On 26/01/2011 01:16, Craig A. James wrote:
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);
As may have been discussed here earlier, maybe this option should output
explicit hydrogen as [H] rather than a hydrogen count on another atom.
SMARTS [CH2] matches a C with/exactly/ two Hs; SMARTS [H]C[H] will match
a carbon with/at least/ two Hs and is more versatile in substructure
searches. Would there be any objections to me changing it in the
development code?
Chris
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