Re: [Cdk-user] InChiKey changing Upon simple conversion of implicit hydrogens
Thanks, Yannick On Thu, Feb 8, 2018 at 2:41 PM, John Mayfieldwrote: > Stereochemistry was not copied properly: https://github.com/ > cdk/cdk/commit/c05d6658dba750467db06a3f46414abe374e33a6#diff- > 0b33035e99ab1a3283d5f24de671e111 > > On 8 February 2018 at 20:00, Yannick .Djoumbou > wrote: > >> Hi John, >> >> I have switched to CDK 2.1.1 and it works properly now. I am wondering >> what caused this discrepancy in the older version. >> >> Thanks, >> >> On Thu, Feb 8, 2018 at 11:12 AM, Yannick .Djoumbou >> wrote: >> >>> Hi John, >>> >>> I am using CDK 1.5.13. I just copy/pasted your code, and I get exactly >>> the response as I did before: 2 different InChIKeys. >>> >>> Thanks, >>> >>> Yannick >>> >>> On Wed, Feb 7, 2018 at 4:20 PM, John Mayfield < >>> john.wilkinson...@gmail.com> wrote: >>> Which version are you using, works okay for me on 2.2-SNAPSHOT and not much should have changed their since a few years: public static void main(String[] args) throws CDKException { String smi = "C[C@]12CC[C@H]3[C@@H](CCC4=CC(O)=CC=C34)[C@@H]1CC[C@@]2(O)C#C"; IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance(); SmilesParser smipar = new SmilesParser(bldr); IAtomContainer mol = smipar.parseSmiles(smi); System.out.println(InChIGeneratorFactory.getInstance().getInChIGenerator(mol).getInchiKey()); // not needed // AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol); AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol); System.out.println(InChIGeneratorFactory.getInstance().getInChIGenerator(mol).getInchiKey()); } You don't need to assign the atom types, but I tried with/without the answer was the same. BFPYWIDHMRZLRN-SLHNCBLASA-N BFPYWIDHMRZLRN-SLHNCBLASA-N John On 7 February 2018 at 22:06, Yannick .Djoumbou wrote: > Hi all, > > I have been under deep debugging more for a few hours, only to find > that there seem the InChIKey of molecules seem to change when I use the > AtomContainerManipulator to convert implicit hydrogens into explicit ones. > > For instance > > I have the following 17-Ethinylestradiol molecule: > > C[C@]12CC[C@H]3[C@@H](CCC4=CC(O)=CC=C34)[C@@H]1CC[C@@]2(O)C#C > > PubChem CID: 5991 > > > If I use > > > InChIGeneratorFactory inchiGenFactory = InChIGeneratorFactory.getInsta > nce(); > > System.out.println("INCHIKEY BEFORE ADDING EXPLICIT HYDROGEN: ") + > inchiGenFactory.getInChIGenerator(molClone).getInchiKey()); > > > AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(" > 17-Ethinylestradiol"); > > AtomContainerManipulator.convertImplicitToExplicitHydrogens(" > 17-Ethinylestradiol"); > > > System.out.println("INCHIKEY AFTER ADDING EXPLICIT HYDROGEN: ") + > inchiGenFactory.getInChIGenerator(molClone).getInchiKey()); > > > I get the following output: > > > INCHIKEY BEFORE ADDING EXPLICIT HYDROGEN: BFPYWIDHMRZLRN-SLHNCBLASA-N > > INCHIKEY AFTER ADDING EXPLICIT HYDROGEN: BFPYWIDHMRZLRN-OQPPHWFISA-N > > This causes a problem down the path for me. > > > An interesting point is that I used the structures generated (via > isomeric SMILES) upon conversion of implicit hydrogen by CDK and > visualized > them using Marvin Sketch (Seee attached file), and the look identical to > me. I also used the isomeric SMILES strings before and after conversion to > search for same stereoisitopes in PubChem, and found the exact same > structure. So I am confused as to why CDK would return different > InChIKeys. > > > Is there an explanation for this, or may be some other steps I should > take to avoid this? > > > Thank you for your consideration. > > > Best, > > > Yannick > > > > > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user > > >>> >> > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
Re: [Cdk-user] InChiKey changing Upon simple conversion of implicit hydrogens
Hi John, I have switched to CDK 2.1.1 and it works properly now. I am wondering what caused this discrepancy in the older version. Thanks, On Thu, Feb 8, 2018 at 11:12 AM, Yannick .Djoumbouwrote: > Hi John, > > I am using CDK 1.5.13. I just copy/pasted your code, and I get exactly the > response as I did before: 2 different InChIKeys. > > Thanks, > > Yannick > > On Wed, Feb 7, 2018 at 4:20 PM, John Mayfield > wrote: > >> Which version are you using, works okay for me on 2.2-SNAPSHOT and not >> much should have changed their since a few years: >> >> public static void main(String[] args) throws CDKException { >> String smi = >> "C[C@]12CC[C@H]3[C@@H](CCC4=CC(O)=CC=C34)[C@@H]1CC[C@@]2(O)C#C"; >> IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance(); >> SmilesParser smipar = new SmilesParser(bldr); >> IAtomContainer mol = smipar.parseSmiles(smi); >> >> System.out.println(InChIGeneratorFactory.getInstance().getInChIGenerator(mol).getInchiKey()); >> // not needed >> // AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol); >> AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol); >> >> System.out.println(InChIGeneratorFactory.getInstance().getInChIGenerator(mol).getInchiKey()); >> } >> >> You don't need to assign the atom types, but I tried with/without the >> answer was the same. >> >> BFPYWIDHMRZLRN-SLHNCBLASA-N >> BFPYWIDHMRZLRN-SLHNCBLASA-N >> >> John >> >> On 7 February 2018 at 22:06, Yannick .Djoumbou >> wrote: >> >>> Hi all, >>> >>> I have been under deep debugging more for a few hours, only to find that >>> there seem the InChIKey of molecules seem to change when I use the >>> AtomContainerManipulator to convert implicit hydrogens into explicit ones. >>> >>> For instance >>> >>> I have the following 17-Ethinylestradiol molecule: >>> >>> C[C@]12CC[C@H]3[C@@H](CCC4=CC(O)=CC=C34)[C@@H]1CC[C@@]2(O)C#C >>> >>> PubChem CID: 5991 >>> >>> >>> If I use >>> >>> >>> InChIGeneratorFactory inchiGenFactory = InChIGeneratorFactory.getInsta >>> nce(); >>> >>> System.out.println("INCHIKEY BEFORE ADDING EXPLICIT HYDROGEN: ") + >>> inchiGenFactory.getInChIGenerator(molClone).getInchiKey()); >>> >>> >>> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(" >>> 17-Ethinylestradiol"); >>> >>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(" >>> 17-Ethinylestradiol"); >>> >>> >>> System.out.println("INCHIKEY AFTER ADDING EXPLICIT HYDROGEN: ") + >>> inchiGenFactory.getInChIGenerator(molClone).getInchiKey()); >>> >>> >>> I get the following output: >>> >>> >>> INCHIKEY BEFORE ADDING EXPLICIT HYDROGEN: BFPYWIDHMRZLRN-SLHNCBLASA-N >>> >>> INCHIKEY AFTER ADDING EXPLICIT HYDROGEN: BFPYWIDHMRZLRN-OQPPHWFISA-N >>> >>> This causes a problem down the path for me. >>> >>> >>> An interesting point is that I used the structures generated (via >>> isomeric SMILES) upon conversion of implicit hydrogen by CDK and visualized >>> them using Marvin Sketch (Seee attached file), and the look identical to >>> me. I also used the isomeric SMILES strings before and after conversion to >>> search for same stereoisitopes in PubChem, and found the exact same >>> structure. So I am confused as to why CDK would return different InChIKeys. >>> >>> >>> Is there an explanation for this, or may be some other steps I should >>> take to avoid this? >>> >>> >>> Thank you for your consideration. >>> >>> >>> Best, >>> >>> >>> Yannick >>> >>> >>> >>> >>> >>> >>> >>> -- >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> ___ >>> Cdk-user mailing list >>> Cdk-user@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>> >>> >> > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
Re: [Cdk-user] InChiKey changing Upon simple conversion of implicit hydrogens
Which version are you using, works okay for me on 2.2-SNAPSHOT and not much should have changed their since a few years: public static void main(String[] args) throws CDKException { String smi = "C[C@]12CC[C@H]3[C@@H](CCC4=CC(O)=CC=C34)[C@@H]1CC[C@@]2(O)C#C"; IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance(); SmilesParser smipar = new SmilesParser(bldr); IAtomContainer mol = smipar.parseSmiles(smi); System.out.println(InChIGeneratorFactory.getInstance().getInChIGenerator(mol).getInchiKey()); // not needed // AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol); AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol); System.out.println(InChIGeneratorFactory.getInstance().getInChIGenerator(mol).getInchiKey()); } You don't need to assign the atom types, but I tried with/without the answer was the same. BFPYWIDHMRZLRN-SLHNCBLASA-N BFPYWIDHMRZLRN-SLHNCBLASA-N John On 7 February 2018 at 22:06, Yannick .Djoumbouwrote: > Hi all, > > I have been under deep debugging more for a few hours, only to find that > there seem the InChIKey of molecules seem to change when I use the > AtomContainerManipulator to convert implicit hydrogens into explicit ones. > > For instance > > I have the following 17-Ethinylestradiol molecule: > > C[C@]12CC[C@H]3[C@@H](CCC4=CC(O)=CC=C34)[C@@H]1CC[C@@]2(O)C#C > > PubChem CID: 5991 > > > If I use > > > InChIGeneratorFactory inchiGenFactory = InChIGeneratorFactory. > getInstance(); > > System.out.println("INCHIKEY BEFORE ADDING EXPLICIT HYDROGEN: ") + > inchiGenFactory.getInChIGenerator(molClone).getInchiKey()); > > > AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(" > 17-Ethinylestradiol"); > > AtomContainerManipulator.convertImplicitToExplicitHydrogens(" > 17-Ethinylestradiol"); > > > System.out.println("INCHIKEY AFTER ADDING EXPLICIT HYDROGEN: ") + > inchiGenFactory.getInChIGenerator(molClone).getInchiKey()); > > > I get the following output: > > > INCHIKEY BEFORE ADDING EXPLICIT HYDROGEN: BFPYWIDHMRZLRN-SLHNCBLASA-N > > INCHIKEY AFTER ADDING EXPLICIT HYDROGEN: BFPYWIDHMRZLRN-OQPPHWFISA-N > > This causes a problem down the path for me. > > > An interesting point is that I used the structures generated (via isomeric > SMILES) upon conversion of implicit hydrogen by CDK and visualized them > using Marvin Sketch (Seee attached file), and the look identical to me. I > also used the isomeric SMILES strings before and after conversion to search > for same stereoisitopes in PubChem, and found the exact same structure. So > I am confused as to why CDK would return different InChIKeys. > > > Is there an explanation for this, or may be some other steps I should take > to avoid this? > > > Thank you for your consideration. > > > Best, > > > Yannick > > > > > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user