Hi Sharang (adding the list as I missed reply-all previously),
Glad to hear that RDKit does what it is supposed to.I am unfortunately not familiar with how Datawarrior processes molecules, so I don't know if it does its own layout. To remove RDKit from the equation - if you can feed Datawarrior a molfile directly from disk, you can see if Datawarrior preserves the layout of the molfile or not.
Cheers -- Jan On 2020-05-09 16:32, Sharang Phatak wrote:
Hi Jan,Thank you for your message. I did go back and check with mol_to_ctab and found out the coordinates are indeed identical. I am using Datawarrior to visualize these structures using Datawarrior's native SQL integration tool. The structures then are displayed a bit differently, flipped / rotated within this tool. Perhaps it's a different issue unrelated to RDKit. If you've experienced such issues and share what you did to overcome them, it would be much appreciated.Cheers, SharangOn Thu, May 7, 2020 at 3:22 AM Jan Holst Jensen <j...@biochemfusion.com <mailto:j...@biochemfusion.com>> wrote:Hi Sharang, A very old version of RDKit ? When I use your form of calling mol_to_ctab() it does preserve coordinates for me. select mol_to_ctab(mol_from_ctab(' 4 3 0 0 0 0 0 0 1 0999 V2000 5.0000 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0000 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0000 3.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 M END '::cstring, true)); RDKit 3D 4 3 0 0 0 0 0 0 0 0999 V2000 5.0000 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0000 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0000 3.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 2 3 1 0 2 4 1 0 M END If I leave out the second optional boolean parameter, which defaults to false, the coordinates are re-generated by RDKit. select mol_to_ctab(mol_from_ctab(' 4 3 0 0 0 0 0 0 1 0999 V2000 5.0000 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0000 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0000 3.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 M END '::cstring)); RDKit 2D 4 3 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 2.2500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 2 3 1 0 2 4 1 0 M END This is on a fairly old RDKit 2016_09_4 on Postgres 9.6. Earlier versions would ignore the second parameter - that was fixed around the 2016_09 release if I recall correctly. Cheers -- Jan Holst Jensen On 2020-05-07 00:21, Sharang Phatak wrote: > Hi, > > I am following the documentation for postgres / rdkit. I have a table > with valid molfiles as confirmed from is_valid_ctab(). I am then > trying to insert into a table 'mols' using > mol_from_ctab(molfile::cstring,true). > > However, the coordinates are not preserved. Is there something I am > missing? > > Thank you, > Sharang
smime.p7s
Description: S/MIME Cryptographic Signature
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
