Re: [Rdkit-discuss] depict R-group property
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Re: [Rdkit-discuss] depict R-group property
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From: Greg L. <gre...@gm...> - 2011-06-14 19:55:40
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Hi Don, On Mon, Jun 13, 2011 at 8:58 PM, Donald Keidel <don...@gm...> wrote: > > Have the following mol file: > > RDKit 2D > > 7 6 0 0 0 0 0 0 0 0999 V2000 > 7.9102 -2.4208 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 6.4770 -2.4208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.0437 -2.4208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 7.1916 -2.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.7583 -2.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.3292 -2.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 7.9148 -3.2458 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 > 2 4 1 0 > 3 5 1 0 > 4 1 1 0 > 5 2 1 0 > 6 3 1 0 > 1 7 1 0 > M RGP 1 7 1 > V 7 * > M END > > > When I use RDKit to depict the molecule I get a * in the image where the > R-group is located. > > Is there a way to define what letter or letter with number combination > is printed for the R-group? A dictionary perhaps? Ideally I would like > the ability to depict R1 thru R9. Here's what's going on currently: By default the rendering code uses atom.GetSymbol() to determine what should show up in the drawing. atom.GetSymbol() using the atomic number, unless the atom has the property "dummyLabel" set. If that property is set, it's used. It should also be checking for the property "_MolFileRLabel". In looking at this I also discovered another problem : there's an error if you call the depiction code using a molecule with R groups and the kekulize argument is True. I've entered a bug about each of these things. They'll be fixed in the next release (planned for end of the month). It's great (for the RDKit) that someone is really using the R group stuff in mol files and reporting the problems; this is an under-utilized/tested piece of the code, so I really appreciate it. Apologies that you're having to suffer through the teething problems. Best, -greg |