Re: [Rdkit-discuss] RDKit Cartridge mol_to_svg parameters

Yes, I'm working on putting that in at the same time as everything else. Dave On Thu, Feb 13, 2020 at 3:54 PM Greg Landrum wrote: > > > On Thu, Feb 13, 2020 at 10:57 AM David Cosgrove < > davidacosgrov...@gmail.com> wrote: > >> >> However, thanks to the generosity of MedChemica, I am currently

Re: [Rdkit-discuss] RDKit Cartridge mol_to_svg parameters

On Thu, Feb 13, 2020 at 10:57 AM David Cosgrove wrote: > > However, thanks to the generosity of MedChemica, I am currently working on > improvements to the drawing code, and have added some extra options to > drawOptions() that will need interpreting in updateDrawerParamsFromJSON. > Whilst doing

Re: [Rdkit-discuss] RDKit Cartridge mol_to_svg parameters

On 2/13/2020 3:56 AM, David Cosgrove wrote: Hi Thomas, I've never used the RDKit cartridge, so have not come across mol_to_svg() before. In the more general case, you can change the bond line width with something like: drawer = rdMolDraw2D.MolDraw2DSVG(200, 200)

Re: [Rdkit-discuss] PDB file format and dummy atoms

Hi Gabriele, this has come up previously: https://sourceforge.net/p/rdkit/mailman/message/36796385/ This gist https://gist.github.com/ptosco/ba11e577a8c616b958c49e23cc42a5e3 shows a possible solution, provided that your molecules do not contain Astatine, otherwise pick another unusual

[Rdkit-discuss] PDB file format and dummy atoms

Hello everybody, I have a list of molecular fragments generated with BRICS and saved in PDB format. When I read them back with Chem.MolFromPDBlock() RDKiT is unable to recognize the dummy atom * and throws a warning (and no molecule is returned). Is it possible add custom atoms to the PDB

Re: [Rdkit-discuss] Extended Huckel Matrices

Basically, to be able to simulate electronic transmission through a molecule we use the retarded greens function. So far we are able to simulate the transmission through pi-bonds, but to extend our simulation to transmission through more than just the pi-bonds, we want to use the extended

Re: [Rdkit-discuss] RDKit Cartridge mol_to_svg parameters

Hi Thomas, I've never used the RDKit cartridge, so have not come across mol_to_svg() before. In the more general case, you can change the bond line width with something like: drawer = rdMolDraw2D.MolDraw2DSVG(200, 200) drawer.drawOptions().bondLineWidth = 10 It may be that you don't have

Re: [Rdkit-discuss] RDKit Cartridge mol_to_svg parameters

OK, I dug into the source code and it seems bondLineWidth simply can't be set: void updateDrawerParamsFromJSON(MolDraw2D , const std::string ) { if (json == "") {

Re: [Rdkit-discuss] Extended Huckel Matrices

Hi Zan, On Wed, Feb 12, 2020 at 7:57 PM Zan Mahmood via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > I am currently working on developing a Virtual Reality simulation platform > for nanosystems. > So far we are able to compute electron transmission through 2D structures >

[Rdkit-discuss] RDKit Cartridge mol_to_svg parameters

Hi All, started to play around with the rdkit cartridge and I was wondering how to correctly use the mol_to_svg function. On rdkit homepage I only found this: mol_to_svg(mol,string default ‘’,int default 250, int default 200, string default ‘’) : returns an SVG with a drawing of the molecule.