Hi Rob,
The results below are quite strange. As John has already pointed out: there
really shouldn't be chirality present on either the N+ or the C that has
two methyls attached.
I tried to reproduce the problem by running corina myself using the same
command-line options you provided (from SMILES instead of SDF, but I don't
think that should make a difference), but I get sensible results;
In [5]: s = Chem.SDMolSupplier('sample.sdf')
In [6]: for m in s:
Chem.AssignAtomChiralTagsFromStructure(m)
Chem.AssignStereochemistry(m,cleanIt=True,force=True)
...: print Chem.MolToSmiles(m,True)
...:
CCN1CCC([N@@H+]2CC[C@@H]2C(C)C)CC1
CCN1CCC([N@@H+]2CC[C@@H]2C(C)C)CC1
CCN1CCC([N@H+]2CC[C@@H]2C(C)C)CC1
CCN1CCC([N@H+]2CC[C@@H]2C(C)C)CC1
CCN1CCC([N@@H+]2CC[C@H]2C(C)C)CC1
CCN1CCC([N@@H+]2CC[C@H]2C(C)C)CC1
CCN1CCC([N@H+]2CC[C@H]2C(C)C)CC1
CCN1CCC([N@H+]2CC[C@H]2C(C)C)CC1
In [7]: s = Chem.SDMolSupplier('sample.sdf')
In [8]: for m in s:
Chem.AssignAtomChiralTagsFromStructure(m)
print Chem.MolToSmiles(m,True)
...:
CCN1CCC([N@@H+]2CC[C@@H]2C(C)C)CC1
CCN1CCC([N@@H+]2CC[C@@H]2C(C)C)CC1
CCN1CCC([N@H+]2CC[C@@H]2C(C)C)CC1
CCN1CCC([N@H+]2CC[C@@H]2C(C)C)CC1
CCN1CCC([N@@H+]2CC[C@H]2C(C)C)CC1
CCN1CCC([N@@H+]2CC[C@H]2C(C)C)CC1
CCN1CCC([N@H+]2CC[C@H]2C(C)C)CC1
CCN1CCC([N@H+]2CC[C@H]2C(C)C)CC1
Could you please send the SDF that corina generates so I can try to
reproduce the problem (or at least try to understand what's gong on) from
that?
Thanks,
-greg
On Wed, Aug 19, 2015 at 3:00 PM, 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)
>
>
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