Re: [Rdkit-discuss] atom indexes and order of atoms in the input file
On 06/15/2017 01:14 PM, Brian Kelley wrote: > Sorry to hear about the flooding. >> Unfortunately we got flooded day before yesterday and the servers doing >> the crunching are currently down. I should have mentioned that the server (URL is in the article), which I'll hopefully get back up today, will output a MOL file with atoms ordered as per the article. The downside is it only works on 3D MOLs. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] atom indexes and order of atoms in the input file
Sorry to hear about the flooding. As an aside if you want to get they smiles atom output order, it is saved as a property on the molecule after a call to MolToSmiles, To get to the property, use mol.GetPropsAsDict(True,True) and it will be there with the key named something like "_smilesAtomOutputOrder" We should probably make a helper function for this. Brian Kelley > On Jun 15, 2017, at 6:27 PM, Dimitri Maziuk wrote: > >> On 06/15/2017 10:13 AM, Maciek Wójcikowski wrote: >> Hi, >> >> If you really want to rely on the order of atom you can renumber them >> anyhow you like with Chem.RenumberAtoms() >> http://rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#RenumberAtoms >> There is also a function which returns canonical order of atoms for >> you: Chem.CanonicalRankAtoms() As I remember correctly the order may differ >> from the canonical smiles, although that might have changed. > > https://www.nature.com/articles/sdata201773 > > Unfortunately we got flooded day before yesterday and the servers doing > the crunching are currently down. > > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] atom indexes and order of atoms in the input file
On 06/15/2017 10:13 AM, Maciek Wójcikowski wrote: > Hi, > > If you really want to rely on the order of atom you can renumber them > anyhow you like with Chem.RenumberAtoms() > http://rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#RenumberAtoms > There is also a function which returns canonical order of atoms for > you: Chem.CanonicalRankAtoms() As I remember correctly the order may differ > from the canonical smiles, although that might have changed. https://www.nature.com/articles/sdata201773 Unfortunately we got flooded day before yesterday and the servers doing the crunching are currently down. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] atom indexes and order of atoms in the input file
Hi, If you really want to rely on the order of atom you can renumber them anyhow you like with Chem.RenumberAtoms() http://rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#RenumberAtoms There is also a function which returns canonical order of atoms for you: Chem.CanonicalRankAtoms() As I remember correctly the order may differ from the canonical smiles, although that might have changed. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-06-15 9:03 GMT+02:00 Brian Kelley : > Yes, atoms are always added in file order. It would take a major change > in rdkit to change/violate this. > > > Brian Kelley > > > On Jun 15, 2017, at 7:52 AM, Francois BERENGER < > beren...@bioreg.kyushu-u.ac.jp> wrote: > > > > Hello, > > > > If I read a molecule from a .sdf file, will the atom indexes be > conserved/preserved? > > > > 1st atom in the file will have index 0, > > 2nd index 1, etc. > > > > And, will this always hold in the future? > > Is this an invariant of rdkit? > > > > Thanks, > > F. > > > > > -- > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > ___ > > Rdkit-discuss mailing list > > Rdkit-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] atom indexes and order of atoms in the input file
Yes, atoms are always added in file order. It would take a major change in rdkit to change/violate this. Brian Kelley > On Jun 15, 2017, at 7:52 AM, Francois BERENGER > wrote: > > Hello, > > If I read a molecule from a .sdf file, will the atom indexes be > conserved/preserved? > > 1st atom in the file will have index 0, > 2nd index 1, etc. > > And, will this always hold in the future? > Is this an invariant of rdkit? > > Thanks, > F. > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss