Re: [Rdkit-discuss] Aligning in 3D

Hi Kirk, Paolo has already pointed out the tools to use if you want to have control over the process. There's also a convenience function available, AllChem.ConstrainedEmbed(), that makes the process a bit easier: http://www.rdkit.org/docs/api/rdkit.Chem.AllChem-module.html#ConstrainedEmbed

[Rdkit-discuss] Aligning in 3D

In working with RDKit I've been able to align 2D structures based upon a common core of MCS using AllChem.GenerateDepictionMatching2DStructure(m,p) The next step for me is to generate 3D structures and align them based upon that same common core. Obviously this leads to multiple steps, not the

[Rdkit-discuss] PyMOL from RDKit? (Resurrection)

Back again! I apologize for resurrecting an old topic, but I'm once again trying to work with PyMOL through RDKit. I've been following the approach in this thread ( http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg00325.html) but it seems not to work any longer. I'm using

Re: [Rdkit-discuss] conformation search and constraints

Dear Rafal, On 22/04/2016 17:15, Rafal Roszak wrote: > Hello, > > I want to find: > A) "global minimum" [*] for given compound(s) and > B) (for the same compound) minimum with constraint(s) (e.g. frozen > angle) > > For problem A) I tried folowing code: > > self.MOLEC=Chem.MolFromSmiles(SMILES)

Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants

Now I think I know and I very much look forward to a more detailed documentation. many thanks, -Monica At 2016-04-22 17:48:39, "Greg Landrum" wrote: There isn't great documentation for this, but the way the current code works is reasonably simple. If your

Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants

There isn't great documentation for this, but the way the current code works is reasonably simple. If your reaction has two products (i.e. two molecules separated by a dot), you will get two products (i.e. two separate molecules) when you call RunReactants(); that's what you asked for. Here's a

Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants

Hi Grégori, Maybe I don't have a clear understanding of this function, I know the dot represent disconncction of two fragments ,and I suppose changes just occurs in mapped molecular fragment, the remaining part of reactant is invariable, in other words, if mapped molecular fragment breaks

Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants

Hi Monica, As Greg stated, why do you expect your product not to be fragmented? I suggest you to have a careful look at the SMARTS definition (for instance from Daylight: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) In SMARTS patterns, the dot indicates disconnected fragments.

[Rdkit-discuss] ReactionFromSmarts and RunReactants

Greg, After changing the pattern into "[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11] , I get the same result .A ring structure just like you said is broken into pieces.