Id=-1,possiblePartners='[#8,#7,#9]',
> possibleHs='[#1][#8,#7,#16]',distThresh=2.5):
> conf = m.GetConformer(confId)
> partners =[x[0] for x in m.GetSubstructMatches(Chem.MolFromSmarts(
> possiblePartners))]
> hs= [x[0] for x in m.GetSubstructMatches(Chem.
>
ngle<=60:
> A60+=1
> elif Angle>60 and Angle<=90:
> A90+=1
> elif Angle>90 and Angle<=102:
> A102+=1
> return (A60,A90,A102)
>
>
> the stats are not perfect but in progress.
>
>
>
>
>
é : mercredi 14 septembre 2016 14:14
À : Guillaume GODIN
Cc : RDKit Discuss
Objet : Re: [Rdkit-discuss] Angstroms Hydrogen bonding
On Wed, Sep 14, 2016 at 4:16 AM, Guillaume GODIN
mailto:guillaume.go...@firmenich.com>> wrote:
Your solution is perfect!
glad it worked
I am cur
or x in m.GetSubstructMatches(Chem.MolFromSmarts(possibleHs))]
res = []
for h in hs:
ph = conf.GetAtomPosition(h)
for partner,linker in zip(partners,linkers):
if m.GetBondBetweenAtoms(h,linker) is not None:
continue
d = conf.GetAtomPosition(partner).
ool, I look forward to trying that out.
Best,
-greg
> BR,
>
> Guillaume
> --
> *De :* Greg Landrum
> *Envoyé :* mercredi 14 septembre 2016 12:16
> *À :* Guillaume GODIN
> *Cc :* RDKit Discuss
> *Objet :* Re: [Rdkit-discuss] Angstroms Hydrog
Hi Guillaume,
Greg's solution is great for intra-molecular H-Bonds. If you want to
achieve inter-molecular ones then it's a bit more complicated. I did such
implementation in my package ODDT [https://github.com/oddt/oddt], which
also uses RDKit. You can find the hbond function in interactions modu
uch
more occurences (ie. a factor of 50-100 more then expected).
When it will be done I will share the code with you guys.
BR,
Guillaume
De : Greg Landrum
Envoyé : mercredi 14 septembre 2016 12:16
À : Guillaume GODIN
Cc : RDKit Discuss
Objet : Re: [Rdkit-dis
Hi Guillaume,
On Tue, Sep 13, 2016 at 10:12 PM, Guillaume GODIN <
guillaume.go...@firmenich.com> wrote:
> 1 Does 3D coordinates of a conformer is in Angstroms ?
>
> If you read the conformer from a file, for example a mol file, then the 3D
coordinates are in whatever units they were in in that fi
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