Re: [Rdkit-discuss] Plotting values next to atoms
On 03/11/2018 04:27, Greg Landrum wrote: Hi Eric, On Fri, Nov 2, 2018 at 2:00 PM Eric Jonas wrote: Hello! I'm trying to figure out if there's any known or sane way to automatically plot numerical values adjacent to atoms using the rdkit drawing machinery. Ideally I'd like to annotate certain atoms programmatically with values. I think the conventional way this is done for publication is post-hoc editing in illustrator but it would be great if there was an automatic or supported mechanism. Hi Eric, One hackish way is to export your molecules in 3D in the PDB format. Then shove your numeric value into the B-factor field. Then, color your molecules by B-factor using your favorite viewer (Chimera, pymol, etc.). For this to work correctly, you may have to scale your values so that they become in the same range than B-factors. Wit a little programming, you could also export your molecules (in 3D, still) directly as balls in the BILD format of UCSF Chimera, and look at them into Chimera. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Regards, Francois. Doing this correctly is on the list of high-priority things to do, and I really hope to have something done for the 2019.03 release, but there's no way I can guarantee that (it's a hard problem). In the meantime, there's a way to at least do something that is, hopefully, better than nothing: https://gist.github.com/greglandrum/8cf8ecc3253abf0a5139a776a5095163 [1] displayed here: https://nbviewer.jupyter.org/gist/greglandrum/8cf8ecc3253abf0a5139a776a5095163 [2] Links: -- [1] https://gist.github.com/greglandrum/8cf8ecc3253abf0a5139a776a5095163 [2] https://nbviewer.jupyter.org/gist/greglandrum/8cf8ecc3253abf0a5139a776a5095163 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Docs intentionally broken?
The change from epydoc to sphinx/autodoc for the python documentation led to some URL changes (most of which I fixed with redirects) and some missing modules. Looks like the rdGeometry module is missing. I will see if I can add it back, but this may take a bit since I'm traveling this week and the beginning of next. -greg On Mon, Nov 5, 2018 at 1:23 PM Brian Cole wrote: > My google search for 'rdkit python point3d' yielded the following as the > top result: > > https://rdkit.org/docs/api/rdkit.Geometry.rdGeometry-module.html > > Which unfortunately now has a 404, page not found. > > Was this an intentional reorganization of the documentation? > > -Brian > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Docs intentionally broken?
My google search for 'rdkit python point3d' yielded the following as the top result: https://rdkit.org/docs/api/rdkit.Geometry.rdGeometry-module.html Which unfortunately now has a 404, page not found. Was this an intentional reorganization of the documentation? -Brian ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] How to increase the quality of image by Draw.MolToImage ?
Hi, rdkit-discuss I'm looking for a way to increase the quality of image made by Draw.MolToImage. Here is my function, but its bonds and atom labels look like up-and-down slightly. I don't use IPython, then are there other options? def draw_img(smiles): from rdkit.Chem import AllChem from rdkit.Chem import Draw from rdkit.Chem.Draw import MolDrawing, DrawingOptions import matplotlib.pyplot as plt from mpl_toolkits.axes_grid1 import ImageGrid m = Chem.MolFromSmiles(smiles) AllChem.Compute2DCoords(m) mHs = AllChem.AddHs(Chem.Mol(m)) m_idx = Chem.Mol(m) mHs_idx = Chem.Mol(mHs) for mol in [m, m_idx, mHs, mHs_idx]: AllChem.GenerateDepictionMatching2DStructure(mol, m) img_m = Draw.MolToImage(m, size=(800, 400), fitImage=True) img_m_idx = Draw.MolToImage(m_idx, size=(800, 400), fitImage=True, includeAtomNumbers=True) img_mHs = Draw.MolToImage(mHs, size=(800, 400), fitImage=True) img_mHs_idx = Draw.MolToImage(mHs_idx, size=(800, 400), fitImage=True, includeAtomNumbers=True) imgs = [img_m, img_m_idx, img_mHs, img_mHs_idx] fig = plt.figure(1, (8, 8)) grid = ImageGrid(fig, 111, # similar to subplot(111) nrows_ncols=(2, 2), # creates 2x2 grid of axes axes_pad=0.1 # pad between axes in inch. ) for i in range(4): grid[i].imshow(imgs[i]) # The AxesGrid object work as a list of axes. plt.show() smiles = 'COc1ccc2[nH]c(nc2c1)S(=O)Cc3ncc(C)c(OC)c3C' draw_img(smiles) Also, I need the function which can close the presented image. The functions from RDkit seem not to support that. Best, Noki ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
