I'm in all-day meetings this week and can't really do an in-depth reply.
This old message was an attempt to explain the confusing aspects of the
topic:
http://www.mail-archive.com/rdkit-devel@lists.sourceforge.net/msg00077.html
On Wed, Jan 15, 2014 at 9:06 AM, JP <jeanpaul.ebe...@inhibox.com> wrote:
> Hi there Chan, Others,
>
> First of all, many thanks for the helpful example and the explanation --
> but I require some further clarification more specifically about the
> following:
>
> m = Chem.MolFromSmiles('O')
> print m.GetAtomWithIdx(0).GetNumImplicitHs()
> print m.GetAtomWithIdx(0).GetNumExplicitHs()
> print m.GetAtomWithIdx(0).GetTotalNumHs()
>
> m = Chem.MolFromSmiles('[OH2]')
> print m.GetAtomWithIdx(0).GetNumImplicitHs()
> print m.GetAtomWithIdx(0).GetNumExplicitHs()
> print m.GetAtomWithIdx(0).GetTotalNumHs()
>
> m = Chem.MolFromSmiles('O([H])[H]')
> print m.GetAtomWithIdx(0).GetNumImplicitHs()
> print m.GetAtomWithIdx(0).GetNumExplicitHs()
> print m.GetAtomWithIdx(0).GetTotalNumHs()
>
> ## Results:
> 2 0 2
> 0 2 2
> 2 # ?? 0 # ?? 2
>
> Why aren't the results of [OH2] and O([H])[H] the same? is this another
> SMILES gotcha? Am I not declaring the Hs explicitly in both cases? You
> see why I am confused?
>
> Your example works fine, unless the user specifies C(=O)[OH] - in that
> case I need to remove the H manually in an editable mol (or I get the
> incorrect valency errors).
>
> Also this must be related to Greg's "Rethinking the RDKit's implicit
> Hydrogen handling" (
> https://www.mail-archive.com/rdkit-devel@lists.sourceforge.net/msg00077.html).
> Does anyone know if this has been implemented? (My guess by reading the
> Atom API doc is no
> http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem.Atom-class.html)
>
> Thank you all for your help!
> JP
>
>
> -
> Jean-Paul Ebejer
> Early Stage Researcher
>
>
> On 15 January 2014 06:28, S.L. Chan <slch...@yahoo.com> wrote:
>
>>
>> ----- Forwarded Message -----
>> *From:* S.L. Chan <slch...@yahoo.com>
>> *To:* JP <jeanpaul.ebe...@inhibox.com>
>> *Sent:* Tuesday, January 14, 2014 10:03 PM
>> *Subject:* Re: [Rdkit-discuss] Add a charge to an atom and modify Hs
>> accordingly (protonation)
>>
>> Hello JP,
>>
>> You need to bear in mind that by default RDKit does not store the
>> hydrogens explicitly. RemoveHs() generally does not do anything on
>> a fresh molecule, and GetNumExplicitHs() generally returns 0 for all
>> atoms.
>>
>> Implicit hydrogens mean the hydrogen atoms implied.
>> GetNumImplicitHs() returns the number of hydrogens EXPECTED to
>> be bonded to that atom. This is why it returned 1 even though
>> your molecule did not have explicit hydrogens.
>>
>> With these in mind you should be able to achieve what you want:
>>
>> >>> m = Chem.MolFromSmiles('C(=O)O')
>> >>> m2 = Chem.AddHs(m)
>> >>> m2.GetNumAtoms()
>> 5
>> >>> m.GetAtomWithIdx(2).SetFormalCharge(-1)
>> >>> Chem.SanitizeMol(m)
>> >>> m3 = Chem.AddHs(m)
>> >>> m3.GetNumAtoms()
>> 4
>> >>> Chem.MolToSmiles(m)
>> 'O=C[O-]'
>>
>> Finally, remember that AddHs() does not generate coordinates for
>> the hydrogens. You need to use AllChem.EmbedMolecule() if you
>> need coordinates for them.
>>
>> Ling
>>
>>
>>
>> ------------------------------
>> *From:* JP <jeanpaul.ebe...@inhibox.com>
>> *To:* "rdkit-discuss@lists.sourceforge.net" <
>> rdkit-discuss@lists.sourceforge.net>
>> *Sent:* Tuesday, January 14, 2014 10:58 AM
>> *Subject:* [Rdkit-discuss] Add a charge to an atom and modify Hs
>> accordingly (protonation)
>>
>> Hi there,
>>
>> This must be really easy -- but anything I am trying is failing and I am
>> losing my mind. I want to add a charge (+ / -) to an atom and add or
>> delete a connected H accordingly.
>>
>> I thought an easy way to do this was to remove all Hs from the molecule
>> (removeHs), add a charge (SetFormalCharge), and re-add all Hs (AddHs).
>> This doesn't work (the sanitization check fails in AddHs, incorrect
>> valence - which I understand) - what is the best way to do this?
>>
>> Also,
>>
>> >>> m = Chem.MolFromSmiles('C(=O)O')
>> >>> m.Debug()
>> Atoms:
>> 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 0 chi: 0
>> 1 8 O chg: 0 deg: 1 exp: 2 imp: 0 hyb: 3 arom?: 0 chi: 0
>> 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0
>> Bonds:
>> 0 0->1 order: 2 conj?: 1 aromatic?: 0
>> 1 0->2 order: 1 conj?: 1 aromatic?: 0
>> >>> m_noHs = Chem.RemoveHs(m)
>> >>> m_noHs.Debug()
>> Atoms:
>> 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 0 chi: 0
>> 1 8 O chg: 0 deg: 1 exp: 2 imp: 0 hyb: 3 arom?: 0 chi: 0
>> 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0
>> Bonds:
>> 0 0->1 order: 2 conj?: 1 aromatic?: 0
>> 1 0->2 order: 1 conj?: 1 aromatic?: 0
>>
>> >>> m_noHs.GetAtomWithIdx(2).GetNumExplicitHs()
>> 0
>> >>> m_noHs.GetAtomWithIdx(2).GetNumImplicitHs()
>> 1
>>
>> Why is there still an implicit H after I "removed" them?
>>
>> I have tried to use ReplaceSubstructs() for this (a bit of an overkill)
>> but I then lose the 3D information of the original atom.
>>
>> Many Thanks... and sorry for the repeated spamming :((((
>>
>> -
>> Jean-Paul Ebejer
>> Early Stage Researcher
>>
>>
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