Re: [Rdkit-discuss] Angstroms Hydrogen bonding

2016-09-15 Thread Greg Landrum
#h.write(str(H)+","+str(abs(H-float(mol.GetProp('deltaH(c)'+'\n') > #print H[1]-float(mol.GetProp('deltaH(c)')) > V.append(H[0]) > return H[1] > > #h = open('Molecules_Score.txt','w') > suppl = > Chem.SDMolSupplier('/Users/mbp/Downloads

Re: [Rdkit-discuss] Angstroms Hydrogen bonding

2016-09-14 Thread Peter Gedeck
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. > > > ​ > > > > BR, > &g

Re: [Rdkit-discuss] Angstroms Hydrogen bonding

2016-09-14 Thread Guillaume GODIN
...@gmail.com> Envoyé : 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 <guillaume.go...@firmenich.com<mailto:guillaume.go...@firmenich.com>> wrote: Your solu

Re: [Rdkit-discuss] Angstroms Hydrogen bonding

2016-09-14 Thread Guillaume GODIN
+41 (0)79 536 1039 Firmenich SA RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 De : Greg Landrum <greg.land...@gmail.com> Envoyé : mercredi 14 septembre 2016 14:14 À : Guillaume GODIN Cc : RDKit Discuss Objet : Re: [Rdkit-discuss] Angstroms Hydrog

Re: [Rdkit-discuss] Angstroms Hydrogen bonding

2016-09-14 Thread Greg Landrum
> > Guillaume > -- > *De :* Greg Landrum <greg.land...@gmail.com> > *Envoyé :* mercredi 14 septembre 2016 12:16 > *À :* Guillaume GODIN > *Cc :* RDKit Discuss > *Objet :* Re: [Rdkit-discuss] Angstroms Hydrogen bonding > > Hi Guillaume

Re: [Rdkit-discuss] Angstroms Hydrogen bonding

2016-09-14 Thread Maciek Wójcikowski
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

Re: [Rdkit-discuss] Angstroms Hydrogen bonding

2016-09-14 Thread Guillaume GODIN
-100 more then expected). When it will be done I will share the code with you guys. BR, Guillaume De : Greg Landrum <greg.land...@gmail.com> Envoyé : mercredi 14 septembre 2016 12:16 À : Guillaume GODIN Cc : RDKit Discuss Objet : Re: [Rdkit-discuss] A

Re: [Rdkit-discuss] Angstroms Hydrogen bonding

2016-09-14 Thread Greg Landrum
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

[Rdkit-discuss] Angstroms Hydrogen bonding

2016-09-13 Thread Guillaume GODIN
Dear RDKiters, I have two question: 1 Does 3D coordinates of a conformer is in Angstroms ? 2 How to enumerate all HBonding to determine the bond length ? Best regards, Guillaume ** DISCLAIMER This email and any files