Hehe, that is why I keep my computers always really cold when I run RDKit ...
------------------------------------- | Markus Sitzmann | [email protected] > On 20.08.2015, at 04:33, Peter Shenkin <[email protected]> wrote: > > Maybe when you have a toolkit as blazingly fast as RDKit it captures the > chirality of N center before it has time to interconvert.... > > -P. > >> On Wed, Aug 19, 2015 at 10:17 PM, John M <[email protected]> wrote: >> More odd is the carbon stereocentre with two methyls... >> >> Generally trivalent nitrogens are not considered chiral due to inversion of >> the lone-pair. The two usual exceptions are when they are a bridgehead or in >> a tight ring (cyclopropane). This is the same in most toolkits, the InChI >> technical documentation provides useful examples. >> >> InChI actually only sees one stereo centre since it strips the proton off: >> InChI=1S/C13H26N2/c1-4-14-8-5-12(6-9-14)15-10-7-13(15)11(2)3/h11-13H,4-10H2,1-3H3/p+1/t13-/m1/s1 >> >> It may well be chiral in this case but since it's not you should also >> strictly remove the other stereocentre in the para position to the nitrogen >> >> For the record just tested and ChemAxon/CDK/OpenBabel do the same. >> >> John >> >> Regards, >> John W May >> [email protected] >> >>> On 19 August 2015 at 09:00, Rob Smith <[email protected]> wrote: >>> Dear RDKit community, >>> >>> I'm trying to use RDKit to read in Corina generated stereoisomers (from a >>> Mol file), assign chiral tags and stereochemistry to the structure and >>> output the canonical smiles string for each isomer of a given molecule (in >>> Python), when I do this, half the canonical smiles strings are not unique. >>> >>> When I read in the output from Corina into an Indigo instance, then use the >>> canonical smiles from Indigo to create an RDKit molecule, canonical smiles >>> strings generated from the molecule objects are all unique. >>> >>> I may be missing an option to enable RDKit to 'visualise' the chiral centre >>> adjacent to the protonated nitrogen, so if someone can spot where I've made >>> a mistake, I'd really appreciate it. I've included the output and Python >>> script below. If you require any further information, please let me know. >>> >>> Many thanks, >>> Rob >>> >>> Output: >>> >>> RDKit Read in of Molecule >>> RDKit Output - CCN1CC[C@@H]([N@@H+]2CC[C@@H]2[C@H](C)C)CC1 >>> RDKit Output - CCN1CC[C@@H]([N@@H+]2CC[C@@H]2[C@H](C)C)CC1 >>> RDKit Output - CCN1CC[C@@H]([N@H+]2CC[C@@H]2[C@H](C)C)CC1 >>> RDKit Output - CCN1CC[C@@H]([N@H+]2CC[C@@H]2[C@H](C)C)CC1 >>> RDKit Output - CCN1CC[C@@H]([N@@H+]2CC[C@H]2[C@H](C)C)CC1 >>> RDKit Output - CCN1CC[C@@H]([N@@H+]2CC[C@H]2[C@H](C)C)CC1 >>> RDKit Output - CCN1CC[C@@H]([N@H+]2CC[C@H]2[C@H](C)C)CC1 >>> RDKit Output - CCN1CC[C@@H]([N@H+]2CC[C@H]2[C@H](C)C)CC1 >>> >>> INDIGO Read in of Molecule >>> RDKit Output - CC[N@]1CC[C@@H]([N@@H+]2CC[C@@H]2C(C)C)CC1 >>> RDKit Output - CC[N@]1CC[C@H]([N@@H+]2CC[C@@H]2C(C)C)CC1 >>> RDKit Output - CC[N@]1CC[C@@H]([N@H+]2CC[C@@H]2C(C)C)CC1 >>> RDKit Output - CC[N@]1CC[C@H]([N@H+]2CC[C@@H]2C(C)C)CC1 >>> RDKit Output - CC[N@]1CC[C@@H]([N@@H+]2CC[C@H]2C(C)C)CC1 >>> RDKit Output - CC[N@]1CC[C@H]([N@@H+]2CC[C@H]2C(C)C)CC1 >>> RDKit Output - CC[N@]1CC[C@@H]([N@H+]2CC[C@H]2C(C)C)CC1 >>> RDKit Output - CC[N@]1CC[C@H]([N@H+]2CC[C@H]2C(C)C)CC1 >>> >>> Python script : >>> >>> from rdkit import Chem >>> import subprocess # Used to run Corina >>> from indigo import * >>> >>> def runCorinaTest(inputMol): >>> indigo = Indigo() >>> >>> molFile = Chem.MolToMolBlock(inputMol) >>> >>> corinaCommand = "echo \'" + molFile + "\' | " >>> # Then Corina - generate stereoisomers... >>> corinaCommand = corinaCommand + "/apps/corina/corina -t n -d >>> canon,stergen,preserve,names,wh,flapn,msc=7,msi=128 -i t=sdf" >>> corinaResult = subprocess.check_output([corinaCommand], shell=True) # >>> Gives the stereoisomer species as an SDF string >>> >>> allMoleculeObjects = [] >>> allMolecules = corinaResult.split("$$$$\n") # Separate Corina output >>> into individual molecules >>> allMolecules = allMolecules[0:len(allMolecules)-1] >>> >>> print("RDKit Read in of Molecule") >>> >>> for eachMolecule in allMolecules: >>> eachMolecule = eachMolecule + "$$$$\n" >>> mol = Chem.MolFromMolBlock(eachMolecule, sanitize=True, >>> removeHs=True, strictParsing=False) >>> Chem.rdmolops.AssignAtomChiralTagsFromStructure(mol, >>> replaceExistingTags=True) >>> Chem.rdmolops.AssignStereochemistry(mol) >>> print("RDKit Output - " + Chem.MolToSmiles(mol, >>> isomericSmiles=True)) >>> >>> print("INDIGO Read in of Molecule") >>> for eachMolecule in allMolecules: >>> eachMolecule = eachMolecule + "$$$$\n" >>> mol = indigo.loadMolecule(eachMolecule) >>> # print("Indigo Output - " + mol.canonicalSmiles()) >>> # Use Indigo Canonical Smiles to create RDKit molecule >>> mol = Chem.MolFromSmiles(mol.canonicalSmiles()) >>> if mol is not None: >>> print("RDKit Output - " + Chem.MolToSmiles(mol, >>> isomericSmiles=True)) >>> >>> return 0 >>> >>> mol = Chem.MolFromSmiles("CC(C)C1[NH+](C2CCN(CC)CC2)CC1") >>> z = runCorinaTest(mol) >>> >>> ------------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Rdkit-discuss mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Rdkit-discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > ------------------------------------------------------------------------------ > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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