Hi Greg,
Yep, the input molecule (a ROMol object read from a SDF) is indeed
protonated. Which was why I was surprised that I didn't see any protons
after I wrote out the PDB object. (I am not doing anything but using RDKit
to pump out independent PDBs for each MOL record in the SD file.) I'll
check to ensure that it is indeed seeing the protons, and get back to you.
Thanks!
Matt
On Thu, May 1, 2014 at 8:44 PM, Greg Landrum <greg.land...@gmail.com> wrote:
> Hi Matt,
>
> On Thu, May 1, 2014 at 11:19 PM, Matthew Lardy <mla...@gmail.com> wrote:
>
>>
>> Hopefully this is easy, but I have an ROMol object that I want to convert
>> into a PDB file. It seems to me that the MolToPDBFile is exactly what I
>> should be using, but I am missing the protons in the resulting file.
>> What's weird is that the input file has protons, and I have added a step to
>> protonate the molecule after reading just to ensure that they are there.
>>
>> Any idea of how to move through this?
>>
>
> If the Hs are there, they should end up being written to the PDB. Here's
> an example:
>
> In [5]: m = Chem.MolFromSmiles('C')
> In [6]: m=Chem.AddHs(m)
> In [7]: print Chem.MolToPDBBlock(m)
> HETATM 1 C1 UNL 1 0.000 0.000 0.000 1.00 0.00
> C
> HETATM 2 H1 UNL 1 0.000 0.000 0.000 1.00 0.00
> H
> HETATM 3 H2 UNL 1 0.000 0.000 0.000 1.00 0.00
> H
> HETATM 4 H3 UNL 1 0.000 0.000 0.000 1.00 0.00
> H
> HETATM 5 H4 UNL 1 0.000 0.000 0.000 1.00 0.00
> H
> CONECT 1 2 3 4 5
> END
>
> Are you sure that the molecule actually has had Hs added? You can check
> this with the Debug() method:
>
> In [8]: m.Debug()
> Atoms:
> 0 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 0
> 1 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 0 arom?: 0 chi: 0
> 2 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 0 arom?: 0 chi: 0
> 3 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 0 arom?: 0 chi: 0
> 4 1 H chg: 0 deg: 1 exp: 1 imp: 0 hyb: 0 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
>
> Note: you mention Hs being removed on reading your input files. If you
> want to preserve the Hs that are present in the input file, you can do this
> from a mol block/file like this:
>
> In [14]: print mb
>
> RDKit
>
> 5 4 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 H 0 0 0 0 0 1 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 H 0 0 0 0 0 1 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 H 0 0 0 0 0 1 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 H 0 0 0 0 0 1 0 0 0 0 0 0
> 1 2 1 0
> 1 3 1 0
> 1 4 1 0
> 1 5 1 0
> M END
>
> In [15]: nm = Chem.MolFromMolBlock(mb,removeHs=False)
> In [16]: nm.GetNumAtoms()
> Out[16]: 5
>
>
> The PDB parsers take a similar argument.
>
> -greg
>
>
>
------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos. Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
