Re: [Rdkit-discuss] rejoining pairs of fragments after fragmenting a molecule

Hi Ling, Having done something similar (but not in RDKit), I would suggest a different algorithm. I think that fragmenting the molecule first and then stitching the bits together is always going to be very complicated. Instead, just fragment the molecule in the ways that you want: - Find the

Re: [Rdkit-discuss] explicit H atoms

I believe it's not possible to represent the chirality of the attached molecule's ring fusion carbons without using an explicit H. Regards, Mark -- Mark Mackey Chief Scientific Officer Cresset New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK tel: +44 (0)1223

Re: [Rdkit-discuss] Reaction SMARTS ring properties

lps, -greg On Tue, Sep 14, 2021 at 12:33 AM Mark Mackey via Rdkit-discuss mailto:rdkit-discuss@lists.sourceforge.net>> wrote: Hi all, I’m trying to run some chemical reactions using the C++ API. Doing something like text = “ [cH1:1]1:[c:2](-[CH2:7]-[CH2:8]-[NH2:9]):[c:3]:[c:4]:[c:5]:[c

[Rdkit-discuss] Reaction SMARTS ring properties

Hi all, I'm trying to run some chemical reactions using the C++ API. Doing something like text = " [cH1:1]1:[c:2](-[CH2:7]-[CH2:8]-[NH2:9]):[c:3]:[c:4]:[c:5]:[c:6]:1.[#6:11]-[CH1;R0:10]=[OD1]>>[c:1]12:[c:2](-[CH2:7]-[CH2:8]-[NH1:9]-[C:10]-2(-[#6:11])):[c:3]:[c:4]:[c:5]:[c:6]:1c1cc(CCN)ccc1";

[Rdkit-discuss] Problem with depicting reaction SMARTS

Hi all, I'm trying to generate an SVG from reaction SMARTS. The code looks like this: QByteArray ChemicalReactionsCalculation::toSvg(const QString , int width, int height) { try { std::string text = reaction.toStdString(); std::unique_ptr

Re: [Rdkit-discuss] Problem with depicting reaction SMARTS

tQuery(const Atom *a) { Cheers, p. On Tue, Feb 8, 2022 at 8:29 PM Mark Mackey via Rdkit-discuss mailto:rdkit-discuss@lists.sourceforge.net>> wrote: Hi all, I’m trying to generate an SVG from reaction SMARTS. The code looks like this: QByteArray ChemicalReactionsCalculation::toSvg(c