Hi JP,
However I am unable to get bond orders for the protein side - am I doing
> something wrong or is this the intended behaviour ?
> I imagine I can use AssignBondOrdersFromTemplate() for the 20 amino acids
> and set these myself -- or is there a better way to do this?
>
I don't know why your protein doesn't get bond orders, the PDBParser should
know the standard amino acids. At least it worked for me when I tried
Chem.MolFromPDB() in the past. Which PDB structure do you try to read?
> Also, is there a way to make AssignBondOrdersFromTemplate assign bond
> orders to all matches?
>
The function was meant for assigning bonds based on an entire molecule. It
would probably not be so difficult to change this (with default = match
only one), if it is really needed.
> Also another thing I don't quite understand is in the following below
> code, I get a "WARNING: More than one matching pattern found - picking one"
> but how can my template match multiple times (this is not symettrical) ?
>
The way the AssignBondOrdersFromTemplate() function works is the following:
1) a copy of the template is generated where all bonds are set to single
bonds
2) this single-bonds copy is used for a substructure match with the query
molecule
3) bond orders are assigned based on this match and the original template
If you get this warning, it means that there is some symmetry in the
"all-single-bonds-stage" of your molecule. In your case, I guess it's the
carboxylic acids which can match two ways when there are only single bonds.
I hope this helps.
Best,
Sereina
>
>
>
> On 13 January 2014 21:02, JP <jeanpaul.ebe...@inhibox.com> wrote:
> >
> > Thanks All - I think I am in a good place now.
> >
> > I can get the SMILES from Paul's mmcif links and then I can use Sereina
> magic three lines to do what I want. I'd cross my fingers - but with RDKit
> you don't need to.
> > This works for all Chemical Components (or what other fashionable name
> they go by these days) in the PDB.
> >
> > For posterity: I have found a post in the mailing list started by James
> which sheds some light on this:
> >
> https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg03481.html
> >
> >
> >
> >
> > On 13 January 2014 19:46, sereina riniker <sereina.rini...@gmail.com>
> wrote:
> >>
> >> Hi JP,
> >>
> >> If you have also a SMILES of the molecule you want to read from PDB,
> you can assign the bond orders based on this template:
> >>
> >> tmp = Chem.MolFromPDBFile(yourfilename)
> >> template = Chem.MolFromSmiles(yoursmiles)
> >> mol = AllChem.AssignBondOrdersFromTemplate(template, tmp)
> >>
> >> Is this what you're looking for?
> >>
> >> Best,
> >> Sereina
> >>
> >>
> >> 2014/1/13 JP <jeanpaul.ebe...@inhibox.com>
> >>>
> >>> RDKitters!
> >>>
> >>> Finally back on the mailing list!
> >>>
> >>> I am sure we've been through this at the UGM (my mind must have
> wandered off!), but a quick question about the PDB reader and bond
> perception. Is this supported with the current PDB reader? I remember
> that someone (PaulE, perhaps?) was saying bond perception was painful, but
> there was some dictionary for PDB ligands which helps (any idea the name of
> this dictionary?).
> >>>
> >>> To the technical details.
> >>>
> >>> I am reading in the following PDB file with a simple MolFromPDBFile()
> call:
> >>>
> >>> HETATM 1 O1P 84T A1862 -27.016 9.387 -72.564 1.00 20.81
> O
> >>> HETATM 2 P 84T A1862 -27.282 9.818 -73.968 1.00 19.65
> P
> >>> HETATM 3 O2P 84T A1862 -27.881 11.176 -74.182 1.00 21.49
> O
> >>> HETATM 4 N 84T A1862 -25.869 9.583 -74.813 1.00 19.78
> N
> >>> HETATM 5 C 84T A1862 -25.759 10.010 -76.075 1.00 19.97
> C
> >>> HETATM 6 CA 84T A1862 -24.493 9.748 -76.807 1.00 19.75
> C
> >>> HETATM 7 CB 84T A1862 -24.794 8.678 -77.847 1.00 19.73
> C
> >>> HETATM 8 CG 84T A1862 -23.571 8.324 -78.681 1.00 19.70
> C
> >>> HETATM 9 CD2 84T A1862 -23.309 9.519 -79.611 1.00 18.49
> C
> >>> HETATM 10 CD1 84T A1862 -23.863 6.932 -79.305 1.00 18.60
> C
> >>> HETATM 11 OHB 84T A1862 -25.210 7.467 -77.223 1.00 19.17
> O
> >>> HETATM 12 OH 84T A1862 -23.549 9.127 -75.984 1.00 20.33
> O
> >>> HETATM 13 O 84T A1862 -26.672 10.517 -76.692 1.00 20.26
> O
> >>> HETATM 14 O5' 84T A1862 -28.377 8.861 -74.619 1.00 19.39
> O
> >>> HETATM 15 C5' 84T A1862 -28.002 7.536 -74.954 1.00 18.47
> C
> >>> HETATM 16 C4' 84T A1862 -28.909 7.000 -76.012 1.00 18.24
> C
> >>> HETATM 17 C3' 84T A1862 -28.901 7.826 -77.298 1.00 18.28
> C
> >>> HETATM 18 C2' 84T A1862 -30.318 7.610 -77.768 1.00 18.69
> C
> >>> HETATM 19 O2' 84T A1862 -30.789 8.641 -78.581 1.00 19.64
> O
> >>> HETATM 20 O4' 84T A1862 -30.262 6.951 -75.529 1.00 18.80
> O
> >>> HETATM 21 C1' 84T A1862 -31.152 7.470 -76.521 1.00 19.01
> C
> >>> HETATM 22 N9 84T A1862 -31.753 8.732 -76.009 1.00 20.08
> N
> >>> HETATM 23 C4 84T A1862 -33.033 9.013 -76.158 1.00 21.10
> C
> >>> HETATM 24 N3 84T A1862 -34.018 8.339 -76.786 1.00 21.58
> N
> >>> HETATM 25 C2 84T A1862 -35.263 8.846 -76.830 1.00 21.95
> C
> >>> HETATM 26 C8 84T A1862 -31.223 9.701 -75.291 1.00 20.27
> C
> >>> HETATM 27 N7 84T A1862 -32.173 10.618 -75.019 1.00 21.28
> N
> >>> HETATM 28 C5 84T A1862 -33.315 10.213 -75.563 1.00 21.81
> C
> >>> HETATM 29 C6 84T A1862 -34.624 10.702 -75.627 1.00 22.85
> C
> >>> HETATM 30 N1 84T A1862 -35.550 10.010 -76.285 1.00 22.44
> N
> >>> HETATM 31 N6 84T A1862 -35.008 11.862 -75.052 1.00 23.86
> N
> >>> TER
> >>> END
> >>>
> >>> But I am losing all the double bond (and aromatic) information:
> >>>
> >>> m = Chem.MolFromPDBFile(sys.argv[1])
> >>> print Chem.MolToSmiles(m)
> >>>
> >>> Gives me:
> >>>
> >>> CC(C)C(O)C(O)C(O)NP(O)(O)OCC1CC(O)C(N2CNC3C2NCNC3N)O1
> >>>
> >>> As usual, many thanks for your time,
> >>>
> >>> -
> >>> Jean-Paul Ebejer
> >>> Early Stage Researcher
> >>>
> >>>
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> >>>
> >>
> >
>
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