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
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