Re: [Rdkit-discuss] Problems building RDKit + JavaWrappers

2020-04-28 Thread Thomas Eckert
That helped, thanks! Didn't realize 'make install' was needed after building the wrappers - I had built without the wrappers first, trying to detect problems iteratively. So now I'm able to use the wrappers in Java but noticed not all "core functionality" is covered by the wrappers. Specifically,

Re: [Rdkit-discuss] Problems building RDKit + JavaWrappers

2020-04-28 Thread Tim Dudgeon
It's availalbe from the org.RDKit.RDKFuncs class. e.g: String RDKFuncs.standardizeSmiles(String smiles)​ RWMol cleanup​(RWMol mol) TIm On 28/04/2020 15:09, Thomas Eckert wrote: That helped, thanks! Didn't realize 'make install' was needed after building the wrappers - I had built without the

Re: [Rdkit-discuss] Restraining torsions whilst generating conformers

2020-04-28 Thread Bruce Milne
Hi Taka, I've been playing with the UFFAddTorsionConstraint suggestion but I can't make it work for my systems (although it is great to know about as I can think of lots of other uses). The problem is that the Embedded geometries are too far from the geometry that I want to enforce on the torsions

Re: [Rdkit-discuss] [*External*] Uniqueness of bonds

2020-04-28 Thread nCloud
That solves the problem. Thank you. --Nimal On Mon, Apr 27, 2020 at 11:32 PM Guillaume GODIN < guillaume.go...@firmenich.com> wrote: > Dear Nimal, > > > > You are using atoms to enumerate bonds and a bond has 2 atoms so the > number of bonds are not the real ones. > > > > Use this instead : > >