On 1/25/11 3:33 PM, Andrew Dalke wrote:
> On Jan 25, 2011, at 4:01 PM, Pascal Muller wrote:
>> Using pybel, I would like to generate a smarts with explicit H before
>> doing a substructure search.
>
> ...
>> scaffoldSmiles = mol.write("can")
>> scaffoldSmarts = pybel.Smarts(scaffoldSmiles)
>
> The problem is this the write("can") step. It converts explicit H:s into
> implicit
>
>>>> mol = pybel.readstring("smi", "C([H])([H])[H]")
>>>> len(mol.atoms)
> 4
>>>> mol.write("can")
> 'C\t\n'
>>>>
>
> I don't know if there's another pybel SMILES output option
> which prevents this unification ...
I don't know about pybel, but for babel(1) there's a command-line option that
may do what you need. It doesn't keep the explicit H atoms as separate atoms,
but it does produce a SMARTS that has the correct H count:
babel -Hcan
...
h Output explicit hydrogens as such
echo "[CH3]C" | babel -i smi -o can -xh
C[CH3]
1 molecule converted
In C++, you do it like this:
OBConversion *pconv = new OBConversion;
pconv->SetInAndOutFormats("smi", "can");
pconv->SetOptions("h", OBCONVERSONI::OUTOPTIONS);
Craig
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