Re: [Rdkit-discuss] Generating 3D Coordinates in already existing coordinate frame...
On Wed, Dec 7, 2011 at 5:06 AM, Greg Landrum greg.land...@gmail.com wrote: Dear JP, I do not see how AddHs will help me when replacing [OH] with [O-], but that might just be me being thick. My problem is that ps = AllChem.ReplaceSubstructs(mol, patt, repl, replaceAll=True) in my original attached code throws away the 3D coordinates (ps[0] atoms are all on 0,0,0) - and I don't know of a way to regain the original co-ordinates back. You need two things here: 1) the coordinates of the input molecule should be copied to the result molecule 2) some way to generate sensible coordinates for the new atoms. The first is already supposed to be happening; the fact that it's not is a bug which I will fix (https://sourceforge.net/tracker/?func=detailaid=3453144group_id=160139atid=814650). This bug is now fixed in svn. -greg -- Systems Optimization Self Assessment Improve efficiency and utilization of IT resources. Drive out cost and improve service delivery. Take 5 minutes to use this Systems Optimization Self Assessment. http://www.accelacomm.com/jaw/sdnl/114/51450054/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Generating 3D Coordinates in already existing coordinate frame...
Just bumping this up ... On 29 November 2011 16:47, JP jeanpaul.ebe...@inhibox.com wrote: Dear Greg, I am not sure that is what I need/I explained myself well. My question is: If you have a 3D molecule, and you replace a part of it with a new group based on some SMARTS expression (with no 3D coorinates) - what is the best way to keep all the 3D info for the atoms in the molecule which have not changed while creating some sensible co-cordinates (in the current frame) for the newly appended atoms to the molecule. I do not see how AddHs will help me when replacing [OH] with [O-], but that might just be me being thick. My problem is that ps = AllChem.ReplaceSubstructs(mol, patt, repl, replaceAll=True) in my original attached code throws away the 3D coordinates (ps[0] atoms are all on 0,0,0) - and I don't know of a way to regain the original co-ordinates back. Is this still a rumble? Many thanks - Jean-Paul Ebejer Early Stage Researcher On 29 November 2011 16:10, Greg Landrum greg.land...@gmail.com wrote: Dear JP, On Tue, Nov 29, 2011 at 3:36 PM, JP jeanpaul.ebe...@inhibox.com wrote: Sorry for the repeated posting -- I had asked a similar question for 2D some time ago (http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01916.html), but now I need the 3D case and I am stuck. Using RDKit 2011_09_01. I am simply protonating a molecule via some simple SMART replacements. I would like the final output molecule to have the same 3D co ordinates as the input one. I have code which works for the 2D case, (basically the below but using GenerateDepictionMatching2DStructure(...) instead. I think you're overcomplicating things. Once you have the molecule ready to be protonated, try doing: Chem.AddHs(mol,addCoords=True) That is *supposed* to do the right thing (assuming I've understood the request correctly). If it doesn't let me know and I will propose a more complicated solution. -greg -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Generating 3D Coordinates in already existing coordinate frame...
Dear JP, On Tue, Nov 29, 2011 at 3:36 PM, JP jeanpaul.ebe...@inhibox.com wrote: Sorry for the repeated posting -- I had asked a similar question for 2D some time ago (http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01916.html), but now I need the 3D case and I am stuck. Using RDKit 2011_09_01. I am simply protonating a molecule via some simple SMART replacements. I would like the final output molecule to have the same 3D co ordinates as the input one. I have code which works for the 2D case, (basically the below but using GenerateDepictionMatching2DStructure(...) instead. I think you're overcomplicating things. Once you have the molecule ready to be protonated, try doing: Chem.AddHs(mol,addCoords=True) That is *supposed* to do the right thing (assuming I've understood the request correctly). If it doesn't let me know and I will propose a more complicated solution. -greg -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Generating 3D Coordinates in already existing coordinate frame...
Dear Greg, I am not sure that is what I need/I explained myself well. My question is: If you have a 3D molecule, and you replace a part of it with a new group based on some SMARTS expression (with no 3D coorinates) - what is the best way to keep all the 3D info for the atoms in the molecule which have not changed while creating some sensible co-cordinates (in the current frame) for the newly appended atoms to the molecule. I do not see how AddHs will help me when replacing [OH] with [O-], but that might just be me being thick. My problem is that ps = AllChem.ReplaceSubstructs(mol, patt, repl, replaceAll=True) in my original attached code throws away the 3D coordinates (ps[0] atoms are all on 0,0,0) - and I don't know of a way to regain the original co-ordinates back. Is this still a rumble? Many thanks - Jean-Paul Ebejer Early Stage Researcher On 29 November 2011 16:10, Greg Landrum greg.land...@gmail.com wrote: Dear JP, On Tue, Nov 29, 2011 at 3:36 PM, JP jeanpaul.ebe...@inhibox.com wrote: Sorry for the repeated posting -- I had asked a similar question for 2D some time ago (http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01916.html), but now I need the 3D case and I am stuck. Using RDKit 2011_09_01. I am simply protonating a molecule via some simple SMART replacements. I would like the final output molecule to have the same 3D co ordinates as the input one. I have code which works for the 2D case, (basically the below but using GenerateDepictionMatching2DStructure(...) instead. I think you're overcomplicating things. Once you have the molecule ready to be protonated, try doing: Chem.AddHs(mol,addCoords=True) That is *supposed* to do the right thing (assuming I've understood the request correctly). If it doesn't let me know and I will propose a more complicated solution. -greg -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Generating 3D coordinates
It's kind of interesting (and encouraging) that the optimizer doesn't completely freak out when you hand it a 2D conformer. :-) Ah... :) What makes 3D coordinates? (I'm guessing it's a one-liner somewhere...) It is indeed a one-liner (two lines with a bit of error checking). To get a 3D conformer, you need to include GraphMol/DistGeomHelpers/Embedder.h and do the following: int cid = DGeomHelpers::EmbedMolecule(*m); if(cid0) // embedding failed, do something There are a bunch of optional arguments to EmbedMolecule, but the defaults normally work reasonably well. So it seems! Fantastic, that did it. It's pretty jaw dropping that so much power can be added with so little code (on my part :) More later. Cheers, Paul. -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing http://p.sf.net/sfu/novell-sfdev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
