Hi Ling,
On Thu, Aug 1, 2013 at 2:56 AM, S.L. Chan <slch...@yahoo.com> wrote:
> Hello folks,
>
> In a way this is a continuation of a previous discussion.
>
> My question is: so is there a simple way to obtain the original
> indexing with all hydrogen atoms included? Do I have to write
> my own function?
>
I guess this means that you want the hydrogens to not be removed from the
molecule?
If so, you just need to tell the RDKit not to remove the Hs.
>From a mol file this is a single extra argument:
In [3]: m = Chem.MolFromMolFile('hmol.mol',removeHs=False)
In [4]: m.Debug()
Atoms:
0 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 0
1 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 0
2 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
3 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
4 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
5 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
6 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
7 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 4 arom?: 0 chi: 0
8 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
Bonds:
0 0->1 order: 1 conj?: 0 aromatic?: 0
1 0->2 order: 1 conj?: 0 aromatic?: 0
2 0->3 order: 1 conj?: 0 aromatic?: 0
3 0->4 order: 1 conj?: 0 aromatic?: 0
4 1->5 order: 1 conj?: 0 aromatic?: 0
5 1->6 order: 1 conj?: 0 aromatic?: 0
6 1->7 order: 1 conj?: 0 aromatic?: 0
7 7->8 order: 1 conj?: 0 aromatic?: 0
but you can also do it from SMILES if you need to:
In [6]: m = Chem.MolFromSmiles('[H]C([H])([H])O[H]',sanitize=False)
In [7]: Chem.SanitizeMol(m)
Out[7]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
In [8]: m.Debug()
Atoms:
0 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
1 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 0
2 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
3 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
4 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 4 arom?: 0 chi: 0
5 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
Bonds:
0 0->1 order: 1 conj?: 0 aromatic?: 0
1 1->2 order: 1 conj?: 0 aromatic?: 0
2 1->3 order: 1 conj?: 0 aromatic?: 0
3 1->4 order: 1 conj?: 0 aromatic?: 0
4 4->5 order: 1 conj?: 0 aromatic?: 0
Does that help?
-greg
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