Re: [Rdkit-discuss] Extracting data of a standard structural formula

Peleg, I was doing something similar using the c++ function compute2DCoords, where you can give a coordinate map as the second argument. It looks like this is exposed in python, using the Compute2DCoords method ( http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem.Mol-class.html#Compute2DCoords),

Re: [Rdkit-discuss] Extracting data of a standard structural formula

To further clarify what I mean: I created a nonanoic acid representation (via the smiles code "C(=O)O"). "Pelarginic_acid.svg.png" is what I expect to get in terms of coordinates, while "test_out.png" are the coordinates I actually get. On Sun, Aug 13, 2017 at 1:30 PM, Peleg Bar-Sapir

Re: [Rdkit-discuss] Extracting data of a standard structural formula

Hi Greg, Thank you for your reply! I tested the method you suggested, but it seems like rdMolDraw2D.PrepareMolForDrawing() has no affect. e.g, I have a molecule m, to which I add hydrogens. I then compute the 2D coordinates of m, and use rdMolDraw2D.PrepareMolForDrawing() as you suggested. To

Re: [Rdkit-discuss] Extracting data of a standard structural formula

Hi Peleg, On Sat, Aug 12, 2017 at 4:08 PM, Peleg Bar-Sapir wrote: > > I'm trying to get the 2D coordinates and info of all the atoms and bonds, > including hydrogens (i.e. atom type, bond type, etc.) of a molecule in a > standard structural formula. To clarify: I'm not