Re: [Rdkit-discuss] Valance Error on Aromatic N atoms.
The molecule has been constructed without problems, but the jupyter rendering code is failing. This isn't particularly surprising, that code is really set up to render non-query molecules, not things constructed from SMARTS. If you want to get a rendering of a molecule build from SMARTS in the notebook, try: from rdkit import Chem from rdkit.Chem.Draw import IPythonConsole from rdkit.Chem import Draw sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1c1)c1c1' mol =Chem.MolFromSmarts(sa) Draw.MolToImage(mol,kekulize=False) Best, -greg On Wed, Jul 12, 2017 at 5:10 PM, Chicago Jiwrote: > the code : > > from rdkit import Chem > from rdkit.Chem.Draw import IPythonConsole > sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1c1)c1c1' > mol =Chem.MolFromSmarts(sa) > mol > - > > The error information: > > RDKit ERROR: [16:07:15] > RDKit ERROR: > RDKit ERROR: > RDKit ERROR: Pre-condition Violation > RDKit ERROR: getExplicitValence() called without call to calcExplicitValence() > RDKit ERROR: Violation occurred on line 162 in file > soft/rdkit/Code/GraphMol/Atom.cpp > RDKit ERROR: Failed Expression: d_explicitValence > -1 > RDKit ERROR: > RDKit ERROR: > RDKit ERROR: [16:07:15] Can't kekulize mol. Unkekulized atoms: 4 5 6 7 8 9 > RDKit ERROR: > > > --- > > > On Wed, Jul 12, 2017 at 2:27 PM, Greg Landrum > wrote: > >> >> >> On Tue, Jul 11, 2017 at 6:53 PM, Chicago Ji wrote: >> >>> Thanks a lot for your code. >>> >>> I met another error. I don't know whether it's Normal. >>> >>> I have a correct SMILES, and read it through MolFromSmarts: >>> >>> >>> sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1c1)c1c1' >>> Chem.MolFromSmarts(sa) >>> >>> >>> >>> Is there something wrong with my input? >>> >> >> Looks fine to me: >> >> In [9]: sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1c1)c1c1' >> >> In [10]: m = Chem.MolFromSmarts(sa) >> >> In [11]: m.GetNumAtoms() >> Out[11]: 35 >> >> >> What error do you see? >> >> -greg >> >> > -- 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] Valance Error on Aromatic N atoms.
Hi, Greg. Thanks a lot for your code. I met another error. I don't know whether it's Normal. I have a correct SMILES, and read it through MolFromSmarts: sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1c1)c1c1' Chem.MolFromSmarts(sa) Is there something wrong with my input? Many Thanks. Best, Changge On Tue, Jul 11, 2017 at 4:53 PM, Greg Landrumwrote: > Here's a simple bit of code that shows how to get only pharmacophore > features whose atoms are contained completely in the MCS: > https://gist.github.com/greglandrum/faf47bd161d9b3af5374c358d0a0786d > > An interesting extension to this, which I may do for a blog post later, is > to further filter things to get the "maximum common pharmacophore" > > -greg > > > On Tue, Jul 11, 2017 at 1:41 PM, Greg Landrum > wrote: > >> Interesting use case. >> >> I can send some sample code for this later this afternoon. >> >> >> On Tue, Jul 11, 2017 at 11:43 AM, Chicago Ji >> wrote: >> >>> Hi, Greg, >>> >>> The SMARTS comes from MCS.FindMCS() analysis. It seems that MCS can only >>> output the result as SMARTS. >>> >>> Maybe I can calculate atom features of the "mother molecule', and then >>> extract those belonging to the common substructure. >>> >>> Or I can delete some atoms of the 'mother molecule', and output as >>> SMILES. >>> >>> Many thanks for your help. >>> >>> Best, >>> Changge >>> >>> >>> On Tue, Jul 11, 2017 at 8:26 AM, Greg Landrum >>> wrote: >>> Using the pharmacophore search code on molecules constructed from SMARTS is, in many circumstances, unlikely to yield the results that you are looking for. Query-Query matching is different than Query-Atom matching. It's more common to look for ph4 features in molecules constructed from SMILES or from a mol file. Is there a particular reason that you need to use SMARTS? -greg On Tue, Jul 11, 2017 at 8:54 AM, Chicago Ji wrote: > Hi Greg, > > I want to get pharmacophore feature for each atom on the molecule > using GetFeaturesForMol(). > > It seems that sanitization is a must before running > GetFeaturesForMol(). > > Many Thanks. > > Best, > Changge > > On Tue, Jul 11, 2017 at 7:31 AM, Greg Landrum > wrote: > >> Hi Changge, >> >> Is there any particular reason that you're calling >> updatePropertyCache on the molecule? That's not an operation that's >> normally necessary. >> >> Best, >> -greg >> >> >> >> On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji >> wrote: >> >>> Dear all, >>> >>> I met a problem with Aromatic N atoms. >>> >>> Here is the code: >>> >>> >>> sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]- >>> !@[#7]-@1-@[#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[ >>> #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1: >>> [#6]:[#6]:[#6]:[#6]:[#6]:1' >>> >>> mc = Chem.MolFromSmarts(sa,False) >>> >>> mc.UpdatePropertyCache() >>> >>> -- >>> >>> The error info says " Explicit valence for atom # 16 N, 4, is >>> greater than permitted" >>> >>> I also tried sanifix3.AdjustAromaticNs, but that doesn't work. >>> >>> Is there an easy way to solve this problem? >>> >>> Many thanks. >>> >>> >>> Best Regards, >>> Changge >>> >>> >>> >>> >>> -- >>> 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] Valance Error on Aromatic N atoms.
Here's a simple bit of code that shows how to get only pharmacophore features whose atoms are contained completely in the MCS: https://gist.github.com/greglandrum/faf47bd161d9b3af5374c358d0a0786d An interesting extension to this, which I may do for a blog post later, is to further filter things to get the "maximum common pharmacophore" -greg On Tue, Jul 11, 2017 at 1:41 PM, Greg Landrumwrote: > Interesting use case. > > I can send some sample code for this later this afternoon. > > > On Tue, Jul 11, 2017 at 11:43 AM, Chicago Ji wrote: > >> Hi, Greg, >> >> The SMARTS comes from MCS.FindMCS() analysis. It seems that MCS can only >> output the result as SMARTS. >> >> Maybe I can calculate atom features of the "mother molecule', and then >> extract those belonging to the common substructure. >> >> Or I can delete some atoms of the 'mother molecule', and output as SMILES. >> >> Many thanks for your help. >> >> Best, >> Changge >> >> >> On Tue, Jul 11, 2017 at 8:26 AM, Greg Landrum >> wrote: >> >>> Using the pharmacophore search code on molecules constructed from SMARTS >>> is, in many circumstances, unlikely to yield the results that you are >>> looking for. Query-Query matching is different than Query-Atom matching. >>> >>> It's more common to look for ph4 features in molecules constructed from >>> SMILES or from a mol file. Is there a particular reason that you need to >>> use SMARTS? >>> >>> -greg >>> >>> >>> On Tue, Jul 11, 2017 at 8:54 AM, Chicago Ji >>> wrote: >>> Hi Greg, I want to get pharmacophore feature for each atom on the molecule using GetFeaturesForMol(). It seems that sanitization is a must before running GetFeaturesForMol(). Many Thanks. Best, Changge On Tue, Jul 11, 2017 at 7:31 AM, Greg Landrum wrote: > Hi Changge, > > Is there any particular reason that you're calling updatePropertyCache > on the molecule? That's not an operation that's normally necessary. > > Best, > -greg > > > > On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji > wrote: > >> Dear all, >> >> I met a problem with Aromatic N atoms. >> >> Here is the code: >> >> >> sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]- >> !@[#7]-@1-@[#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[ >> #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1: >> [#6]:[#6]:[#6]:[#6]:[#6]:1' >> >> mc = Chem.MolFromSmarts(sa,False) >> >> mc.UpdatePropertyCache() >> >> -- >> >> The error info says " Explicit valence for atom # 16 N, 4, is >> greater than permitted" >> >> I also tried sanifix3.AdjustAromaticNs, but that doesn't work. >> >> Is there an easy way to solve this problem? >> >> Many thanks. >> >> >> Best Regards, >> Changge >> >> >> >> >> -- >> 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] Valance Error on Aromatic N atoms.
Interesting use case. I can send some sample code for this later this afternoon. On Tue, Jul 11, 2017 at 11:43 AM, Chicago Jiwrote: > Hi, Greg, > > The SMARTS comes from MCS.FindMCS() analysis. It seems that MCS can only > output the result as SMARTS. > > Maybe I can calculate atom features of the "mother molecule', and then > extract those belonging to the common substructure. > > Or I can delete some atoms of the 'mother molecule', and output as SMILES. > > Many thanks for your help. > > Best, > Changge > > > On Tue, Jul 11, 2017 at 8:26 AM, Greg Landrum > wrote: > >> Using the pharmacophore search code on molecules constructed from SMARTS >> is, in many circumstances, unlikely to yield the results that you are >> looking for. Query-Query matching is different than Query-Atom matching. >> >> It's more common to look for ph4 features in molecules constructed from >> SMILES or from a mol file. Is there a particular reason that you need to >> use SMARTS? >> >> -greg >> >> >> On Tue, Jul 11, 2017 at 8:54 AM, Chicago Ji wrote: >> >>> Hi Greg, >>> >>> I want to get pharmacophore feature for each atom on the molecule using >>> GetFeaturesForMol(). >>> >>> It seems that sanitization is a must before running GetFeaturesForMol(). >>> >>> Many Thanks. >>> >>> Best, >>> Changge >>> >>> On Tue, Jul 11, 2017 at 7:31 AM, Greg Landrum >>> wrote: >>> Hi Changge, Is there any particular reason that you're calling updatePropertyCache on the molecule? That's not an operation that's normally necessary. Best, -greg On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji wrote: > Dear all, > > I met a problem with Aromatic N atoms. > > Here is the code: > > > sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]- > !@[#7]-@1-@[#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[ > #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1: > [#6]:[#6]:[#6]:[#6]:[#6]:1' > > mc = Chem.MolFromSmarts(sa,False) > > mc.UpdatePropertyCache() > > -- > > The error info says " Explicit valence for atom # 16 N, 4, is greater > than permitted" > > I also tried sanifix3.AdjustAromaticNs, but that doesn't work. > > Is there an easy way to solve this problem? > > Many thanks. > > > Best Regards, > Changge > > > > > -- > 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] Valance Error on Aromatic N atoms.
Hi, Greg, The SMARTS comes from MCS.FindMCS() analysis. It seems that MCS can only output the result as SMARTS. Maybe I can calculate atom features of the "mother molecule', and then extract those belonging to the common substructure. Or I can delete some atoms of the 'mother molecule', and output as SMILES. Many thanks for your help. Best, Changge On Tue, Jul 11, 2017 at 8:26 AM, Greg Landrumwrote: > Using the pharmacophore search code on molecules constructed from SMARTS > is, in many circumstances, unlikely to yield the results that you are > looking for. Query-Query matching is different than Query-Atom matching. > > It's more common to look for ph4 features in molecules constructed from > SMILES or from a mol file. Is there a particular reason that you need to > use SMARTS? > > -greg > > > On Tue, Jul 11, 2017 at 8:54 AM, Chicago Ji wrote: > >> Hi Greg, >> >> I want to get pharmacophore feature for each atom on the molecule using >> GetFeaturesForMol(). >> >> It seems that sanitization is a must before running GetFeaturesForMol(). >> >> Many Thanks. >> >> Best, >> Changge >> >> On Tue, Jul 11, 2017 at 7:31 AM, Greg Landrum >> wrote: >> >>> Hi Changge, >>> >>> Is there any particular reason that you're calling updatePropertyCache >>> on the molecule? That's not an operation that's normally necessary. >>> >>> Best, >>> -greg >>> >>> >>> >>> On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji >>> wrote: >>> Dear all, I met a problem with Aromatic N atoms. Here is the code: sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-!@[#7]-@1-@ [#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[ #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1: [#6]:[#6]:[#6]:[#6]:[#6]:1' mc = Chem.MolFromSmarts(sa,False) mc.UpdatePropertyCache() -- The error info says " Explicit valence for atom # 16 N, 4, is greater than permitted" I also tried sanifix3.AdjustAromaticNs, but that doesn't work. Is there an easy way to solve this problem? Many thanks. Best Regards, Changge -- 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] Valance Error on Aromatic N atoms.
Using the pharmacophore search code on molecules constructed from SMARTS is, in many circumstances, unlikely to yield the results that you are looking for. Query-Query matching is different than Query-Atom matching. It's more common to look for ph4 features in molecules constructed from SMILES or from a mol file. Is there a particular reason that you need to use SMARTS? -greg On Tue, Jul 11, 2017 at 8:54 AM, Chicago Jiwrote: > Hi Greg, > > I want to get pharmacophore feature for each atom on the molecule using > GetFeaturesForMol(). > > It seems that sanitization is a must before running GetFeaturesForMol(). > > Many Thanks. > > Best, > Changge > > On Tue, Jul 11, 2017 at 7:31 AM, Greg Landrum > wrote: > >> Hi Changge, >> >> Is there any particular reason that you're calling updatePropertyCache on >> the molecule? That's not an operation that's normally necessary. >> >> Best, >> -greg >> >> >> >> On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji wrote: >> >>> Dear all, >>> >>> I met a problem with Aromatic N atoms. >>> >>> Here is the code: >>> >>> >>> sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-!@[#7]-@1-@ >>> [#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[ >>> #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1: >>> [#6]:[#6]:[#6]:[#6]:[#6]:1' >>> >>> mc = Chem.MolFromSmarts(sa,False) >>> >>> mc.UpdatePropertyCache() >>> >>> -- >>> >>> The error info says " Explicit valence for atom # 16 N, 4, is greater >>> than permitted" >>> >>> I also tried sanifix3.AdjustAromaticNs, but that doesn't work. >>> >>> Is there an easy way to solve this problem? >>> >>> Many thanks. >>> >>> >>> Best Regards, >>> Changge >>> >>> >>> >>> >>> -- >>> 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] Valance Error on Aromatic N atoms.
Hi Greg, I want to get pharmacophore feature for each atom on the molecule using GetFeaturesForMol(). It seems that sanitization is a must before running GetFeaturesForMol(). Many Thanks. Best, Changge On Tue, Jul 11, 2017 at 7:31 AM, Greg Landrumwrote: > Hi Changge, > > Is there any particular reason that you're calling updatePropertyCache on > the molecule? That's not an operation that's normally necessary. > > Best, > -greg > > > > On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji wrote: > >> Dear all, >> >> I met a problem with Aromatic N atoms. >> >> Here is the code: >> >> >> sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-!@[#7]-@1-@ >> [#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[ >> #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1: >> [#6]:[#6]:[#6]:[#6]:[#6]:1' >> >> mc = Chem.MolFromSmarts(sa,False) >> >> mc.UpdatePropertyCache() >> >> -- >> >> The error info says " Explicit valence for atom # 16 N, 4, is greater >> than permitted" >> >> I also tried sanifix3.AdjustAromaticNs, but that doesn't work. >> >> Is there an easy way to solve this problem? >> >> Many thanks. >> >> >> Best Regards, >> Changge >> >> >> >> >> -- >> 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] Valance Error on Aromatic N atoms.
Hi Changge, Is there any particular reason that you're calling updatePropertyCache on the molecule? That's not an operation that's normally necessary. Best, -greg On Mon, Jul 10, 2017 at 8:37 PM, Chicago Jiwrote: > Dear all, > > I met a problem with Aromatic N atoms. > > Here is the code: > > > sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-!@[#7]-@1-@ > [#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[ > #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1: > [#6]:[#6]:[#6]:[#6]:[#6]:1' > > mc = Chem.MolFromSmarts(sa,False) > > mc.UpdatePropertyCache() > > -- > > The error info says " Explicit valence for atom # 16 N, 4, is greater > than permitted" > > I also tried sanifix3.AdjustAromaticNs, but that doesn't work. > > Is there an easy way to solve this problem? > > Many thanks. > > > Best Regards, > Changge > > > > > -- > 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
[Rdkit-discuss] Valance Error on Aromatic N atoms.
Dear all, I met a problem with Aromatic N atoms. Here is the code: sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-!@[#7]-@1-@ [#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[#7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1:[#6]:[#6]:[#6]:[#6]:[#6]:1' mc = Chem.MolFromSmarts(sa,False) mc.UpdatePropertyCache() -- The error info says " Explicit valence for atom # 16 N, 4, is greater than permitted" I also tried sanifix3.AdjustAromaticNs, but that doesn't work. Is there an easy way to solve this problem? Many thanks. Best Regards, Changge -- 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