Re: [Rdkit-discuss] position restraints on all atoms

2017-09-28 Thread Katrina Lexa
Hi Paolo, Thanks so much for your quick response. Hmm… would you mind sharing how you are calculating those RMSDs? I’m seeing RMSDs with constraints of over 1.0 Angstrom, so clearly some detail is still escaping me. My goal here is to reproduce the strain energy calculations that are part of

Re: [Rdkit-discuss] position restraints on all atoms

2017-09-28 Thread Katrina Lexa
Hi Paolo, Thanks so much for this suggestion (ages ago now). Based on Francois’ suggestion and your suggestion I have cobbled together a script that seems like it ought to work to apply position constraints on each atom, minimize, and then return the local minima conformations. Perhaps I’m still

Re: [Rdkit-discuss] position restraints on all atoms

2017-07-26 Thread Paolo Tosco
Hi Katrina, you may add multiple constraints, of the same (e.g., positional) or different kinds. Each of them will result in an additional force field contribution being added to your system. So you may, for example, identify a group that you wish to constrain by a SMARTS pattern, identify

Re: [Rdkit-discuss] position restraints on all atoms

2017-07-26 Thread Katrina Lexa
Thanks Greg! Thanks Francois for your response. Where I’m struggling is with generating locally restrained conformations. Essentially, my question is about this line of code: ff.MMFFAddPositionConstraint(1, 0.3, 1.0e5) My reading of the code page is that the first variable, 1, describes which

Re: [Rdkit-discuss] position restraints on all atoms

2017-07-25 Thread Greg Landrum
Hi Katrina, welcome to the RDKit community! On Mon, Jul 24, 2017 at 10:45 PM, Katrina Lexa wrote: > > I'm relatively new to RDKit, so I apologize for what may be a silly > question. I'd like to generate a set of local minimum conformations around > my input conformation, using

Re: [Rdkit-discuss] position restraints on all atoms

2017-07-25 Thread Francois BERENGER
On 07/25/2017 05:45 AM, Katrina Lexa wrote: Hi All, I'm relatively new to RDKit, so I apologize for what may be a silly question. I'd like to generate a set of local minimum conformations around my input conformation, using a set of defined flat bottom potentials (0.2, 0.6, 1.0, and 1.4), in