Re: [Rdkit-discuss] where to find I-State of atoms

Thanks Greg & Marco, so after reading a little around the Dictionary + 3D descriptors pdf... I-State are in fact "E-state" and are available in rdkit in python (https://github.com/rdkit/rdkit/tree/master/rdkit/Chem/EState) as fingerprint per atom. I will look at it. Best regards, Dr. Guill

[Rdkit-discuss] gromacs force field and topology from SMILES

Hi Rafal, as far as I know the MMFF is not compatible with any contemporary MD forcefield. The usual way to generate topologies for ligands is the generalised amber forcefield (GAFF). What you need are ambertools ( http://ambermd.org/) and acpype (https://github.com/t-/acpype). As input you need a

Re: [Rdkit-discuss] where to find I-State of atoms

Guillaume, I've been using this chapter from the Handbook of Chemoinformatics for the 3D descriptors: http://michem.disat.unimib.it/chm/download/materiale/geometrical_descriptors.pdf Section 2.6 has a discussion of the MoRSE descriptor, along with a definition of the I values. Is there sufficien

Re: [Rdkit-discuss] windows 32 shared library

Hi Steven, On Fri, Oct 14, 2016 at 8:32 PM, Steven Combs wrote: > Has anyone compiled rdkit into a 32bit shared library dll? > > It should be possible. What are you trying to do? -greg -- Check out the vibrant tech comm

Re: [Rdkit-discuss] Issues with rdkit and postgresql cartridge conda installation

Hi Larson, On Fri, Oct 14, 2016 at 6:17 PM, Danes, Larson wrote: > > First and foremost, please excuse any inaccuracies as I am new to the world of Cheminformatics. I'll start with some background on my issue. I've got a MySQL database with chemical information such as CASRNs, Annotation Class, a

[Rdkit-discuss] Solved! (was, Re: Fwd: Jupyter renders only from the outermost level?)

In an earlier thread, I reported that I could not get Jupyter to render except from the outermost level of the notebook. For instance, the following code would not render Benzene: -- from rdkit import Chem from rdkit.Chem import rdDepictor from rdkit.Chem.Draw import rdMolDraw2D from rdkit

Re: [Rdkit-discuss] gromacs force field and topology from SMILES

Hi Rafal, as far as I know the MMFF is not compatible with any contemporary MD forcefield. The usual way to generate topologies for ligands is the generalised amber forcefield (GAFF). What you need are ambertools (http://ambermd.org/ ) and acpype (https://github.com/t-/acpy

Re: [Rdkit-discuss] where to find I-State of atoms

This book >>> http://onlinelibrary.wiley.com/book/10.1002/9783527613106 <<< that look like a bible. Best regards, GMR > On 14 Oct 2016, at 19:28, Guillaume GODIN > wrote: > > ​Dear All, > > I'm looking for the definition & values of the atomic "I-State" used in > Dragon for RDF, MORSE

[Rdkit-discuss] windows 32 shared library

Has anyone compiled rdkit into a 32bit shared library dll? Steven Combs -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___

[Rdkit-discuss] where to find I-State of atoms

?Dear All, I'm looking for the definition & values of the atomic "I-State" used in Dragon for RDF, MORSE descriptors. Do you have a source for those physical descriptors ? best regards, Dr. Guillaume GODIN Principal Scientist Chemoinformatic & Datamining Innovation CORPORATE R&D DIVISION DI

[Rdkit-discuss] Issues with rdkit and postgresql cartridge conda installation

Hello all, First and foremost, please excuse any inaccuracies as I am new to the world of Cheminformatics. I'll start with some background on my issue. I've got a MySQL database with chemical information such as CASRNs, Annotation Class, and SMILE strings. I have a web app currently in develop

Re: [Rdkit-discuss] gromacs force field and topology from SMILES

Dear Rafal, answers below. On 10/14/16 13:53, Rafal Roszak wrote: > Dear all, > > 1. I want to generate gromacs topology with force field parameters > from SMILES. RDKit has two FFs so this should be easy task at least for > this two force fields. Bond and angle parameters can be simply take > fr

[Rdkit-discuss] gromacs force field and topology from SMILES

Dear all, 1. I want to generate gromacs topology with force field parameters from SMILES. RDKit has two FFs so this should be easy task at least for this two force fields. Bond and angle parameters can be simply take from Get*BondStretchParams and Get*StretchBendParams, but vdW and torsian paramet