[Open Babel] generate 3D coordinates based on a scaffold

2012-04-11 Thread Adam Tenderholt
Hi, I'm interested in converting a SMILES string into a 3D structure using another similar molecule as a scaffold. The molecule to be converted may be a substructure of the scaffold molecule with a few modifications (e.g. amines changed to imines), or be protonated at an alternative site (e.g. 4-a

Re: [Open Babel] generate 3D coordinates based on a scaffold

2012-04-12 Thread Adam Tenderholt
> You could probably code something like this using the OBBuilder code, but it > would take some work (i.e, it sounds like you'd need to remove or mutate some > atoms, adjust bond lengths, grow new fragments). > > I assume the idea is to do this in an automated fashion, or I'd suggest doing > it