Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

As a follow up question on this topic, I would like to ask if MurckoScaffold.GetScaffoldForMol(mol) returns the scaffold of mol with different coordinates? I am asking this because when I use the transformation matrix of the alignment of the cores of the probe and the reference molecules, in order

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

HI Thomas, To be sure we're talking about the same thing: rdMolAlign.GetO3A() is an implementation of the Open3DAlign algorithm. This is an unsupervised approach that uses a clever algorithm to come up with an atom-atom mapping between the two molecules you give it. It's not always going to pick

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

I believe (Greg can correct me) to align the bemis-murcko scaffold, you could (1) extract the original atom pairs and send them to the RMSD algorithm (2) take a bemis scaffold and convert it to a substructure query for use in the RMSD algorithm. In either case the RMSD is the rmsd of the

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

​ Greg and Brian, Thank you for your useful hints. All the compounds that I want to align are supposed to belong to the same analogue series so they should shave a common substructure with substantial size. What I want to emulate is the "core restrained docking" with glide, where you specify the

Re: [Rdkit-discuss] problems with installation on conda with python 3.5 32-bit

Hi Michal, We've only ever done python2.7 builds for win32 and we stopped doing those with the 2016.03 release. I will have to check, but I think I probably can start doing these again, but I'm reluctant due to the amount of effort required. How many users do you need to support who are stuck on

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

At least for the MCS calculation, there is an R package for chemistry: https://bioconductor.org/packages/release/bioc/vignettes/fmcsR/inst/doc/fmcsR.html On 02/19/2017 07:33 PM, Thomas Evangelidis wrote: > Dear all, > > I want to align 250 compounds that binding to the same pocket to one of >

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

I don't know the exact glide procedure, but I did write such a system for OpenEye (POSIT). The issue you are facing is that the RMSD portion is just a constraint used for docking, it isn't used as the "score", in fact, it can't tell if the conformation interpenetrates the active site or which

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

With Glide, IIRC, this facility is designed for the use case where the coordinates of a docked ligand are known (typically from an X-ray structure) and the docked ligand shares a SMARTS with the ligands in an input file. The SMARTS-matching atoms of each incoming ligand are superposed upon the

Re: [Rdkit-discuss] problems with installation on conda with python 3.5 32-bit

Hi Greg, Thanks for your reply. Actually, >50% of my (prospective) users are stuck on 32-bit. It would be really nice to have a python3 build (even once a year) but I understand that the demand is low and waning. I guess the solution is to use python2.7 for the time being... Thanks and kind

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

@Peter I am working exactly on the scenario you described. @Brian I have found this thread which is pretty similar to my case and to what you suggested, so now I am adapting my code accordingly. https://sourceforge.net/p/rdkit/mailman/message/35034093/ What you have published sounds

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

Hello Thomas, This publication could be of interest to you. I have not read the whole paper so I don't know how relevant it is. Ling Graph-Based Molecular Alignment (GMA) Marialke, Korner, Tietze, Apostolakis J. Chem. Inf. Model. 47 (2007) 591-601 On Mon, Feb 20, 2017 at 3:32 PM, Thomas

Re: [Rdkit-discuss] problems with installation on conda with python 3.5 32-bit

Hi Greg,    I am using 32-bit python27 and anaconda (with 64-bit windows 10). So I cannot update to latest version and test as you proposed several days ago.     Since it did not trouble me, I plan to upgrade all this environment in the future. BTW, is it necessary to upgrade python into 3.6

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

On Mon, Feb 20, 2017 at 6:17 PM, Thomas Evangelidis wrote: > > Thank you for your useful hints. All the compounds that I want to align > are supposed to belong to the same analogue series so they should shave a > common substructure with substantial size. > In that case,

Re: [Rdkit-discuss] problems with installation on conda with python 3.5 32-bit

On Tue, Feb 21, 2017 at 4:18 AM, 杨弘宾 wrote: > Hi Greg, > I am using 32-bit python27 and anaconda (with 64-bit windows 10). So I > cannot update to latest version and test with "abnormal" operation of rdMolDraw2D> as you proposed several days > ago. > Since it did