov 8, 2017, at 21:00, Chenyang Shi <cs3...@columbia.edu> wrote:
> =C= : [CH0;A;X2;!R](=[$(*)])=[$(*)]
The recursive SMARTS notation, which is the term inside of the [$(...)], finds
a match for the entire pattern and returns the first atom in that pattern.
> For example, if I search "C=C=O" using "[CH0;A;X2;!R](=[$(*)])=[$(*)]",
> >>> from rdkit import Chem
> >>> m = Chem.MolFromSmiles('C=C=O')
> >>> m.GetSubstructMatches(Chem.MolFromSmarts("[CH0;A;X2;!R](=[$(*)])=[$(*)]"))
> ((1, 0, 2),)
>
> it prints out atomic positions 1, 0, 2--three positions. But I would expect
> only one position for the Carbon in the middle.
The $(*) finds the pattern, which is a "*" and in this case the terminal
carbons, and returns it. The substructure search returns 3 positions because
the first is [CH0;A;X2;!R], the second is the first atom of "*", and the third
is the first atom of the other "*".
If you only want the first atom the entire pattern, then put the entire pattern
in a recursive SMARTS, as in:
[$([CH0;A;X2;!R](=*)=*)]
>>> pat = Chem.MolFromSmarts("[$([CH0;A;X2;!R](=*)=*)]")
>>> mol = Chem.MolFromSmiles('C=C=O')
>>> mol.GetSubstructMatches(pat)
((1,),)
> Similarly, if I search "C#C" using "[CH1;A;X2;!R]#[$(*)]",
> >>> from rdkit import Chem
> >>> m = Chem.MolFromSmiles('C#C')
> >>> m.GetSubstructMatches(Chem.MolFromSmarts("[CH1;A;X2;!R]#[$(*)]"))
> ((0, 1),)
> I would expect two separate positions such as (0,), (1,), indicating there
> are two carbon triple bonds (with an hydrogen).
Since you are only looking for a single atom, try putting the entire pattern in
a recursive SMARTS, as in
[$([CH1;A;X2;!R]#*)]
>>> mol = Chem.MolFromSmiles("C#C")
>>> pat = Chem.MolFromSmarts("[$([CH1;A;X2;!R]#*)]")
>>> mol.GetSubstructMatches(pat)
((0,), (1,))
> Then if if I search "CC#CC" using " [CH0;A;X2;!R]#[$(*)]",
I believe you want "[$([CH0;A;X2;!R]#*)]"
Thank you for your clear description of what you expected.
Cheers,
Andrew
da...@dalkescientific.com
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