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From: Nina J. <jel...@gm...> - 2015-04-23 17:54:17
|
Thanks. One more inquiry - could you run mvn dependency:tree on your project with ambit 3.0.0 and tell which net.idea.modbcum-i version is required And possibly check if it is here http://ambit.uni-plovdiv.bg:8083/nexus/#nexus-search;gav~net.idea~modbcum-i~~~~kw,versionexpand Regards, Nina On 23 April 2015 at 20:42, Yannick .Djoumbou <y.d...@gm...> wrote: > Hi Nina, > > I got some help from John regarding kekulization and how to go around type > 4 bonds. I attached the class SmirksTest.java. Some included CDK classes > are not in this code though. > > I changed my code from the previous one, and I am adding implicit H > atoms., converting them to explicit ones, and I kekulize the molecule. > John suggested setting the flag of each bond to ISAROMATIC when its is set > to SINGLE_OR_DOUBLE, as well as seeting the flag for the 2 participant > atoms to ISAROMATIC. this is done before kekulaiation (from the > Kekulization class). > > Now, I get metabolites when the input structure is in aromatic (not > kekule) form (see MOL1, output_1, and mol1_metabolites). however, when I > submit the structure in kekule form (MOL2, output_2), I do not get any > metabolite. > > The SMIRKS I used is: [c:1][H:2]>>[c:1][OX2][H:2] (I also tried > [c;H1:1]>>[c:1][OX2H1]) > > Thank you for your help. > > Regards, > > > On Thu, Apr 23, 2015 at 11:07 AM, Nina Jeliazkova < > jel...@gm...> wrote: > >> Hi Yannick, >> >> On 23 April 2015 at 19:17, Yannick .Djoumbou <y.d...@gm...> >> wrote: >> >>> Hi Nina, >>> >>> You mentioned early that SMIRKS needs the structures to be kekulized. I >>> assumed that it means every bond of type 4 will be changed to type 1 or 2, >>> but still be labeled as aromatic. Am I right? >>> This means, I should not used the Aromatize function then. I should make >>> sure the structure is always kekulize. Therefore, I should use the >>> kekuliseAromaticRings() from FixBondOrdersTool, right? >>> >> >> No, FixBondOrdersTool is deprecated, don't use it. Use the new >> Kekulization class. John May may help with how to use it. >> >> >> http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Kekulization.html >> >> >>> >>> Moreover, I have the following error when using ambit2 3.0.0. It >>> tdoesn't mattr whether I use CDK 1.5.6 (as I did before with ambit 2.5.6) >>> or 1.5.10. >>> >>> Exception in thread "main" java.lang.NoClassDefFoundError: >>> net/idea/modbcum/i/exceptions/AmbitException >>> at Metabolize.main(Metabolize.java:35) >>> Caused by: java.lang.ClassNotFoundException: >>> net.idea.modbcum.i.exceptions.AmbitException >>> at java.net.URLClassLoader$1.run(URLClassLoader.java:366) >>> at java.net.URLClassLoader$1.run(URLClassLoader.java:355) >>> at java.security.AccessController.doPrivileged(Native Method) >>> at java.net.URLClassLoader.findClass(URLClassLoader.java:354) >>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424) >>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) >>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357) >>> ... 1 more >>> >>> Metabolize.java is the class where I call the main function that uses >>> the AMBIT and CDK modules. I did not have this error before moving to 3.0.0. >>> >> >> Can you give a piece of code we can test? It looks like a missing/ not >> loaded dependency. >> >> Regards, >> Nina >> >> >> >>> Please let me know. >>> >>> Regards, >>> >>> On Tue, Apr 21, 2015 at 10:54 PM, Yannick .Djoumbou < >>> y.d...@gm...> wrote: >>> >>>> Thanks for letting me know. >>>> Regards, >>>> >>>> Yannick >>>> >>>> On Tue, Apr 21, 2015 at 10:44 PM, Nina Jeliazkova < >>>> jel...@gm...> wrote: >>>> >>>>> Yannick, >>>>> >>>>> Just a warning, 3.0.0 is still being tested and not released yet, but >>>>> the SMIRKS package was tested by another group as well and appears to work >>>>> well. >>>>> >>>>> Best regards, >>>>> Nina >>>>> >>>>> >>>>> On 22 April 2015 at 07:38, Yannick .Djoumbou <y.d...@gm...> >>>>> wrote: >>>>> >>>>>> Thanks Nina, >>>>>> >>>>>> first of all, I am really happy that a new release of AMBIT was >>>>>> released and is working with CDK 1.5.10. I'll try that out and also use the >>>>>> aromaticity class. >>>>>> I a looking forward to reading Nick's reply. >>>>>> >>>>>> Regards, >>>>>> >>>>>> Yannick >>>>>> >>>>>> On Tue, Apr 21, 2015 at 10:32 PM, Nina Jeliazkova < >>>>>> jel...@gm...> wrote: >>>>>> >>>>>>> Yannick, >>>>>>> >>>>>>> Nick may reply later this week, but could you please try ambit >>>>>>> 3.0.0-SNAPSHOT (CDK 1.5.10) dependency >>>>>>> >>>>>>> >>>>>>> http://ambit.uni-plovdiv.bg:8083/nexus/#nexus-search;gav~ambit~~3.0.0-SNAPSHOT~~ >>>>>>> >>>>>>> The version you work with is quite outdated and there have been >>>>>>> number of improvements. >>>>>>> >>>>>>> Last but not least, the SMIRKS package expects Kekule structures. >>>>>>> You will NOT get same results if structures are not kekulized. Fortunately, >>>>>>> in CDK 1.5.10 the kekulization works quite well. >>>>>>> >>>>>>> In any case please do not use SMSD* package, it is already >>>>>>> deprecated in CDK as far as I know. Use the new Aromaticity class >>>>>>> >>>>>>> >>>>>>> http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Aromaticity.html >>>>>>> >>>>>>> Best regards, >>>>>>> Nina >>>>>>> >>>>>>> >>>>>>> On 21 April 2015 at 21:07, Yannick .Djoumbou <y.d...@gm...> >>>>>>> wrote: >>>>>>> >>>>>>>> Hello guys, >>>>>>>> >>>>>>>> I am dealing with an issue here. I would like to apply a >>>>>>>> transformation on the attached molecules. Below is a function that I wrote >>>>>>>> to apply a transformation with single copy for each position (with >>>>>>>> smrkMan.applyTransformationWithSingleCopyForEachPos). Because CDK has >>>>>>>> issues dealing with bond type 4, I tried to transform the same molecule >>>>>>>> (aniline) using different bond types. >>>>>>>> In test1.sdf, the bond types in the benzene ring have type 1 and 2, >>>>>>>> alternatively. This, however produces 5 metabolites. In test2.sdf, >>>>>>>> the aromatic bonds of the molecule are of type 4. The transformation does >>>>>>>> not produce any product, which is wrong. >>>>>>>> >>>>>>>> Procedure: >>>>>>>> ---------- >>>>>>>> (1) I tested whether CDK viewed the input molecule as aromatic or >>>>>>>> not, by checking the bond types. For my own preference, I also >>>>>>>> added explicit hydrogen atoms in order to use my smirks pattern more >>>>>>>> efficiently. For test1, aniline is not first viewed as aromatic. >>>>>>>> Thus, I aromatized it using CDK's SMSDNormalizer.aromatizeMolecule. In >>>>>>>> test2, aniline is viewed as aromatic. Because the bonds in the benzene ring >>>>>>>> are of type 4, I decided to kekulize it, so that CDK with better >>>>>>>> deal with the molecule. Somehow, the resulting molecule still has bond type >>>>>>>> 4. The resulting molecules after these edits are stored in >>>>>>>> test1_after_aromatizing_and_adding_hydrogen.sdf and >>>>>>>> test2_after_kekulizing_and_adding_hydrogen.sdf. Somehow, the molecule in >>>>>>>> the later files does not have explicit hydrogen atoms attached to the >>>>>>>> benzene ring. >>>>>>>> >>>>>>>> (2) Following the first step, I ran >>>>>>>> smrkMan.applyTransformationWithSingleCopyForEachPos on the container >>>>>>>> obtained after the first step, where smrkMan is an instance of the SMRIKS >>>>>>>> Manager. As mentioned earlier, aniline in the first form (ring bonds with >>>>>>>> types 1 and 2) was transformed. the five products are in the file >>>>>>>> test1_metabolites.sdf. In the second file (ring bonds with type 4) >>>>>>>> is not transformed. >>>>>>>> I used the smirks: [c;H1:1]>>[c:1][OX2H1] and [c:1]>>[c:1][OX2H1] >>>>>>>> foe each molecule, which returned the same output. >>>>>>>> This procedure was implemented in the function transform_from_sdf >>>>>>>> below. >>>>>>>> >>>>>>>> >>>>>>>> Could you please help me here? How can I get the same results >>>>>>>> whether I submit my molecule in the kekule or the aromatic form? I have >>>>>>>> tried different things, but without success. by the way, I am using the >>>>>>>> AMBIT 2.6.0 and CDK version 1.5.6 versions. I really need help >>>>>>>> here. >>>>>>>> >>>>>>>> Thank you for your consideration. >>>>>>>> >>>>>>>> Best regards, >>>>>>>> >>>>>>>> Yannick >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> public LinkedHashMap<String, IAtomContainerSet> >>>>>>>> transform_from_sdf(File sdf_input, SMIRKSReaction reaction) throws >>>>>>>> Exception{ >>>>>>>> >>>>>>>> LinkedHashMap<String, IAtomContainerSet> sdf_metabolites = new >>>>>>>> LinkedHashMap<String, IAtomContainerSet>(); >>>>>>>> IteratingSDFReader reader = new IteratingSDFReader(new >>>>>>>> FileInputStream(sdf_input), DefaultChemObjectBuilder.getInstance()); >>>>>>>> SMIRKSManager smrkMan = new >>>>>>>> SMIRKSManager(SilentChemObjectBuilder.getInstance()); >>>>>>>> >>>>>>>> StringWriter writer=new StringWriter(); // >>>>>>>> http://www.programcreek.com/java-api-examples/index.php?api=org.openscience.cdk.AtomContainerSet >>>>>>>> >>>>>>>> StructureDiagramGenerator sdg = new >>>>>>>> StructureDiagramGenerator(); >>>>>>>> DeduceBondSystemTool dbst = new DeduceBondSystemTool(); >>>>>>>> FixBondOrdersTool kekulizer = new FixBondOrdersTool(); >>>>>>>> >>>>>>>> int i = 0; >>>>>>>> while (reader.hasNext()) { >>>>>>>> i = i+1; >>>>>>>> >>>>>>>> IAtomContainer molecule = (IAtomContainer)reader.next(); >>>>>>>> System.out.println("Query molecule: " + molecule); >>>>>>>> >>>>>>>> boolean aromatic_0 = false; >>>>>>>> for (IBond bond : molecule.bonds()) if >>>>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_0 = true; break;} >>>>>>>> >>>>>>>> System.out.println("IS THE ORIGINAL MOLECULE AROMATIC?: " + >>>>>>>> aromatic_0); >>>>>>>> >>>>>>>> >>>>>>>> StringWriter w = new StringWriter(); >>>>>>>> MDLWriter mw = new MDLWriter(w); >>>>>>>> mw.write(molecule); >>>>>>>> System.out.println("ORIGINAL MOLECULE" + w.toString()); >>>>>>>> >>>>>>>> >>>>>>>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule); >>>>>>>> sdg.setMolecule(molecule); >>>>>>>> sdg.generateCoordinates(); >>>>>>>> IAtomContainer mol_with_hydrogen = sdg.getMolecule(); >>>>>>>> >>>>>>>> >>>>>>>> if(!aromatic_0){ >>>>>>>> SMSDNormalizer.aromatizeMolecule(mol_with_hydrogen); >>>>>>>> boolean aromatic = false; >>>>>>>> for (IBond bond : mol_with_hydrogen.bonds()) if >>>>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic = true; break;} >>>>>>>> System.out.println("HAS THE MOLECULE BEEN AROMATIZED?: >>>>>>>> " + aromatic); >>>>>>>> mw.write(mol_with_hydrogen); >>>>>>>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >>>>>>>> EXPLICIT ATOMS" + w.toString()); >>>>>>>> >>>>>>>> } >>>>>>>> else{ >>>>>>>> >>>>>>>> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol_with_hydrogen); >>>>>>>> mol_with_hydrogen = >>>>>>>> kekulizer.kekuliseAromaticRings(mol_with_hydrogen); >>>>>>>> mw.write(mol_with_hydrogen); >>>>>>>> System.out.println(mol_with_hydrogen); >>>>>>>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >>>>>>>> EXPLICIT ATOMS" + w.toString()); >>>>>>>> >>>>>>>> boolean aromatic_3 = false; >>>>>>>> for (IBond bond : mol_with_hydrogen.bonds()) if >>>>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_3 = true; break;} >>>>>>>> System.out.println("IS AROMATIC AFTER HYDRO?? " + >>>>>>>> aromatic_3); >>>>>>>> } >>>>>>>> >>>>>>>> >>>>>>>> System.out.println(mol_with_hydrogen); >>>>>>>> SmilesGenerator sg = new SmilesGenerator(); >>>>>>>> System.out.println(sg.create(mol_with_hydrogen)); >>>>>>>> >>>>>>>> >>>>>>>> String name = (String) >>>>>>>> molecule.getProperty(CDKConstants.TITLE); >>>>>>>> IAtomContainerSet metabolites = >>>>>>>> generateAllMetabolitesFromAtomContainer(mol_with_hydrogen, reaction, >>>>>>>> smrkMan); >>>>>>>> System.out.println("METABOLITES" + metabolites); >>>>>>>> } >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > |
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From: Yannick .D. <y.d...@gm...> - 2015-04-23 17:44:09
|
Again, this is done with AMBIT 2 2.6 .0 and CDK 1.5.10. I get errors when using AMBIT2 3.0.0. Regards, On Thu, Apr 23, 2015 at 11:42 AM, Yannick .Djoumbou <y.d...@gm...> wrote: > Hi Nina, > > I got some help from John regarding kekulization and how to go around type > 4 bonds. I attached the class SmirksTest.java. Some included CDK classes > are not in this code though. > > I changed my code from the previous one, and I am adding implicit H > atoms., converting them to explicit ones, and I kekulize the molecule. > John suggested setting the flag of each bond to ISAROMATIC when its is set > to SINGLE_OR_DOUBLE, as well as seeting the flag for the 2 participant > atoms to ISAROMATIC. this is done before kekulaiation (from the > Kekulization class). > > Now, I get metabolites when the input structure is in aromatic (not > kekule) form (see MOL1, output_1, and mol1_metabolites). however, when I > submit the structure in kekule form (MOL2, output_2), I do not get any > metabolite. > > The SMIRKS I used is: [c:1][H:2]>>[c:1][OX2][H:2] (I also tried > [c;H1:1]>>[c:1][OX2H1]) > > Thank you for your help. > > Regards, > > > On Thu, Apr 23, 2015 at 11:07 AM, Nina Jeliazkova < > jel...@gm...> wrote: > >> Hi Yannick, >> >> On 23 April 2015 at 19:17, Yannick .Djoumbou <y.d...@gm...> >> wrote: >> >>> Hi Nina, >>> >>> You mentioned early that SMIRKS needs the structures to be kekulized. I >>> assumed that it means every bond of type 4 will be changed to type 1 or 2, >>> but still be labeled as aromatic. Am I right? >>> This means, I should not used the Aromatize function then. I should make >>> sure the structure is always kekulize. Therefore, I should use the >>> kekuliseAromaticRings() from FixBondOrdersTool, right? >>> >> >> No, FixBondOrdersTool is deprecated, don't use it. Use the new >> Kekulization class. John May may help with how to use it. >> >> >> http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Kekulization.html >> >> >>> >>> Moreover, I have the following error when using ambit2 3.0.0. It >>> tdoesn't mattr whether I use CDK 1.5.6 (as I did before with ambit 2.5.6) >>> or 1.5.10. >>> >>> Exception in thread "main" java.lang.NoClassDefFoundError: >>> net/idea/modbcum/i/exceptions/AmbitException >>> at Metabolize.main(Metabolize.java:35) >>> Caused by: java.lang.ClassNotFoundException: >>> net.idea.modbcum.i.exceptions.AmbitException >>> at java.net.URLClassLoader$1.run(URLClassLoader.java:366) >>> at java.net.URLClassLoader$1.run(URLClassLoader.java:355) >>> at java.security.AccessController.doPrivileged(Native Method) >>> at java.net.URLClassLoader.findClass(URLClassLoader.java:354) >>> at java.lang.ClassLoader.loadClass(ClassLoader.java:424) >>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) >>> at java.lang.ClassLoader.loadClass(ClassLoader.java:357) >>> ... 1 more >>> >>> Metabolize.java is the class where I call the main function that uses >>> the AMBIT and CDK modules. I did not have this error before moving to 3.0.0. >>> >> >> Can you give a piece of code we can test? It looks like a missing/ not >> loaded dependency. >> >> Regards, >> Nina >> >> >> >>> Please let me know. >>> >>> Regards, >>> >>> On Tue, Apr 21, 2015 at 10:54 PM, Yannick .Djoumbou < >>> y.d...@gm...> wrote: >>> >>>> Thanks for letting me know. >>>> Regards, >>>> >>>> Yannick >>>> >>>> On Tue, Apr 21, 2015 at 10:44 PM, Nina Jeliazkova < >>>> jel...@gm...> wrote: >>>> >>>>> Yannick, >>>>> >>>>> Just a warning, 3.0.0 is still being tested and not released yet, but >>>>> the SMIRKS package was tested by another group as well and appears to work >>>>> well. >>>>> >>>>> Best regards, >>>>> Nina >>>>> >>>>> >>>>> On 22 April 2015 at 07:38, Yannick .Djoumbou <y.d...@gm...> >>>>> wrote: >>>>> >>>>>> Thanks Nina, >>>>>> >>>>>> first of all, I am really happy that a new release of AMBIT was >>>>>> released and is working with CDK 1.5.10. I'll try that out and also use the >>>>>> aromaticity class. >>>>>> I a looking forward to reading Nick's reply. >>>>>> >>>>>> Regards, >>>>>> >>>>>> Yannick >>>>>> >>>>>> On Tue, Apr 21, 2015 at 10:32 PM, Nina Jeliazkova < >>>>>> jel...@gm...> wrote: >>>>>> >>>>>>> Yannick, >>>>>>> >>>>>>> Nick may reply later this week, but could you please try ambit >>>>>>> 3.0.0-SNAPSHOT (CDK 1.5.10) dependency >>>>>>> >>>>>>> >>>>>>> http://ambit.uni-plovdiv.bg:8083/nexus/#nexus-search;gav~ambit~~3.0.0-SNAPSHOT~~ >>>>>>> >>>>>>> The version you work with is quite outdated and there have been >>>>>>> number of improvements. >>>>>>> >>>>>>> Last but not least, the SMIRKS package expects Kekule structures. >>>>>>> You will NOT get same results if structures are not kekulized. Fortunately, >>>>>>> in CDK 1.5.10 the kekulization works quite well. >>>>>>> >>>>>>> In any case please do not use SMSD* package, it is already >>>>>>> deprecated in CDK as far as I know. Use the new Aromaticity class >>>>>>> >>>>>>> >>>>>>> http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Aromaticity.html >>>>>>> >>>>>>> Best regards, >>>>>>> Nina >>>>>>> >>>>>>> >>>>>>> On 21 April 2015 at 21:07, Yannick .Djoumbou <y.d...@gm...> >>>>>>> wrote: >>>>>>> >>>>>>>> Hello guys, >>>>>>>> >>>>>>>> I am dealing with an issue here. I would like to apply a >>>>>>>> transformation on the attached molecules. Below is a function that I wrote >>>>>>>> to apply a transformation with single copy for each position (with >>>>>>>> smrkMan.applyTransformationWithSingleCopyForEachPos). Because CDK has >>>>>>>> issues dealing with bond type 4, I tried to transform the same molecule >>>>>>>> (aniline) using different bond types. >>>>>>>> In test1.sdf, the bond types in the benzene ring have type 1 and 2, >>>>>>>> alternatively. This, however produces 5 metabolites. In test2.sdf, >>>>>>>> the aromatic bonds of the molecule are of type 4. The transformation does >>>>>>>> not produce any product, which is wrong. >>>>>>>> >>>>>>>> Procedure: >>>>>>>> ---------- >>>>>>>> (1) I tested whether CDK viewed the input molecule as aromatic or >>>>>>>> not, by checking the bond types. For my own preference, I also >>>>>>>> added explicit hydrogen atoms in order to use my smirks pattern more >>>>>>>> efficiently. For test1, aniline is not first viewed as aromatic. >>>>>>>> Thus, I aromatized it using CDK's SMSDNormalizer.aromatizeMolecule. In >>>>>>>> test2, aniline is viewed as aromatic. Because the bonds in the benzene ring >>>>>>>> are of type 4, I decided to kekulize it, so that CDK with better >>>>>>>> deal with the molecule. Somehow, the resulting molecule still has bond type >>>>>>>> 4. The resulting molecules after these edits are stored in >>>>>>>> test1_after_aromatizing_and_adding_hydrogen.sdf and >>>>>>>> test2_after_kekulizing_and_adding_hydrogen.sdf. Somehow, the molecule in >>>>>>>> the later files does not have explicit hydrogen atoms attached to the >>>>>>>> benzene ring. >>>>>>>> >>>>>>>> (2) Following the first step, I ran >>>>>>>> smrkMan.applyTransformationWithSingleCopyForEachPos on the container >>>>>>>> obtained after the first step, where smrkMan is an instance of the SMRIKS >>>>>>>> Manager. As mentioned earlier, aniline in the first form (ring bonds with >>>>>>>> types 1 and 2) was transformed. the five products are in the file >>>>>>>> test1_metabolites.sdf. In the second file (ring bonds with type 4) >>>>>>>> is not transformed. >>>>>>>> I used the smirks: [c;H1:1]>>[c:1][OX2H1] and [c:1]>>[c:1][OX2H1] >>>>>>>> foe each molecule, which returned the same output. >>>>>>>> This procedure was implemented in the function transform_from_sdf >>>>>>>> below. >>>>>>>> >>>>>>>> >>>>>>>> Could you please help me here? How can I get the same results >>>>>>>> whether I submit my molecule in the kekule or the aromatic form? I have >>>>>>>> tried different things, but without success. by the way, I am using the >>>>>>>> AMBIT 2.6.0 and CDK version 1.5.6 versions. I really need help >>>>>>>> here. >>>>>>>> >>>>>>>> Thank you for your consideration. >>>>>>>> >>>>>>>> Best regards, >>>>>>>> >>>>>>>> Yannick >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> public LinkedHashMap<String, IAtomContainerSet> >>>>>>>> transform_from_sdf(File sdf_input, SMIRKSReaction reaction) throws >>>>>>>> Exception{ >>>>>>>> >>>>>>>> LinkedHashMap<String, IAtomContainerSet> sdf_metabolites = new >>>>>>>> LinkedHashMap<String, IAtomContainerSet>(); >>>>>>>> IteratingSDFReader reader = new IteratingSDFReader(new >>>>>>>> FileInputStream(sdf_input), DefaultChemObjectBuilder.getInstance()); >>>>>>>> SMIRKSManager smrkMan = new >>>>>>>> SMIRKSManager(SilentChemObjectBuilder.getInstance()); >>>>>>>> >>>>>>>> StringWriter writer=new StringWriter(); // >>>>>>>> http://www.programcreek.com/java-api-examples/index.php?api=org.openscience.cdk.AtomContainerSet >>>>>>>> >>>>>>>> StructureDiagramGenerator sdg = new >>>>>>>> StructureDiagramGenerator(); >>>>>>>> DeduceBondSystemTool dbst = new DeduceBondSystemTool(); >>>>>>>> FixBondOrdersTool kekulizer = new FixBondOrdersTool(); >>>>>>>> >>>>>>>> int i = 0; >>>>>>>> while (reader.hasNext()) { >>>>>>>> i = i+1; >>>>>>>> >>>>>>>> IAtomContainer molecule = (IAtomContainer)reader.next(); >>>>>>>> System.out.println("Query molecule: " + molecule); >>>>>>>> >>>>>>>> boolean aromatic_0 = false; >>>>>>>> for (IBond bond : molecule.bonds()) if >>>>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_0 = true; break;} >>>>>>>> >>>>>>>> System.out.println("IS THE ORIGINAL MOLECULE AROMATIC?: " + >>>>>>>> aromatic_0); >>>>>>>> >>>>>>>> >>>>>>>> StringWriter w = new StringWriter(); >>>>>>>> MDLWriter mw = new MDLWriter(w); >>>>>>>> mw.write(molecule); >>>>>>>> System.out.println("ORIGINAL MOLECULE" + w.toString()); >>>>>>>> >>>>>>>> >>>>>>>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule); >>>>>>>> sdg.setMolecule(molecule); >>>>>>>> sdg.generateCoordinates(); >>>>>>>> IAtomContainer mol_with_hydrogen = sdg.getMolecule(); >>>>>>>> >>>>>>>> >>>>>>>> if(!aromatic_0){ >>>>>>>> SMSDNormalizer.aromatizeMolecule(mol_with_hydrogen); >>>>>>>> boolean aromatic = false; >>>>>>>> for (IBond bond : mol_with_hydrogen.bonds()) if >>>>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic = true; break;} >>>>>>>> System.out.println("HAS THE MOLECULE BEEN AROMATIZED?: >>>>>>>> " + aromatic); >>>>>>>> mw.write(mol_with_hydrogen); >>>>>>>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >>>>>>>> EXPLICIT ATOMS" + w.toString()); >>>>>>>> >>>>>>>> } >>>>>>>> else{ >>>>>>>> >>>>>>>> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol_with_hydrogen); >>>>>>>> mol_with_hydrogen = >>>>>>>> kekulizer.kekuliseAromaticRings(mol_with_hydrogen); >>>>>>>> mw.write(mol_with_hydrogen); >>>>>>>> System.out.println(mol_with_hydrogen); >>>>>>>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >>>>>>>> EXPLICIT ATOMS" + w.toString()); >>>>>>>> >>>>>>>> boolean aromatic_3 = false; >>>>>>>> for (IBond bond : mol_with_hydrogen.bonds()) if >>>>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_3 = true; break;} >>>>>>>> System.out.println("IS AROMATIC AFTER HYDRO?? " + >>>>>>>> aromatic_3); >>>>>>>> } >>>>>>>> >>>>>>>> >>>>>>>> System.out.println(mol_with_hydrogen); >>>>>>>> SmilesGenerator sg = new SmilesGenerator(); >>>>>>>> System.out.println(sg.create(mol_with_hydrogen)); >>>>>>>> >>>>>>>> >>>>>>>> String name = (String) >>>>>>>> molecule.getProperty(CDKConstants.TITLE); >>>>>>>> IAtomContainerSet metabolites = >>>>>>>> generateAllMetabolitesFromAtomContainer(mol_with_hydrogen, reaction, >>>>>>>> smrkMan); >>>>>>>> System.out.println("METABOLITES" + metabolites); >>>>>>>> } >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > |
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From: Yannick .D. <y.d...@gm...> - 2015-04-23 17:42:22
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Query molecule: AtomContainer(1350215963, #A:7, Atom(619992292, S:C, SP:0, 2D:[(-2.1214, -1.65)], AtomType(619992292, FC:0, Isotope(619992292, Element(619992292, S:C, AN:6)))), Atom(1385819957, S:C, SP:0, 2D:[(-2.8359, -2.0625)], AtomType(1385819957, FC:0, Isotope(1385819957, Element(1385819957, S:C, AN:6)))), Atom(2015865584, S:C, SP:0, 2D:[(-2.8359, -2.8875)], AtomType(2015865584, FC:0, Isotope(2015865584, Element(2015865584, S:C, AN:6)))), Atom(1950855216, S:C, SP:0, 2D:[(-2.1214, -3.3)], AtomType(1950855216, FC:0, Isotope(1950855216, Element(1950855216, S:C, AN:6)))), Atom(243292916, S:C, SP:0, 2D:[(-1.407, -2.8875)], AtomType(243292916, FC:0, Isotope(243292916, Element(243292916, S:C, AN:6)))), Atom(215175324, S:C, SP:0, 2D:[(-1.407, -2.0625)], AtomType(215175324, FC:0, Isotope(215175324, Element(215175324, S:C, AN:6)))), Atom(89208920, S:N, H:2, SP:0, 2D:[(-2.1214, -0.825)], AtomType(89208920, FC:0, EV:3, Isotope(89208920, Element(89208920, S:N, AN:7)))), #B:7, Bond(390732834, #O:UNSET, #S:NONE, #A:2, Atom(619992292, S:C, SP:0, 2D:[(-2.1214, -1.65)], AtomType(619992292, FC:0, Isotope(619992292, Element(619992292, S:C, AN:6)))), Atom(1385819957, S:C, SP:0, 2D:[(-2.8359, -2.0625)], AtomType(1385819957, FC:0, Isotope(1385819957, Element(1385819957, S:C, AN:6)))), ElectronContainer(390732834EC:0)), Bond(41748512, #O:UNSET, #S:NONE, #A:2, Atom(1385819957, S:C, SP:0, 2D:[(-2.8359, -2.0625)], AtomType(1385819957, FC:0, Isotope(1385819957, Element(1385819957, S:C, AN:6)))), Atom(2015865584, S:C, SP:0, 2D:[(-2.8359, -2.8875)], AtomType(2015865584, FC:0, Isotope(2015865584, Element(2015865584, S:C, AN:6)))), ElectronContainer(41748512EC:0)), Bond(1587572262, #O:UNSET, #S:NONE, #A:2, Atom(2015865584, S:C, SP:0, 2D:[(-2.8359, -2.8875)], AtomType(2015865584, FC:0, Isotope(2015865584, Element(2015865584, S:C, AN:6)))), Atom(1950855216, S:C, SP:0, 2D:[(-2.1214, -3.3)], AtomType(1950855216, FC:0, Isotope(1950855216, Element(1950855216, S:C, AN:6)))), ElectronContainer(1587572262EC:0)), Bond(1990177106, #O:UNSET, #S:NONE, #A:2, Atom(1950855216, S:C, SP:0, 2D:[(-2.1214, -3.3)], AtomType(1950855216, FC:0, Isotope(1950855216, Element(1950855216, S:C, AN:6)))), Atom(243292916, S:C, SP:0, 2D:[(-1.407, -2.8875)], AtomType(243292916, FC:0, Isotope(243292916, Element(243292916, S:C, AN:6)))), ElectronContainer(1990177106EC:0)), Bond(1848818517, #O:UNSET, #S:NONE, #A:2, Atom(243292916, S:C, SP:0, 2D:[(-1.407, -2.8875)], AtomType(243292916, FC:0, Isotope(243292916, Element(243292916, S:C, AN:6)))), Atom(215175324, S:C, SP:0, 2D:[(-1.407, -2.0625)], AtomType(215175324, FC:0, Isotope(215175324, Element(215175324, S:C, AN:6)))), ElectronContainer(1848818517EC:0)), Bond(1151926776, #O:UNSET, #S:NONE, #A:2, Atom(619992292, S:C, SP:0, 2D:[(-2.1214, -1.65)], AtomType(619992292, FC:0, Isotope(619992292, Element(619992292, S:C, AN:6)))), Atom(215175324, S:C, SP:0, 2D:[(-1.407, -2.0625)], AtomType(215175324, FC:0, Isotope(215175324, Element(215175324, S:C, AN:6)))), ElectronContainer(1151926776EC:0)), Bond(868246527, #O:SINGLE, #S:NONE, #A:2, Atom(619992292, S:C, SP:0, 2D:[(-2.1214, -1.65)], AtomType(619992292, FC:0, Isotope(619992292, Element(619992292, S:C, AN:6)))), Atom(89208920, S:N, H:2, SP:0, 2D:[(-2.1214, -0.825)], AtomType(89208920, FC:0, EV:3, Isotope(89208920, Element(89208920, S:N, AN:7)))), ElectronContainer(868246527EC:2)))
IS THE ORIGINAL MOLECULE AROMATIC?: true
ORIGINAL MOLECULE
CDK 0423151106
7 7 0 0 0 0 0 0 0 0999 V2000
-2.1214 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8359 -2.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8359 -2.8875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1214 -3.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4070 -2.8875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4070 -2.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1214 -0.8250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
1 6 4 0 0 0 0
1 7 1 0 0 0 0
M END
KEKULIZED MOLECULE WITH HYDROGEN EXPLICIT ATOMS
CDK 0423151106
7 7 0 0 0 0 0 0 0 0999 V2000
-2.1214 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8359 -2.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8359 -2.8875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1214 -3.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4070 -2.8875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4070 -2.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1214 -0.8250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
1 6 4 0 0 0 0
1 7 1 0 0 0 0
M END
$$$$
CDK 0423151106
14 14 0 0 0 0 0 0 0 0999 V2000
0.0000 1.0710 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2990 0.3210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2990 -1.1790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.9290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 -1.1790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.3210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 2.5710 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.5980 1.0710 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5980 -1.9290 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0000 -3.4290 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.5980 -1.9290 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.5980 1.0710 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2990 3.3210 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 3.3210 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
1 6 4 0 0 0 0
1 7 1 0 0 0 0
2 8 1 0 0 0 0
3 9 1 0 0 0 0
4 10 1 0 0 0 0
5 11 1 0 0 0 0
6 12 1 0 0 0 0
7 13 1 0 0 0 0
7 14 1 0 0 0 0
M END
$$$$
AtomContainer(1972313122, #A:14, Atom(207043258, S:C, H:0, SP:0, 2D:[(0.0, 1.071)], AtomType(207043258, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(207043258, Element(207043258, S:C, AN:6)))), Atom(852529066, S:C, H:0, SP:0, 2D:[(-1.299, 0.321)], AtomType(852529066, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(852529066, Element(852529066, S:C, AN:6)))), Atom(445119478, S:C, H:0, SP:0, 2D:[(-1.299, -1.179)], AtomType(445119478, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(445119478, Element(445119478, S:C, AN:6)))), Atom(1437524245, S:C, H:0, SP:0, 2D:[(0.0, -1.929)], AtomType(1437524245, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1437524245, Element(1437524245, S:C, AN:6)))), Atom(1278956965, S:C, H:0, SP:0, 2D:[(1.299, -1.179)], AtomType(1278956965, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1278956965, Element(1278956965, S:C, AN:6)))), Atom(1265887932, S:C, H:0, SP:0, 2D:[(1.299, 0.321)], AtomType(1265887932, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1265887932, Element(1265887932, S:C, AN:6)))), Atom(657982295, S:N, H:0, SP:0, 2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(657982295, N:N.sp3, MBO:SINGLE, BOS:3.0, FC:0, H:SP3, NC:3, EV:3, Isotope(657982295, Element(657982295, S:N, AN:7)))), Atom(109066362, S:H, H:0, 2D:[(-2.5980428689648356, 1.070991749682361)], AtomType(109066362, N:H, FC:0, Isotope(109066362, Element(109066362, S:H, AN:1)))), Atom(1274795243, S:H, H:0, 2D:[(-2.598042868964835, -1.9289917496823614)], AtomType(1274795243, N:H, FC:0, Isotope(1274795243, Element(1274795243, S:H, AN:1)))), Atom(39302982, S:H, H:0, 2D:[(-2.755455298081545E-16, -3.4290000000000003)], AtomType(39302982, N:H, FC:0, Isotope(39302982, Element(39302982, S:H, AN:1)))), Atom(1287738845, S:H, H:0, 2D:[(2.598042868964835, -1.9289917496823614)], AtomType(1287738845, N:H, FC:0, Isotope(1287738845, Element(1287738845, S:H, AN:1)))), Atom(686573449, S:H, H:0, 2D:[(2.5980428689648356, 1.070991749682361)], AtomType(686573449, N:H, FC:0, Isotope(686573449, Element(686573449, S:H, AN:1)))), Atom(810322012, S:H, H:0, 2D:[(-1.299038105676657, 3.3210000000000015)], AtomType(810322012, N:H, FC:0, Isotope(810322012, Element(810322012, S:H, AN:1)))), Atom(1888250057, S:H, H:0, 2D:[(1.2990381056766584, 3.320999999999999)], AtomType(1888250057, N:H, FC:0, Isotope(1888250057, Element(1888250057, S:H, AN:1)))), #B:14, Bond(305372633, #O:DOUBLE, #S:NONE, #A:2, Atom(207043258, S:C, H:0, SP:0, 2D:[(0.0, 1.071)], AtomType(207043258, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(207043258, Element(207043258, S:C, AN:6)))), Atom(852529066, S:C, H:0, SP:0, 2D:[(-1.299, 0.321)], AtomType(852529066, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(852529066, Element(852529066, S:C, AN:6)))), ElectronContainer(305372633EC:4)), Bond(2059410148, #O:SINGLE, #S:NONE, #A:2, Atom(852529066, S:C, H:0, SP:0, 2D:[(-1.299, 0.321)], AtomType(852529066, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(852529066, Element(852529066, S:C, AN:6)))), Atom(445119478, S:C, H:0, SP:0, 2D:[(-1.299, -1.179)], AtomType(445119478, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(445119478, Element(445119478, S:C, AN:6)))), ElectronContainer(2059410148EC:2)), Bond(1512418737, #O:DOUBLE, #S:NONE, #A:2, Atom(445119478, S:C, H:0, SP:0, 2D:[(-1.299, -1.179)], AtomType(445119478, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(445119478, Element(445119478, S:C, AN:6)))), Atom(1437524245, S:C, H:0, SP:0, 2D:[(0.0, -1.929)], AtomType(1437524245, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1437524245, Element(1437524245, S:C, AN:6)))), ElectronContainer(1512418737EC:4)), Bond(1605266867, #O:SINGLE, #S:NONE, #A:2, Atom(1437524245, S:C, H:0, SP:0, 2D:[(0.0, -1.929)], AtomType(1437524245, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1437524245, Element(1437524245, S:C, AN:6)))), Atom(1278956965, S:C, H:0, SP:0, 2D:[(1.299, -1.179)], AtomType(1278956965, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1278956965, Element(1278956965, S:C, AN:6)))), ElectronContainer(1605266867EC:2)), Bond(883176408, #O:DOUBLE, #S:NONE, #A:2, Atom(1278956965, S:C, H:0, SP:0, 2D:[(1.299, -1.179)], AtomType(1278956965, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1278956965, Element(1278956965, S:C, AN:6)))), Atom(1265887932, S:C, H:0, SP:0, 2D:[(1.299, 0.321)], AtomType(1265887932, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1265887932, Element(1265887932, S:C, AN:6)))), ElectronContainer(883176408EC:4)), Bond(138921192, #O:SINGLE, #S:NONE, #A:2, Atom(207043258, S:C, H:0, SP:0, 2D:[(0.0, 1.071)], AtomType(207043258, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(207043258, Element(207043258, S:C, AN:6)))), Atom(1265887932, S:C, H:0, SP:0, 2D:[(1.299, 0.321)], AtomType(1265887932, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1265887932, Element(1265887932, S:C, AN:6)))), ElectronContainer(138921192EC:2)), Bond(533749655, #O:SINGLE, #S:NONE, #A:2, Atom(207043258, S:C, H:0, SP:0, 2D:[(0.0, 1.071)], AtomType(207043258, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(207043258, Element(207043258, S:C, AN:6)))), Atom(657982295, S:N, H:0, SP:0, 2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(657982295, N:N.sp3, MBO:SINGLE, BOS:3.0, FC:0, H:SP3, NC:3, EV:3, Isotope(657982295, Element(657982295, S:N, AN:7)))), ElectronContainer(533749655EC:2)), Bond(691258066, #O:SINGLE, #S:NONE, #A:2, Atom(852529066, S:C, H:0, SP:0, 2D:[(-1.299, 0.321)], AtomType(852529066, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(852529066, Element(852529066, S:C, AN:6)))), Atom(109066362, S:H, H:0, 2D:[(-2.5980428689648356, 1.070991749682361)], AtomType(109066362, N:H, FC:0, Isotope(109066362, Element(109066362, S:H, AN:1)))), ElectronContainer(691258066EC:2)), Bond(87784992, #O:SINGLE, #S:NONE, #A:2, Atom(445119478, S:C, H:0, SP:0, 2D:[(-1.299, -1.179)], AtomType(445119478, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(445119478, Element(445119478, S:C, AN:6)))), Atom(1274795243, S:H, H:0, 2D:[(-2.598042868964835, -1.9289917496823614)], AtomType(1274795243, N:H, FC:0, Isotope(1274795243, Element(1274795243, S:H, AN:1)))), ElectronContainer(87784992EC:2)), Bond(81095055, #O:SINGLE, #S:NONE, #A:2, Atom(1437524245, S:C, H:0, SP:0, 2D:[(0.0, -1.929)], AtomType(1437524245, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1437524245, Element(1437524245, S:C, AN:6)))), Atom(39302982, S:H, H:0, 2D:[(-2.755455298081545E-16, -3.4290000000000003)], AtomType(39302982, N:H, FC:0, Isotope(39302982, Element(39302982, S:H, AN:1)))), ElectronContainer(81095055EC:2)), Bond(1459957187, #O:SINGLE, #S:NONE, #A:2, Atom(1278956965, S:C, H:0, SP:0, 2D:[(1.299, -1.179)], AtomType(1278956965, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1278956965, Element(1278956965, S:C, AN:6)))), Atom(1287738845, S:H, H:0, 2D:[(2.598042868964835, -1.9289917496823614)], AtomType(1287738845, N:H, FC:0, Isotope(1287738845, Element(1287738845, S:H, AN:1)))), ElectronContainer(1459957187EC:2)), Bond(352291287, #O:SINGLE, #S:NONE, #A:2, Atom(1265887932, S:C, H:0, SP:0, 2D:[(1.299, 0.321)], AtomType(1265887932, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1265887932, Element(1265887932, S:C, AN:6)))), Atom(686573449, S:H, H:0, 2D:[(2.5980428689648356, 1.070991749682361)], AtomType(686573449, N:H, FC:0, Isotope(686573449, Element(686573449, S:H, AN:1)))), ElectronContainer(352291287EC:2)), Bond(347245830, #O:SINGLE, #S:NONE, #A:2, Atom(657982295, S:N, H:0, SP:0, 2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(657982295, N:N.sp3, MBO:SINGLE, BOS:3.0, FC:0, H:SP3, NC:3, EV:3, Isotope(657982295, Element(657982295, S:N, AN:7)))), Atom(810322012, S:H, H:0, 2D:[(-1.299038105676657, 3.3210000000000015)], AtomType(810322012, N:H, FC:0, Isotope(810322012, Element(810322012, S:H, AN:1)))), ElectronContainer(347245830EC:2)), Bond(1447595911, #O:SINGLE, #S:NONE, #A:2, Atom(657982295, S:N, H:0, SP:0, 2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(657982295, N:N.sp3, MBO:SINGLE, BOS:3.0, FC:0, H:SP3, NC:3, EV:3, Isotope(657982295, Element(657982295, S:N, AN:7)))), Atom(1888250057, S:H, H:0, 2D:[(1.2990381056766584, 3.320999999999999)], AtomType(1888250057, N:H, FC:0, Isotope(1888250057, Element(1888250057, S:H, AN:1)))), ElectronContainer(1447595911EC:2)))
C1(=C(C(=C(C(=C1[H])[H])[H])[H])[H])N([H])[H]
<---------------->
METABOLITESAtomContainerSet(230824171, M=5, AtomContainer(1106375515, #A:15, Atom(1939864879, S:C, H:0, SP:0, 2D:[(0.0, 1.071)], AtomType(1939864879, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1939864879, Element(1939864879, S:C, AN:6)))), Atom(212292599, S:C, H:0, SP:0, 2D:[(-1.299, 0.321)], AtomType(212292599, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(212292599, Element(212292599, S:C, AN:6)))), Atom(1031373726, S:C, H:0, SP:0, 2D:[(-1.299, -1.179)], AtomType(1031373726, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1031373726, Element(1031373726, S:C, AN:6)))), Atom(1957697945, S:C, H:0, SP:0, 2D:[(0.0, -1.929)], AtomType(1957697945, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1957697945, Element(1957697945, S:C, AN:6)))), Atom(1432405928, S:C, H:0, SP:0, 2D:[(1.299, -1.179)], AtomType(1432405928, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1432405928, Element(1432405928, S:C, AN:6)))), 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MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1479616934, Element(1479616934, S:C, AN:6)))), Atom(763309998, S:C, H:0, SP:0, 2D:[(1.299, 0.321)], AtomType(763309998, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(763309998, Element(763309998, S:C, AN:6)))), ElectronContainer(1157307426EC:2)), Bond(1106517903, #O:SINGLE, #S:NONE, #A:2, Atom(1479616934, S:C, H:0, SP:0, 2D:[(0.0, 1.071)], AtomType(1479616934, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1479616934, Element(1479616934, S:C, AN:6)))), Atom(2031312855, S:N, H:0, SP:0, 2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(2031312855, N:N.sp3, MBO:SINGLE, BOS:3.0, FC:0, H:SP3, NC:3, EV:3, Isotope(2031312855, Element(2031312855, S:N, AN:7)))), ElectronContainer(1106517903EC:2)), Bond(38012701, #O:SINGLE, #S:NONE, #A:2, Atom(61177478, S:C, H:0, SP:0, 2D:[(-1.299, 0.321)], AtomType(61177478, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(61177478, Element(61177478, S:C, AN:6)))), Atom(1727617626, S:H, H:0, 2D:[(-2.5980428689648356, 1.070991749682361)], AtomType(1727617626, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1727617626, Element(1727617626, S:H, AN:1)))), ElectronContainer(38012701EC:2)), Bond(1076822548, #O:SINGLE, #S:NONE, #A:2, Atom(1712689480, S:C, H:0, SP:0, 2D:[(-1.299, -1.179)], AtomType(1712689480, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1712689480, Element(1712689480, S:C, AN:6)))), Atom(2090532742, S:H, H:0, 2D:[(-2.598042868964835, -1.9289917496823614)], AtomType(2090532742, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(2090532742, Element(2090532742, S:H, AN:1)))), ElectronContainer(1076822548EC:2)), Bond(1311870967, #O:SINGLE, #S:NONE, #A:2, Atom(301285972, S:C, H:0, SP:0, 2D:[(0.0, -1.929)], AtomType(301285972, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(301285972, Element(301285972, S:C, AN:6)))), Atom(603846227, S:H, H:0, 2D:[(-2.755455298081545E-16, -3.4290000000000003)], AtomType(603846227, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(603846227, Element(603846227, S:H, AN:1)))), ElectronContainer(1311870967EC:2)), Bond(400738620, #O:SINGLE, #S:NONE, #A:2, Atom(763309998, S:C, H:0, SP:0, 2D:[(1.299, 0.321)], AtomType(763309998, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(763309998, Element(763309998, S:C, AN:6)))), Atom(167882264, S:H, H:0, 2D:[(2.5980428689648356, 1.070991749682361)], AtomType(167882264, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(167882264, Element(167882264, S:H, AN:1)))), ElectronContainer(400738620EC:2)), Bond(705269348, #O:SINGLE, #S:NONE, #A:2, Atom(2031312855, S:N, H:0, SP:0, 2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(2031312855, N:N.sp3, MBO:SINGLE, BOS:3.0, FC:0, H:SP3, NC:3, EV:3, Isotope(2031312855, Element(2031312855, S:N, AN:7)))), Atom(1951182537, S:H, H:0, 2D:[(-1.299038105676657, 3.3210000000000015)], AtomType(1951182537, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1951182537, Element(1951182537, S:H, AN:1)))), ElectronContainer(705269348EC:2)), Bond(1499684043, #O:SINGLE, #S:NONE, #A:2, Atom(2031312855, S:N, H:0, SP:0, 2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(2031312855, N:N.sp3, MBO:SINGLE, BOS:3.0, FC:0, H:SP3, NC:3, EV:3, Isotope(2031312855, Element(2031312855, S:N, AN:7)))), Atom(1449609669, S:H, H:0, 2D:[(1.2990381056766584, 3.320999999999999)], AtomType(1449609669, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1449609669, Element(1449609669, S:H, AN:1)))), ElectronContainer(1499684043EC:2)), Bond(174145862, #O:SINGLE, #S:NONE, #A:2, Atom(2094375425, S:C, H:0, SP:0, 2D:[(1.299, -1.179)], AtomType(2094375425, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(2094375425, Element(2094375425, S:C, AN:6)))), Atom(387731668, S:O, AtomType(387731668, N:O.sp3, MBO:SINGLE, BOS:2.0, FC:0, H:SP3, NC:2, EV:2, Isotope(387731668, Element(387731668, S:O, AN:8)))), ElectronContainer(174145862EC:2)), Bond(1996775420, #O:SINGLE, #S:NONE, #A:2, Atom(387731668, S:O, AtomType(387731668, N:O.sp3, MBO:SINGLE, BOS:2.0, FC:0, H:SP3, NC:2, EV:2, Isotope(387731668, Element(387731668, S:O, AN:8)))), Atom(1983305114, S:H, H:0, 2D:[(2.598042868964835, -1.9289917496823614)], AtomType(1983305114, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1983305114, Element(1983305114, S:H, AN:1)))), ElectronContainer(1996775420EC:2))), AtomContainer(1077532271, #A:15, Atom(355283546, S:C, H:0, SP:0, 2D:[(0.0, 1.071)], AtomType(355283546, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(355283546, Element(355283546, S:C, AN:6)))), Atom(1246018962, S:C, H:0, SP:0, 2D:[(-1.299, 0.321)], AtomType(1246018962, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1246018962, Element(1246018962, S:C, AN:6)))), Atom(1727652437, S:C, H:0, SP:0, 2D:[(-1.299, -1.179)], AtomType(1727652437, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1727652437, Element(1727652437, S:C, AN:6)))), Atom(528117572, S:C, H:0, SP:0, 2D:[(0.0, -1.929)], AtomType(528117572, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(528117572, Element(528117572, S:C, AN:6)))), Atom(522119553, S:C, H:0, SP:0, 2D:[(1.299, -1.179)], AtomType(522119553, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(522119553, Element(522119553, S:C, AN:6)))), Atom(645145629, S:C, H:0, SP:0, 2D:[(1.299, 0.321)], AtomType(645145629, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(645145629, Element(645145629, S:C, AN:6)))), Atom(317652900, S:N, H:0, SP:0, 2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(317652900, N:N.sp3, MBO:SINGLE, BOS:3.0, FC:0, H:SP3, NC:3, EV:3, Isotope(317652900, Element(317652900, S:N, AN:7)))), Atom(147943858, S:H, H:0, 2D:[(-2.5980428689648356, 1.070991749682361)], AtomType(147943858, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(147943858, Element(147943858, S:H, AN:1)))), Atom(1853841827, S:H, H:0, 2D:[(-2.598042868964835, -1.9289917496823614)], AtomType(1853841827, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1853841827, Element(1853841827, S:H, AN:1)))), Atom(1826835713, S:H, H:0, 2D:[(-2.755455298081545E-16, -3.4290000000000003)], AtomType(1826835713, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1826835713, Element(1826835713, S:H, AN:1)))), Atom(1054127232, S:H, H:0, 2D:[(2.598042868964835, -1.9289917496823614)], AtomType(1054127232, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1054127232, Element(1054127232, S:H, AN:1)))), Atom(2123784121, S:H, H:0, 2D:[(2.5980428689648356, 1.070991749682361)], AtomType(2123784121, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(2123784121, Element(2123784121, S:H, AN:1)))), Atom(1114024860, S:H, H:0, 2D:[(-1.299038105676657, 3.3210000000000015)], AtomType(1114024860, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1114024860, Element(1114024860, S:H, AN:1)))), Atom(1653387474, S:H, H:0, 2D:[(1.2990381056766584, 3.320999999999999)], AtomType(1653387474, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1653387474, Element(1653387474, S:H, AN:1)))), Atom(44883338, S:O, AtomType(44883338, N:O.sp3, MBO:SINGLE, BOS:2.0, FC:0, H:SP3, NC:2, EV:2, Isotope(44883338, Element(44883338, S:O, AN:8)))), #B:15, Bond(587501669, #O:DOUBLE, #S:NONE, #A:2, Atom(355283546, S:C, H:0, SP:0, 2D:[(0.0, 1.071)], AtomType(355283546, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(355283546, Element(355283546, S:C, AN:6)))), Atom(1246018962, S:C, H:0, SP:0, 2D:[(-1.299, 0.321)], AtomType(1246018962, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1246018962, Element(1246018962, S:C, AN:6)))), ElectronContainer(587501669EC:4)), Bond(10741977, #O:SINGLE, #S:NONE, #A:2, Atom(1246018962, S:C, H:0, SP:0, 2D:[(-1.299, 0.321)], AtomType(1246018962, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1246018962, Element(1246018962, S:C, AN:6)))), Atom(1727652437, S:C, H:0, SP:0, 2D:[(-1.299, -1.179)], AtomType(1727652437, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1727652437, Element(1727652437, S:C, AN:6)))), ElectronContainer(10741977EC:2)), Bond(151781091, #O:DOUBLE, #S:NONE, #A:2, Atom(1727652437, S:C, H:0, SP:0, 2D:[(-1.299, -1.179)], AtomType(1727652437, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1727652437, Element(1727652437, S:C, AN:6)))), Atom(528117572, S:C, H:0, SP:0, 2D:[(0.0, -1.929)], AtomType(528117572, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(528117572, Element(528117572, S:C, AN:6)))), ElectronContainer(151781091EC:4)), Bond(1921707448, #O:SINGLE, #S:NONE, #A:2, Atom(528117572, S:C, H:0, SP:0, 2D:[(0.0, -1.929)], AtomType(528117572, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(528117572, Element(528117572, S:C, AN:6)))), Atom(522119553, S:C, H:0, SP:0, 2D:[(1.299, -1.179)], AtomType(522119553, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(522119553, Element(522119553, S:C, AN:6)))), ElectronContainer(1921707448EC:2)), Bond(2130511303, #O:DOUBLE, #S:NONE, #A:2, Atom(522119553, S:C, H:0, SP:0, 2D:[(1.299, -1.179)], AtomType(522119553, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(522119553, Element(522119553, S:C, AN:6)))), Atom(645145629, S:C, H:0, SP:0, 2D:[(1.299, 0.321)], AtomType(645145629, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(645145629, Element(645145629, S:C, AN:6)))), ElectronContainer(2130511303EC:4)), Bond(361139443, #O:SINGLE, #S:NONE, #A:2, Atom(355283546, S:C, H:0, SP:0, 2D:[(0.0, 1.071)], AtomType(355283546, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(355283546, Element(355283546, S:C, AN:6)))), Atom(645145629, S:C, H:0, SP:0, 2D:[(1.299, 0.321)], AtomType(645145629, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(645145629, Element(645145629, S:C, AN:6)))), ElectronContainer(361139443EC:2)), Bond(881832079, #O:SINGLE, #S:NONE, #A:2, Atom(355283546, S:C, H:0, SP:0, 2D:[(0.0, 1.071)], AtomType(355283546, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(355283546, Element(355283546, S:C, AN:6)))), Atom(317652900, S:N, H:0, SP:0, 2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(317652900, N:N.sp3, MBO:SINGLE, BOS:3.0, FC:0, H:SP3, NC:3, EV:3, Isotope(317652900, Element(317652900, S:N, AN:7)))), ElectronContainer(881832079EC:2)), Bond(1167103806, #O:SINGLE, #S:NONE, #A:2, Atom(1246018962, S:C, H:0, SP:0, 2D:[(-1.299, 0.321)], AtomType(1246018962, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1246018962, Element(1246018962, S:C, AN:6)))), Atom(147943858, S:H, H:0, 2D:[(-2.5980428689648356, 1.070991749682361)], AtomType(147943858, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(147943858, Element(147943858, S:H, AN:1)))), ElectronContainer(1167103806EC:2)), Bond(398035744, #O:SINGLE, #S:NONE, #A:2, Atom(1727652437, S:C, H:0, SP:0, 2D:[(-1.299, -1.179)], AtomType(1727652437, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1727652437, Element(1727652437, S:C, AN:6)))), Atom(1853841827, S:H, H:0, 2D:[(-2.598042868964835, -1.9289917496823614)], AtomType(1853841827, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1853841827, Element(1853841827, S:H, AN:1)))), ElectronContainer(398035744EC:2)), Bond(375189003, #O:SINGLE, #S:NONE, #A:2, Atom(522119553, S:C, H:0, SP:0, 2D:[(1.299, -1.179)], AtomType(522119553, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(522119553, Element(522119553, S:C, AN:6)))), Atom(1054127232, S:H, H:0, 2D:[(2.598042868964835, -1.9289917496823614)], AtomType(1054127232, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1054127232, Element(1054127232, S:H, AN:1)))), ElectronContainer(375189003EC:2)), Bond(789585829, #O:SINGLE, #S:NONE, #A:2, Atom(645145629, S:C, H:0, SP:0, 2D:[(1.299, 0.321)], AtomType(645145629, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(645145629, Element(645145629, S:C, AN:6)))), Atom(2123784121, S:H, H:0, 2D:[(2.5980428689648356, 1.070991749682361)], AtomType(2123784121, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(2123784121, Element(2123784121, S:H, AN:1)))), ElectronContainer(789585829EC:2)), Bond(1267573190, #O:SINGLE, #S:NONE, #A:2, Atom(317652900, S:N, H:0, SP:0, 2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(317652900, N:N.sp3, MBO:SINGLE, BOS:3.0, FC:0, H:SP3, NC:3, EV:3, Isotope(317652900, Element(317652900, S:N, AN:7)))), Atom(1114024860, S:H, H:0, 2D:[(-1.299038105676657, 3.3210000000000015)], AtomType(1114024860, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1114024860, Element(1114024860, S:H, AN:1)))), ElectronContainer(1267573190EC:2)), Bond(1064826090, #O:SINGLE, #S:NONE, #A:2, Atom(317652900, S:N, H:0, SP:0, 2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(317652900, N:N.sp3, MBO:SINGLE, 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AtomType(1826835713, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1826835713, Element(1826835713, S:H, AN:1)))), ElectronContainer(1365232814EC:2))), AtomContainer(1752620350, #A:15, Atom(1404520198, S:C, H:0, SP:0, 2D:[(0.0, 1.071)], AtomType(1404520198, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1404520198, Element(1404520198, S:C, AN:6)))), Atom(630719962, S:C, H:0, SP:0, 2D:[(-1.299, 0.321)], AtomType(630719962, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(630719962, Element(630719962, S:C, AN:6)))), Atom(531119742, S:C, H:0, SP:0, 2D:[(-1.299, -1.179)], AtomType(531119742, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(531119742, Element(531119742, S:C, AN:6)))), Atom(1587466862, S:C, H:0, SP:0, 2D:[(0.0, -1.929)], AtomType(1587466862, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1587466862, Element(1587466862, S:C, AN:6)))), Atom(218719306, S:C, H:0, SP:0, 2D:[(1.299, -1.179)], AtomType(218719306, 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AtomType(915530020, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(915530020, Element(915530020, S:H, AN:1)))), Atom(592715385, S:H, H:0, 2D:[(2.598042868964835, -1.9289917496823614)], AtomType(592715385, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(592715385, Element(592715385, S:H, AN:1)))), Atom(1738320909, S:H, H:0, 2D:[(2.5980428689648356, 1.070991749682361)], AtomType(1738320909, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1738320909, Element(1738320909, S:H, AN:1)))), Atom(1591983775, S:H, H:0, 2D:[(-1.299038105676657, 3.3210000000000015)], AtomType(1591983775, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1591983775, Element(1591983775, S:H, AN:1)))), Atom(972548452, S:H, H:0, 2D:[(1.2990381056766584, 3.320999999999999)], AtomType(972548452, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(972548452, Element(972548452, S:H, AN:1)))), Atom(1123795447, S:O, AtomType(1123795447, N:O.sp3, MBO:SINGLE, BOS:2.0, FC:0, H:SP3, NC:2, 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2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(1579363303, N:N.sp3, MBO:SINGLE, BOS:3.0, FC:0, H:SP3, NC:3, EV:3, Isotope(1579363303, Element(1579363303, S:N, AN:7)))), ElectronContainer(1090281493EC:2)), Bond(2030576647, #O:SINGLE, #S:NONE, #A:2, Atom(630719962, S:C, H:0, SP:0, 2D:[(-1.299, 0.321)], AtomType(630719962, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(630719962, Element(630719962, S:C, AN:6)))), Atom(1461156601, S:H, H:0, 2D:[(-2.5980428689648356, 1.070991749682361)], AtomType(1461156601, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1461156601, Element(1461156601, S:H, AN:1)))), ElectronContainer(2030576647EC:2)), Bond(91588005, #O:SINGLE, #S:NONE, #A:2, Atom(1587466862, S:C, H:0, SP:0, 2D:[(0.0, -1.929)], AtomType(1587466862, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1587466862, Element(1587466862, S:C, AN:6)))), Atom(915530020, S:H, H:0, 2D:[(-2.755455298081545E-16, -3.4290000000000003)], AtomType(915530020, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(915530020, Element(915530020, S:H, AN:1)))), ElectronContainer(91588005EC:2)), Bond(1721308783, #O:SINGLE, #S:NONE, #A:2, Atom(218719306, S:C, H:0, SP:0, 2D:[(1.299, -1.179)], AtomType(218719306, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(218719306, Element(218719306, S:C, AN:6)))), Atom(592715385, S:H, H:0, 2D:[(2.598042868964835, -1.9289917496823614)], AtomType(592715385, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(592715385, Element(592715385, S:H, AN:1)))), ElectronContainer(1721308783EC:2)), Bond(1284507144, #O:SINGLE, #S:NONE, #A:2, Atom(1670855925, S:C, H:0, SP:0, 2D:[(1.299, 0.321)], AtomType(1670855925, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(1670855925, Element(1670855925, S:C, AN:6)))), Atom(1738320909, S:H, H:0, 2D:[(2.5980428689648356, 1.070991749682361)], AtomType(1738320909, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1738320909, Element(1738320909, S:H, AN:1)))), ElectronContainer(1284507144EC:2)), Bond(58465917, #O:SINGLE, #S:NONE, #A:2, Atom(1579363303, S:N, H:0, SP:0, 2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(1579363303, N:N.sp3, MBO:SINGLE, BOS:3.0, FC:0, H:SP3, NC:3, EV:3, Isotope(1579363303, Element(1579363303, S:N, AN:7)))), Atom(1591983775, S:H, H:0, 2D:[(-1.299038105676657, 3.3210000000000015)], AtomType(1591983775, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1591983775, Element(1591983775, S:H, AN:1)))), ElectronContainer(58465917EC:2)), Bond(1236640340, #O:SINGLE, #S:NONE, #A:2, Atom(1579363303, S:N, H:0, SP:0, 2D:[(9.184850993605148E-17, 2.5709999999999997)], AtomType(1579363303, N:N.sp3, MBO:SINGLE, BOS:3.0, FC:0, H:SP3, NC:3, EV:3, Isotope(1579363303, Element(1579363303, S:N, AN:7)))), Atom(972548452, S:H, H:0, 2D:[(1.2990381056766584, 3.320999999999999)], AtomType(972548452, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(972548452, Element(972548452, S:H, AN:1)))), ElectronContainer(1236640340EC:2)), Bond(867458714, #O:SINGLE, #S:NONE, #A:2, Atom(531119742, S:C, H:0, SP:0, 2D:[(-1.299, -1.179)], AtomType(531119742, N:C.sp2, MBO:DOUBLE, BOS:4.0, FC:0, H:SP2, NC:3, EV:4, Isotope(531119742, Element(531119742, S:C, AN:6)))), Atom(1123795447, S:O, AtomType(1123795447, N:O.sp3, MBO:SINGLE, BOS:2.0, FC:0, H:SP3, NC:2, EV:2, Isotope(1123795447, Element(1123795447, S:O, AN:8)))), ElectronContainer(867458714EC:2)), Bond(112126715, #O:SINGLE, #S:NONE, #A:2, Atom(1123795447, S:O, AtomType(1123795447, N:O.sp3, MBO:SINGLE, BOS:2.0, FC:0, H:SP3, NC:2, EV:2, Isotope(1123795447, Element(1123795447, S:O, AN:8)))), Atom(1183489562, S:H, H:0, 2D:[(-2.598042868964835, -1.9289917496823614)], AtomType(1183489562, N:H, MBO:SINGLE, BOS:1.0, FC:0, H:S, NC:1, EV:1, Isotope(1183489562, Element(1183489562, S:H, AN:1)))), ElectronContainer(112126715EC:2))), AtomContainer(1170540586, #A:15, Atom(177938735, S:C, H:0, SP:0, 2D:[(0.0, 1.071)], AtomType(177938735, 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[truncated message content] |
|
From: Nina J. <jel...@gm...> - 2015-04-23 17:07:51
|
Hi Yannick, On 23 April 2015 at 19:17, Yannick .Djoumbou <y.d...@gm...> wrote: > Hi Nina, > > You mentioned early that SMIRKS needs the structures to be kekulized. I > assumed that it means every bond of type 4 will be changed to type 1 or 2, > but still be labeled as aromatic. Am I right? > This means, I should not used the Aromatize function then. I should make > sure the structure is always kekulize. Therefore, I should use the > kekuliseAromaticRings() from FixBondOrdersTool, right? > No, FixBondOrdersTool is deprecated, don't use it. Use the new Kekulization class. John May may help with how to use it. http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Kekulization.html > > Moreover, I have the following error when using ambit2 3.0.0. It tdoesn't > mattr whether I use CDK 1.5.6 (as I did before with ambit 2.5.6) or 1.5.10. > > Exception in thread "main" java.lang.NoClassDefFoundError: > net/idea/modbcum/i/exceptions/AmbitException > at Metabolize.main(Metabolize.java:35) > Caused by: java.lang.ClassNotFoundException: > net.idea.modbcum.i.exceptions.AmbitException > at java.net.URLClassLoader$1.run(URLClassLoader.java:366) > at java.net.URLClassLoader$1.run(URLClassLoader.java:355) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(URLClassLoader.java:354) > at java.lang.ClassLoader.loadClass(ClassLoader.java:424) > at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) > at java.lang.ClassLoader.loadClass(ClassLoader.java:357) > ... 1 more > > Metabolize.java is the class where I call the main function that uses the > AMBIT and CDK modules. I did not have this error before moving to 3.0.0. > Can you give a piece of code we can test? It looks like a missing/ not loaded dependency. Regards, Nina > Please let me know. > > Regards, > > On Tue, Apr 21, 2015 at 10:54 PM, Yannick .Djoumbou <y.d...@gm...> > wrote: > >> Thanks for letting me know. >> Regards, >> >> Yannick >> >> On Tue, Apr 21, 2015 at 10:44 PM, Nina Jeliazkova < >> jel...@gm...> wrote: >> >>> Yannick, >>> >>> Just a warning, 3.0.0 is still being tested and not released yet, but >>> the SMIRKS package was tested by another group as well and appears to work >>> well. >>> >>> Best regards, >>> Nina >>> >>> >>> On 22 April 2015 at 07:38, Yannick .Djoumbou <y.d...@gm...> >>> wrote: >>> >>>> Thanks Nina, >>>> >>>> first of all, I am really happy that a new release of AMBIT was >>>> released and is working with CDK 1.5.10. I'll try that out and also use the >>>> aromaticity class. >>>> I a looking forward to reading Nick's reply. >>>> >>>> Regards, >>>> >>>> Yannick >>>> >>>> On Tue, Apr 21, 2015 at 10:32 PM, Nina Jeliazkova < >>>> jel...@gm...> wrote: >>>> >>>>> Yannick, >>>>> >>>>> Nick may reply later this week, but could you please try ambit >>>>> 3.0.0-SNAPSHOT (CDK 1.5.10) dependency >>>>> >>>>> >>>>> http://ambit.uni-plovdiv.bg:8083/nexus/#nexus-search;gav~ambit~~3.0.0-SNAPSHOT~~ >>>>> >>>>> The version you work with is quite outdated and there have been number >>>>> of improvements. >>>>> >>>>> Last but not least, the SMIRKS package expects Kekule structures. You >>>>> will NOT get same results if structures are not kekulized. Fortunately, in >>>>> CDK 1.5.10 the kekulization works quite well. >>>>> >>>>> In any case please do not use SMSD* package, it is already deprecated >>>>> in CDK as far as I know. Use the new Aromaticity class >>>>> >>>>> >>>>> http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Aromaticity.html >>>>> >>>>> Best regards, >>>>> Nina >>>>> >>>>> >>>>> On 21 April 2015 at 21:07, Yannick .Djoumbou <y.d...@gm...> >>>>> wrote: >>>>> >>>>>> Hello guys, >>>>>> >>>>>> I am dealing with an issue here. I would like to apply a >>>>>> transformation on the attached molecules. Below is a function that I wrote >>>>>> to apply a transformation with single copy for each position (with >>>>>> smrkMan.applyTransformationWithSingleCopyForEachPos). Because CDK has >>>>>> issues dealing with bond type 4, I tried to transform the same molecule >>>>>> (aniline) using different bond types. >>>>>> In test1.sdf, the bond types in the benzene ring have type 1 and 2, >>>>>> alternatively. This, however produces 5 metabolites. In test2.sdf, >>>>>> the aromatic bonds of the molecule are of type 4. The transformation does >>>>>> not produce any product, which is wrong. >>>>>> >>>>>> Procedure: >>>>>> ---------- >>>>>> (1) I tested whether CDK viewed the input molecule as aromatic or >>>>>> not, by checking the bond types. For my own preference, I also added >>>>>> explicit hydrogen atoms in order to use my smirks pattern more efficiently. For >>>>>> test1, aniline is not first viewed as aromatic. Thus, I aromatized it using >>>>>> CDK's SMSDNormalizer.aromatizeMolecule. In test2, aniline is viewed as >>>>>> aromatic. Because the bonds in the benzene ring are of type 4, I >>>>>> decided to kekulize it, so that CDK with better deal with the molecule. >>>>>> Somehow, the resulting molecule still has bond type 4. The resulting >>>>>> molecules after these edits are stored in >>>>>> test1_after_aromatizing_and_adding_hydrogen.sdf and >>>>>> test2_after_kekulizing_and_adding_hydrogen.sdf. Somehow, the molecule in >>>>>> the later files does not have explicit hydrogen atoms attached to the >>>>>> benzene ring. >>>>>> >>>>>> (2) Following the first step, I ran >>>>>> smrkMan.applyTransformationWithSingleCopyForEachPos on the container >>>>>> obtained after the first step, where smrkMan is an instance of the SMRIKS >>>>>> Manager. As mentioned earlier, aniline in the first form (ring bonds with >>>>>> types 1 and 2) was transformed. the five products are in the file >>>>>> test1_metabolites.sdf. In the second file (ring bonds with type 4) >>>>>> is not transformed. >>>>>> I used the smirks: [c;H1:1]>>[c:1][OX2H1] and [c:1]>>[c:1][OX2H1] foe >>>>>> each molecule, which returned the same output. >>>>>> This procedure was implemented in the function transform_from_sdf >>>>>> below. >>>>>> >>>>>> >>>>>> Could you please help me here? How can I get the same results whether >>>>>> I submit my molecule in the kekule or the aromatic form? I have tried >>>>>> different things, but without success. by the way, I am using the AMBIT >>>>>> 2.6.0 and CDK version 1.5.6 versions. I really need help here. >>>>>> >>>>>> Thank you for your consideration. >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Yannick >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> public LinkedHashMap<String, IAtomContainerSet> >>>>>> transform_from_sdf(File sdf_input, SMIRKSReaction reaction) throws >>>>>> Exception{ >>>>>> >>>>>> LinkedHashMap<String, IAtomContainerSet> sdf_metabolites = new >>>>>> LinkedHashMap<String, IAtomContainerSet>(); >>>>>> IteratingSDFReader reader = new IteratingSDFReader(new >>>>>> FileInputStream(sdf_input), DefaultChemObjectBuilder.getInstance()); >>>>>> SMIRKSManager smrkMan = new >>>>>> SMIRKSManager(SilentChemObjectBuilder.getInstance()); >>>>>> >>>>>> StringWriter writer=new StringWriter(); // >>>>>> http://www.programcreek.com/java-api-examples/index.php?api=org.openscience.cdk.AtomContainerSet >>>>>> >>>>>> StructureDiagramGenerator sdg = new StructureDiagramGenerator(); >>>>>> DeduceBondSystemTool dbst = new DeduceBondSystemTool(); >>>>>> FixBondOrdersTool kekulizer = new FixBondOrdersTool(); >>>>>> >>>>>> int i = 0; >>>>>> while (reader.hasNext()) { >>>>>> i = i+1; >>>>>> >>>>>> IAtomContainer molecule = (IAtomContainer)reader.next(); >>>>>> System.out.println("Query molecule: " + molecule); >>>>>> >>>>>> boolean aromatic_0 = false; >>>>>> for (IBond bond : molecule.bonds()) if >>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_0 = true; break;} >>>>>> >>>>>> System.out.println("IS THE ORIGINAL MOLECULE AROMATIC?: " + >>>>>> aromatic_0); >>>>>> >>>>>> >>>>>> StringWriter w = new StringWriter(); >>>>>> MDLWriter mw = new MDLWriter(w); >>>>>> mw.write(molecule); >>>>>> System.out.println("ORIGINAL MOLECULE" + w.toString()); >>>>>> >>>>>> >>>>>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule); >>>>>> sdg.setMolecule(molecule); >>>>>> sdg.generateCoordinates(); >>>>>> IAtomContainer mol_with_hydrogen = sdg.getMolecule(); >>>>>> >>>>>> >>>>>> if(!aromatic_0){ >>>>>> SMSDNormalizer.aromatizeMolecule(mol_with_hydrogen); >>>>>> boolean aromatic = false; >>>>>> for (IBond bond : mol_with_hydrogen.bonds()) if >>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic = true; break;} >>>>>> System.out.println("HAS THE MOLECULE BEEN AROMATIZED?: " >>>>>> + aromatic); >>>>>> mw.write(mol_with_hydrogen); >>>>>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >>>>>> EXPLICIT ATOMS" + w.toString()); >>>>>> >>>>>> } >>>>>> else{ >>>>>> >>>>>> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol_with_hydrogen); >>>>>> mol_with_hydrogen = >>>>>> kekulizer.kekuliseAromaticRings(mol_with_hydrogen); >>>>>> mw.write(mol_with_hydrogen); >>>>>> System.out.println(mol_with_hydrogen); >>>>>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >>>>>> EXPLICIT ATOMS" + w.toString()); >>>>>> >>>>>> boolean aromatic_3 = false; >>>>>> for (IBond bond : mol_with_hydrogen.bonds()) if >>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_3 = true; break;} >>>>>> System.out.println("IS AROMATIC AFTER HYDRO?? " + >>>>>> aromatic_3); >>>>>> } >>>>>> >>>>>> >>>>>> System.out.println(mol_with_hydrogen); >>>>>> SmilesGenerator sg = new SmilesGenerator(); >>>>>> System.out.println(sg.create(mol_with_hydrogen)); >>>>>> >>>>>> >>>>>> String name = (String) >>>>>> molecule.getProperty(CDKConstants.TITLE); >>>>>> IAtomContainerSet metabolites = >>>>>> generateAllMetabolitesFromAtomContainer(mol_with_hydrogen, reaction, >>>>>> smrkMan); >>>>>> System.out.println("METABOLITES" + metabolites); >>>>>> } >>>>>> >>>>> >>>>> >>>> >>> >> > |
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From: Yannick .D. <y.d...@gm...> - 2015-04-23 16:22:17
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erratum: In regard to the mail I sent a few minutes ago, I used AMBIT 2.6.0 before and not 2.5.6. Regards, Yannick On Thu, Apr 23, 2015 at 10:17 AM, Yannick .Djoumbou <y.d...@gm...> wrote: > Hi Nina, > > You mentioned early that SMIRKS needs the structures to be kekulized. I > assumed that it means every bond of type 4 will be changed to type 1 or 2, > but still be labeled as aromatic. Am I right? > This means, I should not used the Aromatize function then. I should make > sure the structure is always kekulize. Therefore, I should use the > kekuliseAromaticRings() from FixBondOrdersTool, right? > > Moreover, I have the following error when using ambit2 3.0.0. It tdoesn't > mattr whether I use CDK 1.5.6 (as I did before with ambit 2.5.6) or 1.5.10. > > Exception in thread "main" java.lang.NoClassDefFoundError: > net/idea/modbcum/i/exceptions/AmbitException > at Metabolize.main(Metabolize.java:35) > Caused by: java.lang.ClassNotFoundException: > net.idea.modbcum.i.exceptions.AmbitException > at java.net.URLClassLoader$1.run(URLClassLoader.java:366) > at java.net.URLClassLoader$1.run(URLClassLoader.java:355) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(URLClassLoader.java:354) > at java.lang.ClassLoader.loadClass(ClassLoader.java:424) > at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) > at java.lang.ClassLoader.loadClass(ClassLoader.java:357) > ... 1 more > > Metabolize.java is the class where I call the main function that uses the > AMBIT and CDK modules. I did not have this error before moving to 3.0.0. > > Please let me know. > > Regards, > > On Tue, Apr 21, 2015 at 10:54 PM, Yannick .Djoumbou <y.d...@gm...> > wrote: > >> Thanks for letting me know. >> Regards, >> >> Yannick >> >> On Tue, Apr 21, 2015 at 10:44 PM, Nina Jeliazkova < >> jel...@gm...> wrote: >> >>> Yannick, >>> >>> Just a warning, 3.0.0 is still being tested and not released yet, but >>> the SMIRKS package was tested by another group as well and appears to work >>> well. >>> >>> Best regards, >>> Nina >>> >>> >>> On 22 April 2015 at 07:38, Yannick .Djoumbou <y.d...@gm...> >>> wrote: >>> >>>> Thanks Nina, >>>> >>>> first of all, I am really happy that a new release of AMBIT was >>>> released and is working with CDK 1.5.10. I'll try that out and also use the >>>> aromaticity class. >>>> I a looking forward to reading Nick's reply. >>>> >>>> Regards, >>>> >>>> Yannick >>>> >>>> On Tue, Apr 21, 2015 at 10:32 PM, Nina Jeliazkova < >>>> jel...@gm...> wrote: >>>> >>>>> Yannick, >>>>> >>>>> Nick may reply later this week, but could you please try ambit >>>>> 3.0.0-SNAPSHOT (CDK 1.5.10) dependency >>>>> >>>>> >>>>> http://ambit.uni-plovdiv.bg:8083/nexus/#nexus-search;gav~ambit~~3.0.0-SNAPSHOT~~ >>>>> >>>>> The version you work with is quite outdated and there have been number >>>>> of improvements. >>>>> >>>>> Last but not least, the SMIRKS package expects Kekule structures. You >>>>> will NOT get same results if structures are not kekulized. Fortunately, in >>>>> CDK 1.5.10 the kekulization works quite well. >>>>> >>>>> In any case please do not use SMSD* package, it is already deprecated >>>>> in CDK as far as I know. Use the new Aromaticity class >>>>> >>>>> >>>>> http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Aromaticity.html >>>>> >>>>> Best regards, >>>>> Nina >>>>> >>>>> >>>>> On 21 April 2015 at 21:07, Yannick .Djoumbou <y.d...@gm...> >>>>> wrote: >>>>> >>>>>> Hello guys, >>>>>> >>>>>> I am dealing with an issue here. I would like to apply a >>>>>> transformation on the attached molecules. Below is a function that I wrote >>>>>> to apply a transformation with single copy for each position (with >>>>>> smrkMan.applyTransformationWithSingleCopyForEachPos). Because CDK has >>>>>> issues dealing with bond type 4, I tried to transform the same molecule >>>>>> (aniline) using different bond types. >>>>>> In test1.sdf, the bond types in the benzene ring have type 1 and 2, >>>>>> alternatively. This, however produces 5 metabolites. In test2.sdf, >>>>>> the aromatic bonds of the molecule are of type 4. The transformation does >>>>>> not produce any product, which is wrong. >>>>>> >>>>>> Procedure: >>>>>> ---------- >>>>>> (1) I tested whether CDK viewed the input molecule as aromatic or >>>>>> not, by checking the bond types. For my own preference, I also added >>>>>> explicit hydrogen atoms in order to use my smirks pattern more efficiently. For >>>>>> test1, aniline is not first viewed as aromatic. Thus, I aromatized it using >>>>>> CDK's SMSDNormalizer.aromatizeMolecule. In test2, aniline is viewed as >>>>>> aromatic. Because the bonds in the benzene ring are of type 4, I >>>>>> decided to kekulize it, so that CDK with better deal with the molecule. >>>>>> Somehow, the resulting molecule still has bond type 4. The resulting >>>>>> molecules after these edits are stored in >>>>>> test1_after_aromatizing_and_adding_hydrogen.sdf and >>>>>> test2_after_kekulizing_and_adding_hydrogen.sdf. Somehow, the molecule in >>>>>> the later files does not have explicit hydrogen atoms attached to the >>>>>> benzene ring. >>>>>> >>>>>> (2) Following the first step, I ran >>>>>> smrkMan.applyTransformationWithSingleCopyForEachPos on the container >>>>>> obtained after the first step, where smrkMan is an instance of the SMRIKS >>>>>> Manager. As mentioned earlier, aniline in the first form (ring bonds with >>>>>> types 1 and 2) was transformed. the five products are in the file >>>>>> test1_metabolites.sdf. In the second file (ring bonds with type 4) >>>>>> is not transformed. >>>>>> I used the smirks: [c;H1:1]>>[c:1][OX2H1] and [c:1]>>[c:1][OX2H1] foe >>>>>> each molecule, which returned the same output. >>>>>> This procedure was implemented in the function transform_from_sdf >>>>>> below. >>>>>> >>>>>> >>>>>> Could you please help me here? How can I get the same results whether >>>>>> I submit my molecule in the kekule or the aromatic form? I have tried >>>>>> different things, but without success. by the way, I am using the AMBIT >>>>>> 2.6.0 and CDK version 1.5.6 versions. I really need help here. >>>>>> >>>>>> Thank you for your consideration. >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Yannick >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> public LinkedHashMap<String, IAtomContainerSet> >>>>>> transform_from_sdf(File sdf_input, SMIRKSReaction reaction) throws >>>>>> Exception{ >>>>>> >>>>>> LinkedHashMap<String, IAtomContainerSet> sdf_metabolites = new >>>>>> LinkedHashMap<String, IAtomContainerSet>(); >>>>>> IteratingSDFReader reader = new IteratingSDFReader(new >>>>>> FileInputStream(sdf_input), DefaultChemObjectBuilder.getInstance()); >>>>>> SMIRKSManager smrkMan = new >>>>>> SMIRKSManager(SilentChemObjectBuilder.getInstance()); >>>>>> >>>>>> StringWriter writer=new StringWriter(); // >>>>>> http://www.programcreek.com/java-api-examples/index.php?api=org.openscience.cdk.AtomContainerSet >>>>>> >>>>>> StructureDiagramGenerator sdg = new StructureDiagramGenerator(); >>>>>> DeduceBondSystemTool dbst = new DeduceBondSystemTool(); >>>>>> FixBondOrdersTool kekulizer = new FixBondOrdersTool(); >>>>>> >>>>>> int i = 0; >>>>>> while (reader.hasNext()) { >>>>>> i = i+1; >>>>>> >>>>>> IAtomContainer molecule = (IAtomContainer)reader.next(); >>>>>> System.out.println("Query molecule: " + molecule); >>>>>> >>>>>> boolean aromatic_0 = false; >>>>>> for (IBond bond : molecule.bonds()) if >>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_0 = true; break;} >>>>>> >>>>>> System.out.println("IS THE ORIGINAL MOLECULE AROMATIC?: " + >>>>>> aromatic_0); >>>>>> >>>>>> >>>>>> StringWriter w = new StringWriter(); >>>>>> MDLWriter mw = new MDLWriter(w); >>>>>> mw.write(molecule); >>>>>> System.out.println("ORIGINAL MOLECULE" + w.toString()); >>>>>> >>>>>> >>>>>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule); >>>>>> sdg.setMolecule(molecule); >>>>>> sdg.generateCoordinates(); >>>>>> IAtomContainer mol_with_hydrogen = sdg.getMolecule(); >>>>>> >>>>>> >>>>>> if(!aromatic_0){ >>>>>> SMSDNormalizer.aromatizeMolecule(mol_with_hydrogen); >>>>>> boolean aromatic = false; >>>>>> for (IBond bond : mol_with_hydrogen.bonds()) if >>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic = true; break;} >>>>>> System.out.println("HAS THE MOLECULE BEEN AROMATIZED?: " >>>>>> + aromatic); >>>>>> mw.write(mol_with_hydrogen); >>>>>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >>>>>> EXPLICIT ATOMS" + w.toString()); >>>>>> >>>>>> } >>>>>> else{ >>>>>> >>>>>> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol_with_hydrogen); >>>>>> mol_with_hydrogen = >>>>>> kekulizer.kekuliseAromaticRings(mol_with_hydrogen); >>>>>> mw.write(mol_with_hydrogen); >>>>>> System.out.println(mol_with_hydrogen); >>>>>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >>>>>> EXPLICIT ATOMS" + w.toString()); >>>>>> >>>>>> boolean aromatic_3 = false; >>>>>> for (IBond bond : mol_with_hydrogen.bonds()) if >>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_3 = true; break;} >>>>>> System.out.println("IS AROMATIC AFTER HYDRO?? " + >>>>>> aromatic_3); >>>>>> } >>>>>> >>>>>> >>>>>> System.out.println(mol_with_hydrogen); >>>>>> SmilesGenerator sg = new SmilesGenerator(); >>>>>> System.out.println(sg.create(mol_with_hydrogen)); >>>>>> >>>>>> >>>>>> String name = (String) >>>>>> molecule.getProperty(CDKConstants.TITLE); >>>>>> IAtomContainerSet metabolites = >>>>>> generateAllMetabolitesFromAtomContainer(mol_with_hydrogen, reaction, >>>>>> smrkMan); >>>>>> System.out.println("METABOLITES" + metabolites); >>>>>> } >>>>>> >>>>> >>>>> >>>> >>> >> > |
|
From: Yannick .D. <y.d...@gm...> - 2015-04-23 16:17:48
|
Hi Nina,
You mentioned early that SMIRKS needs the structures to be kekulized. I
assumed that it means every bond of type 4 will be changed to type 1 or 2,
but still be labeled as aromatic. Am I right?
This means, I should not used the Aromatize function then. I should make
sure the structure is always kekulize. Therefore, I should use the
kekuliseAromaticRings() from FixBondOrdersTool, right?
Moreover, I have the following error when using ambit2 3.0.0. It tdoesn't
mattr whether I use CDK 1.5.6 (as I did before with ambit 2.5.6) or 1.5.10.
Exception in thread "main" java.lang.NoClassDefFoundError:
net/idea/modbcum/i/exceptions/AmbitException
at Metabolize.main(Metabolize.java:35)
Caused by: java.lang.ClassNotFoundException:
net.idea.modbcum.i.exceptions.AmbitException
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 1 more
Metabolize.java is the class where I call the main function that uses the
AMBIT and CDK modules. I did not have this error before moving to 3.0.0.
Please let me know.
Regards,
On Tue, Apr 21, 2015 at 10:54 PM, Yannick .Djoumbou <y.d...@gm...>
wrote:
> Thanks for letting me know.
> Regards,
>
> Yannick
>
> On Tue, Apr 21, 2015 at 10:44 PM, Nina Jeliazkova <
> jel...@gm...> wrote:
>
>> Yannick,
>>
>> Just a warning, 3.0.0 is still being tested and not released yet, but the
>> SMIRKS package was tested by another group as well and appears to work well.
>>
>> Best regards,
>> Nina
>>
>>
>> On 22 April 2015 at 07:38, Yannick .Djoumbou <y.d...@gm...>
>> wrote:
>>
>>> Thanks Nina,
>>>
>>> first of all, I am really happy that a new release of AMBIT was released
>>> and is working with CDK 1.5.10. I'll try that out and also use the
>>> aromaticity class.
>>> I a looking forward to reading Nick's reply.
>>>
>>> Regards,
>>>
>>> Yannick
>>>
>>> On Tue, Apr 21, 2015 at 10:32 PM, Nina Jeliazkova <
>>> jel...@gm...> wrote:
>>>
>>>> Yannick,
>>>>
>>>> Nick may reply later this week, but could you please try ambit
>>>> 3.0.0-SNAPSHOT (CDK 1.5.10) dependency
>>>>
>>>>
>>>> http://ambit.uni-plovdiv.bg:8083/nexus/#nexus-search;gav~ambit~~3.0.0-SNAPSHOT~~
>>>>
>>>> The version you work with is quite outdated and there have been number
>>>> of improvements.
>>>>
>>>> Last but not least, the SMIRKS package expects Kekule structures. You
>>>> will NOT get same results if structures are not kekulized. Fortunately, in
>>>> CDK 1.5.10 the kekulization works quite well.
>>>>
>>>> In any case please do not use SMSD* package, it is already deprecated
>>>> in CDK as far as I know. Use the new Aromaticity class
>>>>
>>>>
>>>> http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Aromaticity.html
>>>>
>>>> Best regards,
>>>> Nina
>>>>
>>>>
>>>> On 21 April 2015 at 21:07, Yannick .Djoumbou <y.d...@gm...>
>>>> wrote:
>>>>
>>>>> Hello guys,
>>>>>
>>>>> I am dealing with an issue here. I would like to apply a
>>>>> transformation on the attached molecules. Below is a function that I wrote
>>>>> to apply a transformation with single copy for each position (with
>>>>> smrkMan.applyTransformationWithSingleCopyForEachPos). Because CDK has
>>>>> issues dealing with bond type 4, I tried to transform the same molecule
>>>>> (aniline) using different bond types.
>>>>> In test1.sdf, the bond types in the benzene ring have type 1 and 2,
>>>>> alternatively. This, however produces 5 metabolites. In test2.sdf,
>>>>> the aromatic bonds of the molecule are of type 4. The transformation does
>>>>> not produce any product, which is wrong.
>>>>>
>>>>> Procedure:
>>>>> ----------
>>>>> (1) I tested whether CDK viewed the input molecule as aromatic or not,
>>>>> by checking the bond types. For my own preference, I also added
>>>>> explicit hydrogen atoms in order to use my smirks pattern more efficiently. For
>>>>> test1, aniline is not first viewed as aromatic. Thus, I aromatized it using
>>>>> CDK's SMSDNormalizer.aromatizeMolecule. In test2, aniline is viewed as
>>>>> aromatic. Because the bonds in the benzene ring are of type 4, I
>>>>> decided to kekulize it, so that CDK with better deal with the molecule.
>>>>> Somehow, the resulting molecule still has bond type 4. The resulting
>>>>> molecules after these edits are stored in
>>>>> test1_after_aromatizing_and_adding_hydrogen.sdf and
>>>>> test2_after_kekulizing_and_adding_hydrogen.sdf. Somehow, the molecule in
>>>>> the later files does not have explicit hydrogen atoms attached to the
>>>>> benzene ring.
>>>>>
>>>>> (2) Following the first step, I ran
>>>>> smrkMan.applyTransformationWithSingleCopyForEachPos on the container
>>>>> obtained after the first step, where smrkMan is an instance of the SMRIKS
>>>>> Manager. As mentioned earlier, aniline in the first form (ring bonds with
>>>>> types 1 and 2) was transformed. the five products are in the file
>>>>> test1_metabolites.sdf. In the second file (ring bonds with type 4) is
>>>>> not transformed.
>>>>> I used the smirks: [c;H1:1]>>[c:1][OX2H1] and [c:1]>>[c:1][OX2H1] foe
>>>>> each molecule, which returned the same output.
>>>>> This procedure was implemented in the function transform_from_sdf
>>>>> below.
>>>>>
>>>>>
>>>>> Could you please help me here? How can I get the same results whether
>>>>> I submit my molecule in the kekule or the aromatic form? I have tried
>>>>> different things, but without success. by the way, I am using the AMBIT
>>>>> 2.6.0 and CDK version 1.5.6 versions. I really need help here.
>>>>>
>>>>> Thank you for your consideration.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Yannick
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> public LinkedHashMap<String, IAtomContainerSet>
>>>>> transform_from_sdf(File sdf_input, SMIRKSReaction reaction) throws
>>>>> Exception{
>>>>>
>>>>> LinkedHashMap<String, IAtomContainerSet> sdf_metabolites = new
>>>>> LinkedHashMap<String, IAtomContainerSet>();
>>>>> IteratingSDFReader reader = new IteratingSDFReader(new
>>>>> FileInputStream(sdf_input), DefaultChemObjectBuilder.getInstance());
>>>>> SMIRKSManager smrkMan = new
>>>>> SMIRKSManager(SilentChemObjectBuilder.getInstance());
>>>>>
>>>>> StringWriter writer=new StringWriter(); //
>>>>> http://www.programcreek.com/java-api-examples/index.php?api=org.openscience.cdk.AtomContainerSet
>>>>>
>>>>> StructureDiagramGenerator sdg = new StructureDiagramGenerator();
>>>>> DeduceBondSystemTool dbst = new DeduceBondSystemTool();
>>>>> FixBondOrdersTool kekulizer = new FixBondOrdersTool();
>>>>>
>>>>> int i = 0;
>>>>> while (reader.hasNext()) {
>>>>> i = i+1;
>>>>>
>>>>> IAtomContainer molecule = (IAtomContainer)reader.next();
>>>>> System.out.println("Query molecule: " + molecule);
>>>>>
>>>>> boolean aromatic_0 = false;
>>>>> for (IBond bond : molecule.bonds()) if
>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_0 = true; break;}
>>>>>
>>>>> System.out.println("IS THE ORIGINAL MOLECULE AROMATIC?: " +
>>>>> aromatic_0);
>>>>>
>>>>>
>>>>> StringWriter w = new StringWriter();
>>>>> MDLWriter mw = new MDLWriter(w);
>>>>> mw.write(molecule);
>>>>> System.out.println("ORIGINAL MOLECULE" + w.toString());
>>>>>
>>>>>
>>>>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);
>>>>> sdg.setMolecule(molecule);
>>>>> sdg.generateCoordinates();
>>>>> IAtomContainer mol_with_hydrogen = sdg.getMolecule();
>>>>>
>>>>>
>>>>> if(!aromatic_0){
>>>>> SMSDNormalizer.aromatizeMolecule(mol_with_hydrogen);
>>>>> boolean aromatic = false;
>>>>> for (IBond bond : mol_with_hydrogen.bonds()) if
>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic = true; break;}
>>>>> System.out.println("HAS THE MOLECULE BEEN AROMATIZED?: " +
>>>>> aromatic);
>>>>> mw.write(mol_with_hydrogen);
>>>>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN
>>>>> EXPLICIT ATOMS" + w.toString());
>>>>>
>>>>> }
>>>>> else{
>>>>>
>>>>> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol_with_hydrogen);
>>>>> mol_with_hydrogen =
>>>>> kekulizer.kekuliseAromaticRings(mol_with_hydrogen);
>>>>> mw.write(mol_with_hydrogen);
>>>>> System.out.println(mol_with_hydrogen);
>>>>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN
>>>>> EXPLICIT ATOMS" + w.toString());
>>>>>
>>>>> boolean aromatic_3 = false;
>>>>> for (IBond bond : mol_with_hydrogen.bonds()) if
>>>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_3 = true; break;}
>>>>> System.out.println("IS AROMATIC AFTER HYDRO?? " +
>>>>> aromatic_3);
>>>>> }
>>>>>
>>>>>
>>>>> System.out.println(mol_with_hydrogen);
>>>>> SmilesGenerator sg = new SmilesGenerator();
>>>>> System.out.println(sg.create(mol_with_hydrogen));
>>>>>
>>>>>
>>>>> String name = (String)
>>>>> molecule.getProperty(CDKConstants.TITLE);
>>>>> IAtomContainerSet metabolites =
>>>>> generateAllMetabolitesFromAtomContainer(mol_with_hydrogen, reaction,
>>>>> smrkMan);
>>>>> System.out.println("METABOLITES" + metabolites);
>>>>> }
>>>>>
>>>>
>>>>
>>>
>>
>
|
|
From: Yannick .D. <y.d...@gm...> - 2015-04-22 05:02:13
|
Thanks Nina, first of all, I am really happy that a new release of AMBIT was released and is working with CDK 1.5.10. I'll try that out and also use the aromaticity class. I a looking forward to reading Nick's reply. Regards, Yannick On Tue, Apr 21, 2015 at 10:32 PM, Nina Jeliazkova <jel...@gm... > wrote: > Yannick, > > Nick may reply later this week, but could you please try ambit > 3.0.0-SNAPSHOT (CDK 1.5.10) dependency > > > http://ambit.uni-plovdiv.bg:8083/nexus/#nexus-search;gav~ambit~~3.0.0-SNAPSHOT~~ > > The version you work with is quite outdated and there have been number of > improvements. > > Last but not least, the SMIRKS package expects Kekule structures. You will > NOT get same results if structures are not kekulized. Fortunately, in CDK > 1.5.10 the kekulization works quite well. > > In any case please do not use SMSD* package, it is already deprecated in > CDK as far as I know. Use the new Aromaticity class > > > http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Aromaticity.html > > Best regards, > Nina > > > On 21 April 2015 at 21:07, Yannick .Djoumbou <y.d...@gm...> wrote: > >> Hello guys, >> >> I am dealing with an issue here. I would like to apply a transformation >> on the attached molecules. Below is a function that I wrote to apply a >> transformation with single copy for each position (with >> smrkMan.applyTransformationWithSingleCopyForEachPos). Because CDK has >> issues dealing with bond type 4, I tried to transform the same molecule >> (aniline) using different bond types. >> In test1.sdf, the bond types in the benzene ring have type 1 and 2, >> alternatively. This, however produces 5 metabolites. In test2.sdf, the >> aromatic bonds of the molecule are of type 4. The transformation does not >> produce any product, which is wrong. >> >> Procedure: >> ---------- >> (1) I tested whether CDK viewed the input molecule as aromatic or not, by >> checking the bond types. For my own preference, I also added explicit >> hydrogen atoms in order to use my smirks pattern more efficiently. For >> test1, aniline is not first viewed as aromatic. Thus, I aromatized it using >> CDK's SMSDNormalizer.aromatizeMolecule. In test2, aniline is viewed as >> aromatic. Because the bonds in the benzene ring are of type 4, I decided >> to kekulize it, so that CDK with better deal with the molecule. Somehow, >> the resulting molecule still has bond type 4. The resulting molecules after >> these edits are stored in test1_after_aromatizing_and_adding_hydrogen.sdf >> and test2_after_kekulizing_and_adding_hydrogen.sdf. Somehow, the molecule >> in the later files does not have explicit hydrogen atoms attached to the >> benzene ring. >> >> (2) Following the first step, I ran >> smrkMan.applyTransformationWithSingleCopyForEachPos on the container >> obtained after the first step, where smrkMan is an instance of the SMRIKS >> Manager. As mentioned earlier, aniline in the first form (ring bonds with >> types 1 and 2) was transformed. the five products are in the file >> test1_metabolites.sdf. In the second file (ring bonds with type 4) is >> not transformed. >> I used the smirks: [c;H1:1]>>[c:1][OX2H1] and [c:1]>>[c:1][OX2H1] foe >> each molecule, which returned the same output. >> This procedure was implemented in the function transform_from_sdf below. >> >> >> Could you please help me here? How can I get the same results whether I >> submit my molecule in the kekule or the aromatic form? I have tried >> different things, but without success. by the way, I am using the AMBIT >> 2.6.0 and CDK version 1.5.6 versions. I really need help here. >> >> Thank you for your consideration. >> >> Best regards, >> >> Yannick >> >> >> >> >> >> >> >> >> public LinkedHashMap<String, IAtomContainerSet> transform_from_sdf(File >> sdf_input, SMIRKSReaction reaction) throws Exception{ >> >> LinkedHashMap<String, IAtomContainerSet> sdf_metabolites = new >> LinkedHashMap<String, IAtomContainerSet>(); >> IteratingSDFReader reader = new IteratingSDFReader(new >> FileInputStream(sdf_input), DefaultChemObjectBuilder.getInstance()); >> SMIRKSManager smrkMan = new >> SMIRKSManager(SilentChemObjectBuilder.getInstance()); >> >> StringWriter writer=new StringWriter(); // >> http://www.programcreek.com/java-api-examples/index.php?api=org.openscience.cdk.AtomContainerSet >> >> StructureDiagramGenerator sdg = new StructureDiagramGenerator(); >> DeduceBondSystemTool dbst = new DeduceBondSystemTool(); >> FixBondOrdersTool kekulizer = new FixBondOrdersTool(); >> >> int i = 0; >> while (reader.hasNext()) { >> i = i+1; >> >> IAtomContainer molecule = (IAtomContainer)reader.next(); >> System.out.println("Query molecule: " + molecule); >> >> boolean aromatic_0 = false; >> for (IBond bond : molecule.bonds()) if >> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_0 = true; break;} >> >> System.out.println("IS THE ORIGINAL MOLECULE AROMATIC?: " + >> aromatic_0); >> >> >> StringWriter w = new StringWriter(); >> MDLWriter mw = new MDLWriter(w); >> mw.write(molecule); >> System.out.println("ORIGINAL MOLECULE" + w.toString()); >> >> >> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule); >> sdg.setMolecule(molecule); >> sdg.generateCoordinates(); >> IAtomContainer mol_with_hydrogen = sdg.getMolecule(); >> >> >> if(!aromatic_0){ >> SMSDNormalizer.aromatizeMolecule(mol_with_hydrogen); >> boolean aromatic = false; >> for (IBond bond : mol_with_hydrogen.bonds()) if >> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic = true; break;} >> System.out.println("HAS THE MOLECULE BEEN AROMATIZED?: " + >> aromatic); >> mw.write(mol_with_hydrogen); >> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >> EXPLICIT ATOMS" + w.toString()); >> >> } >> else{ >> >> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol_with_hydrogen); >> mol_with_hydrogen = >> kekulizer.kekuliseAromaticRings(mol_with_hydrogen); >> mw.write(mol_with_hydrogen); >> System.out.println(mol_with_hydrogen); >> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >> EXPLICIT ATOMS" + w.toString()); >> >> boolean aromatic_3 = false; >> for (IBond bond : mol_with_hydrogen.bonds()) if >> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_3 = true; break;} >> System.out.println("IS AROMATIC AFTER HYDRO?? " + >> aromatic_3); >> } >> >> >> System.out.println(mol_with_hydrogen); >> SmilesGenerator sg = new SmilesGenerator(); >> System.out.println(sg.create(mol_with_hydrogen)); >> >> >> String name = (String) molecule.getProperty(CDKConstants.TITLE); >> IAtomContainerSet metabolites = >> generateAllMetabolitesFromAtomContainer(mol_with_hydrogen, reaction, >> smrkMan); >> System.out.println("METABOLITES" + metabolites); >> } >> > > |
|
From: Yannick .D. <y.d...@gm...> - 2015-04-22 04:54:16
|
Thanks for letting me know. Regards, Yannick On Tue, Apr 21, 2015 at 10:44 PM, Nina Jeliazkova <jel...@gm... > wrote: > Yannick, > > Just a warning, 3.0.0 is still being tested and not released yet, but the > SMIRKS package was tested by another group as well and appears to work well. > > Best regards, > Nina > > > On 22 April 2015 at 07:38, Yannick .Djoumbou <y.d...@gm...> wrote: > >> Thanks Nina, >> >> first of all, I am really happy that a new release of AMBIT was released >> and is working with CDK 1.5.10. I'll try that out and also use the >> aromaticity class. >> I a looking forward to reading Nick's reply. >> >> Regards, >> >> Yannick >> >> On Tue, Apr 21, 2015 at 10:32 PM, Nina Jeliazkova < >> jel...@gm...> wrote: >> >>> Yannick, >>> >>> Nick may reply later this week, but could you please try ambit >>> 3.0.0-SNAPSHOT (CDK 1.5.10) dependency >>> >>> >>> http://ambit.uni-plovdiv.bg:8083/nexus/#nexus-search;gav~ambit~~3.0.0-SNAPSHOT~~ >>> >>> The version you work with is quite outdated and there have been number >>> of improvements. >>> >>> Last but not least, the SMIRKS package expects Kekule structures. You >>> will NOT get same results if structures are not kekulized. Fortunately, in >>> CDK 1.5.10 the kekulization works quite well. >>> >>> In any case please do not use SMSD* package, it is already deprecated in >>> CDK as far as I know. Use the new Aromaticity class >>> >>> >>> http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Aromaticity.html >>> >>> Best regards, >>> Nina >>> >>> >>> On 21 April 2015 at 21:07, Yannick .Djoumbou <y.d...@gm...> >>> wrote: >>> >>>> Hello guys, >>>> >>>> I am dealing with an issue here. I would like to apply a transformation >>>> on the attached molecules. Below is a function that I wrote to apply a >>>> transformation with single copy for each position (with >>>> smrkMan.applyTransformationWithSingleCopyForEachPos). Because CDK has >>>> issues dealing with bond type 4, I tried to transform the same molecule >>>> (aniline) using different bond types. >>>> In test1.sdf, the bond types in the benzene ring have type 1 and 2, >>>> alternatively. This, however produces 5 metabolites. In test2.sdf, the >>>> aromatic bonds of the molecule are of type 4. The transformation does not >>>> produce any product, which is wrong. >>>> >>>> Procedure: >>>> ---------- >>>> (1) I tested whether CDK viewed the input molecule as aromatic or not, >>>> by checking the bond types. For my own preference, I also added >>>> explicit hydrogen atoms in order to use my smirks pattern more efficiently. For >>>> test1, aniline is not first viewed as aromatic. Thus, I aromatized it using >>>> CDK's SMSDNormalizer.aromatizeMolecule. In test2, aniline is viewed as >>>> aromatic. Because the bonds in the benzene ring are of type 4, I >>>> decided to kekulize it, so that CDK with better deal with the molecule. >>>> Somehow, the resulting molecule still has bond type 4. The resulting >>>> molecules after these edits are stored in >>>> test1_after_aromatizing_and_adding_hydrogen.sdf and >>>> test2_after_kekulizing_and_adding_hydrogen.sdf. Somehow, the molecule in >>>> the later files does not have explicit hydrogen atoms attached to the >>>> benzene ring. >>>> >>>> (2) Following the first step, I ran >>>> smrkMan.applyTransformationWithSingleCopyForEachPos on the container >>>> obtained after the first step, where smrkMan is an instance of the SMRIKS >>>> Manager. As mentioned earlier, aniline in the first form (ring bonds with >>>> types 1 and 2) was transformed. the five products are in the file >>>> test1_metabolites.sdf. In the second file (ring bonds with type 4) is >>>> not transformed. >>>> I used the smirks: [c;H1:1]>>[c:1][OX2H1] and [c:1]>>[c:1][OX2H1] foe >>>> each molecule, which returned the same output. >>>> This procedure was implemented in the function transform_from_sdf >>>> below. >>>> >>>> >>>> Could you please help me here? How can I get the same results whether I >>>> submit my molecule in the kekule or the aromatic form? I have tried >>>> different things, but without success. by the way, I am using the AMBIT >>>> 2.6.0 and CDK version 1.5.6 versions. I really need help here. >>>> >>>> Thank you for your consideration. >>>> >>>> Best regards, >>>> >>>> Yannick >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> public LinkedHashMap<String, IAtomContainerSet> transform_from_sdf(File >>>> sdf_input, SMIRKSReaction reaction) throws Exception{ >>>> >>>> LinkedHashMap<String, IAtomContainerSet> sdf_metabolites = new >>>> LinkedHashMap<String, IAtomContainerSet>(); >>>> IteratingSDFReader reader = new IteratingSDFReader(new >>>> FileInputStream(sdf_input), DefaultChemObjectBuilder.getInstance()); >>>> SMIRKSManager smrkMan = new >>>> SMIRKSManager(SilentChemObjectBuilder.getInstance()); >>>> >>>> StringWriter writer=new StringWriter(); // >>>> http://www.programcreek.com/java-api-examples/index.php?api=org.openscience.cdk.AtomContainerSet >>>> >>>> StructureDiagramGenerator sdg = new StructureDiagramGenerator(); >>>> DeduceBondSystemTool dbst = new DeduceBondSystemTool(); >>>> FixBondOrdersTool kekulizer = new FixBondOrdersTool(); >>>> >>>> int i = 0; >>>> while (reader.hasNext()) { >>>> i = i+1; >>>> >>>> IAtomContainer molecule = (IAtomContainer)reader.next(); >>>> System.out.println("Query molecule: " + molecule); >>>> >>>> boolean aromatic_0 = false; >>>> for (IBond bond : molecule.bonds()) if >>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_0 = true; break;} >>>> >>>> System.out.println("IS THE ORIGINAL MOLECULE AROMATIC?: " + >>>> aromatic_0); >>>> >>>> >>>> StringWriter w = new StringWriter(); >>>> MDLWriter mw = new MDLWriter(w); >>>> mw.write(molecule); >>>> System.out.println("ORIGINAL MOLECULE" + w.toString()); >>>> >>>> >>>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule); >>>> sdg.setMolecule(molecule); >>>> sdg.generateCoordinates(); >>>> IAtomContainer mol_with_hydrogen = sdg.getMolecule(); >>>> >>>> >>>> if(!aromatic_0){ >>>> SMSDNormalizer.aromatizeMolecule(mol_with_hydrogen); >>>> boolean aromatic = false; >>>> for (IBond bond : mol_with_hydrogen.bonds()) if >>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic = true; break;} >>>> System.out.println("HAS THE MOLECULE BEEN AROMATIZED?: " + >>>> aromatic); >>>> mw.write(mol_with_hydrogen); >>>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >>>> EXPLICIT ATOMS" + w.toString()); >>>> >>>> } >>>> else{ >>>> >>>> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol_with_hydrogen); >>>> mol_with_hydrogen = >>>> kekulizer.kekuliseAromaticRings(mol_with_hydrogen); >>>> mw.write(mol_with_hydrogen); >>>> System.out.println(mol_with_hydrogen); >>>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >>>> EXPLICIT ATOMS" + w.toString()); >>>> >>>> boolean aromatic_3 = false; >>>> for (IBond bond : mol_with_hydrogen.bonds()) if >>>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_3 = true; break;} >>>> System.out.println("IS AROMATIC AFTER HYDRO?? " + >>>> aromatic_3); >>>> } >>>> >>>> >>>> System.out.println(mol_with_hydrogen); >>>> SmilesGenerator sg = new SmilesGenerator(); >>>> System.out.println(sg.create(mol_with_hydrogen)); >>>> >>>> >>>> String name = (String) molecule.getProperty(CDKConstants.TITLE); >>>> IAtomContainerSet metabolites = >>>> generateAllMetabolitesFromAtomContainer(mol_with_hydrogen, reaction, >>>> smrkMan); >>>> System.out.println("METABOLITES" + metabolites); >>>> } >>>> >>> >>> >> > |
|
From: Nina J. <jel...@gm...> - 2015-04-22 04:51:18
|
Yannick, Just a warning, 3.0.0 is still being tested and not released yet, but the SMIRKS package was tested by another group as well and appears to work well. Best regards, Nina On 22 April 2015 at 07:38, Yannick .Djoumbou <y.d...@gm...> wrote: > Thanks Nina, > > first of all, I am really happy that a new release of AMBIT was released > and is working with CDK 1.5.10. I'll try that out and also use the > aromaticity class. > I a looking forward to reading Nick's reply. > > Regards, > > Yannick > > On Tue, Apr 21, 2015 at 10:32 PM, Nina Jeliazkova < > jel...@gm...> wrote: > >> Yannick, >> >> Nick may reply later this week, but could you please try ambit >> 3.0.0-SNAPSHOT (CDK 1.5.10) dependency >> >> >> http://ambit.uni-plovdiv.bg:8083/nexus/#nexus-search;gav~ambit~~3.0.0-SNAPSHOT~~ >> >> The version you work with is quite outdated and there have been number of >> improvements. >> >> Last but not least, the SMIRKS package expects Kekule structures. You >> will NOT get same results if structures are not kekulized. Fortunately, in >> CDK 1.5.10 the kekulization works quite well. >> >> In any case please do not use SMSD* package, it is already deprecated in >> CDK as far as I know. Use the new Aromaticity class >> >> >> http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Aromaticity.html >> >> Best regards, >> Nina >> >> >> On 21 April 2015 at 21:07, Yannick .Djoumbou <y.d...@gm...> >> wrote: >> >>> Hello guys, >>> >>> I am dealing with an issue here. I would like to apply a transformation >>> on the attached molecules. Below is a function that I wrote to apply a >>> transformation with single copy for each position (with >>> smrkMan.applyTransformationWithSingleCopyForEachPos). Because CDK has >>> issues dealing with bond type 4, I tried to transform the same molecule >>> (aniline) using different bond types. >>> In test1.sdf, the bond types in the benzene ring have type 1 and 2, >>> alternatively. This, however produces 5 metabolites. In test2.sdf, the >>> aromatic bonds of the molecule are of type 4. The transformation does not >>> produce any product, which is wrong. >>> >>> Procedure: >>> ---------- >>> (1) I tested whether CDK viewed the input molecule as aromatic or not, >>> by checking the bond types. For my own preference, I also added >>> explicit hydrogen atoms in order to use my smirks pattern more efficiently. For >>> test1, aniline is not first viewed as aromatic. Thus, I aromatized it using >>> CDK's SMSDNormalizer.aromatizeMolecule. In test2, aniline is viewed as >>> aromatic. Because the bonds in the benzene ring are of type 4, I >>> decided to kekulize it, so that CDK with better deal with the molecule. >>> Somehow, the resulting molecule still has bond type 4. The resulting >>> molecules after these edits are stored in >>> test1_after_aromatizing_and_adding_hydrogen.sdf and >>> test2_after_kekulizing_and_adding_hydrogen.sdf. Somehow, the molecule in >>> the later files does not have explicit hydrogen atoms attached to the >>> benzene ring. >>> >>> (2) Following the first step, I ran >>> smrkMan.applyTransformationWithSingleCopyForEachPos on the container >>> obtained after the first step, where smrkMan is an instance of the SMRIKS >>> Manager. As mentioned earlier, aniline in the first form (ring bonds with >>> types 1 and 2) was transformed. the five products are in the file >>> test1_metabolites.sdf. In the second file (ring bonds with type 4) is >>> not transformed. >>> I used the smirks: [c;H1:1]>>[c:1][OX2H1] and [c:1]>>[c:1][OX2H1] foe >>> each molecule, which returned the same output. >>> This procedure was implemented in the function transform_from_sdf >>> below. >>> >>> >>> Could you please help me here? How can I get the same results whether I >>> submit my molecule in the kekule or the aromatic form? I have tried >>> different things, but without success. by the way, I am using the AMBIT >>> 2.6.0 and CDK version 1.5.6 versions. I really need help here. >>> >>> Thank you for your consideration. >>> >>> Best regards, >>> >>> Yannick >>> >>> >>> >>> >>> >>> >>> >>> >>> public LinkedHashMap<String, IAtomContainerSet> transform_from_sdf(File >>> sdf_input, SMIRKSReaction reaction) throws Exception{ >>> >>> LinkedHashMap<String, IAtomContainerSet> sdf_metabolites = new >>> LinkedHashMap<String, IAtomContainerSet>(); >>> IteratingSDFReader reader = new IteratingSDFReader(new >>> FileInputStream(sdf_input), DefaultChemObjectBuilder.getInstance()); >>> SMIRKSManager smrkMan = new >>> SMIRKSManager(SilentChemObjectBuilder.getInstance()); >>> >>> StringWriter writer=new StringWriter(); // >>> http://www.programcreek.com/java-api-examples/index.php?api=org.openscience.cdk.AtomContainerSet >>> >>> StructureDiagramGenerator sdg = new StructureDiagramGenerator(); >>> DeduceBondSystemTool dbst = new DeduceBondSystemTool(); >>> FixBondOrdersTool kekulizer = new FixBondOrdersTool(); >>> >>> int i = 0; >>> while (reader.hasNext()) { >>> i = i+1; >>> >>> IAtomContainer molecule = (IAtomContainer)reader.next(); >>> System.out.println("Query molecule: " + molecule); >>> >>> boolean aromatic_0 = false; >>> for (IBond bond : molecule.bonds()) if >>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_0 = true; break;} >>> >>> System.out.println("IS THE ORIGINAL MOLECULE AROMATIC?: " + >>> aromatic_0); >>> >>> >>> StringWriter w = new StringWriter(); >>> MDLWriter mw = new MDLWriter(w); >>> mw.write(molecule); >>> System.out.println("ORIGINAL MOLECULE" + w.toString()); >>> >>> >>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule); >>> sdg.setMolecule(molecule); >>> sdg.generateCoordinates(); >>> IAtomContainer mol_with_hydrogen = sdg.getMolecule(); >>> >>> >>> if(!aromatic_0){ >>> SMSDNormalizer.aromatizeMolecule(mol_with_hydrogen); >>> boolean aromatic = false; >>> for (IBond bond : mol_with_hydrogen.bonds()) if >>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic = true; break;} >>> System.out.println("HAS THE MOLECULE BEEN AROMATIZED?: " + >>> aromatic); >>> mw.write(mol_with_hydrogen); >>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >>> EXPLICIT ATOMS" + w.toString()); >>> >>> } >>> else{ >>> >>> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol_with_hydrogen); >>> mol_with_hydrogen = >>> kekulizer.kekuliseAromaticRings(mol_with_hydrogen); >>> mw.write(mol_with_hydrogen); >>> System.out.println(mol_with_hydrogen); >>> System.out.println("AROMATIZED MOLECULE WITH HYDROGEN >>> EXPLICIT ATOMS" + w.toString()); >>> >>> boolean aromatic_3 = false; >>> for (IBond bond : mol_with_hydrogen.bonds()) if >>> (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_3 = true; break;} >>> System.out.println("IS AROMATIC AFTER HYDRO?? " + >>> aromatic_3); >>> } >>> >>> >>> System.out.println(mol_with_hydrogen); >>> SmilesGenerator sg = new SmilesGenerator(); >>> System.out.println(sg.create(mol_with_hydrogen)); >>> >>> >>> String name = (String) molecule.getProperty(CDKConstants.TITLE); >>> IAtomContainerSet metabolites = >>> generateAllMetabolitesFromAtomContainer(mol_with_hydrogen, reaction, >>> smrkMan); >>> System.out.println("METABOLITES" + metabolites); >>> } >>> >> >> > |
|
From: Nina J. <jel...@gm...> - 2015-04-22 04:32:20
|
Yannick, Nick may reply later this week, but could you please try ambit 3.0.0-SNAPSHOT (CDK 1.5.10) dependency http://ambit.uni-plovdiv.bg:8083/nexus/#nexus-search;gav~ambit~~3.0.0-SNAPSHOT~~ The version you work with is quite outdated and there have been number of improvements. Last but not least, the SMIRKS package expects Kekule structures. You will NOT get same results if structures are not kekulized. Fortunately, in CDK 1.5.10 the kekulization works quite well. In any case please do not use SMSD* package, it is already deprecated in CDK as far as I know. Use the new Aromaticity class http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Aromaticity.html Best regards, Nina On 21 April 2015 at 21:07, Yannick .Djoumbou <y.d...@gm...> wrote: > Hello guys, > > I am dealing with an issue here. I would like to apply a transformation on > the attached molecules. Below is a function that I wrote to apply a > transformation with single copy for each position (with > smrkMan.applyTransformationWithSingleCopyForEachPos). Because CDK has > issues dealing with bond type 4, I tried to transform the same molecule > (aniline) using different bond types. > In test1.sdf, the bond types in the benzene ring have type 1 and 2, > alternatively. This, however produces 5 metabolites. In test2.sdf, the > aromatic bonds of the molecule are of type 4. The transformation does not > produce any product, which is wrong. > > Procedure: > ---------- > (1) I tested whether CDK viewed the input molecule as aromatic or not, by > checking the bond types. For my own preference, I also added explicit > hydrogen atoms in order to use my smirks pattern more efficiently. For > test1, aniline is not first viewed as aromatic. Thus, I aromatized it using > CDK's SMSDNormalizer.aromatizeMolecule. In test2, aniline is viewed as > aromatic. Because the bonds in the benzene ring are of type 4, I decided > to kekulize it, so that CDK with better deal with the molecule. Somehow, > the resulting molecule still has bond type 4. The resulting molecules after > these edits are stored in test1_after_aromatizing_and_adding_hydrogen.sdf > and test2_after_kekulizing_and_adding_hydrogen.sdf. Somehow, the molecule > in the later files does not have explicit hydrogen atoms attached to the > benzene ring. > > (2) Following the first step, I ran > smrkMan.applyTransformationWithSingleCopyForEachPos on the container > obtained after the first step, where smrkMan is an instance of the SMRIKS > Manager. As mentioned earlier, aniline in the first form (ring bonds with > types 1 and 2) was transformed. the five products are in the file > test1_metabolites.sdf. In the second file (ring bonds with type 4) is not > transformed. > I used the smirks: [c;H1:1]>>[c:1][OX2H1] and [c:1]>>[c:1][OX2H1] foe each > molecule, which returned the same output. > This procedure was implemented in the function transform_from_sdf below. > > > Could you please help me here? How can I get the same results whether I > submit my molecule in the kekule or the aromatic form? I have tried > different things, but without success. by the way, I am using the AMBIT > 2.6.0 and CDK version 1.5.6 versions. I really need help here. > > Thank you for your consideration. > > Best regards, > > Yannick > > > > > > > > > public LinkedHashMap<String, IAtomContainerSet> transform_from_sdf(File > sdf_input, SMIRKSReaction reaction) throws Exception{ > > LinkedHashMap<String, IAtomContainerSet> sdf_metabolites = new > LinkedHashMap<String, IAtomContainerSet>(); > IteratingSDFReader reader = new IteratingSDFReader(new > FileInputStream(sdf_input), DefaultChemObjectBuilder.getInstance()); > SMIRKSManager smrkMan = new > SMIRKSManager(SilentChemObjectBuilder.getInstance()); > > StringWriter writer=new StringWriter(); // > http://www.programcreek.com/java-api-examples/index.php?api=org.openscience.cdk.AtomContainerSet > > StructureDiagramGenerator sdg = new StructureDiagramGenerator(); > DeduceBondSystemTool dbst = new DeduceBondSystemTool(); > FixBondOrdersTool kekulizer = new FixBondOrdersTool(); > > int i = 0; > while (reader.hasNext()) { > i = i+1; > > IAtomContainer molecule = (IAtomContainer)reader.next(); > System.out.println("Query molecule: " + molecule); > > boolean aromatic_0 = false; > for (IBond bond : molecule.bonds()) if > (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_0 = true; break;} > > System.out.println("IS THE ORIGINAL MOLECULE AROMATIC?: " + > aromatic_0); > > > StringWriter w = new StringWriter(); > MDLWriter mw = new MDLWriter(w); > mw.write(molecule); > System.out.println("ORIGINAL MOLECULE" + w.toString()); > > > AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule); > sdg.setMolecule(molecule); > sdg.generateCoordinates(); > IAtomContainer mol_with_hydrogen = sdg.getMolecule(); > > > if(!aromatic_0){ > SMSDNormalizer.aromatizeMolecule(mol_with_hydrogen); > boolean aromatic = false; > for (IBond bond : mol_with_hydrogen.bonds()) if > (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic = true; break;} > System.out.println("HAS THE MOLECULE BEEN AROMATIZED?: " + > aromatic); > mw.write(mol_with_hydrogen); > System.out.println("AROMATIZED MOLECULE WITH HYDROGEN EXPLICIT > ATOMS" + w.toString()); > > } > else{ > > AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol_with_hydrogen); > mol_with_hydrogen = > kekulizer.kekuliseAromaticRings(mol_with_hydrogen); > mw.write(mol_with_hydrogen); > System.out.println(mol_with_hydrogen); > System.out.println("AROMATIZED MOLECULE WITH HYDROGEN EXPLICIT > ATOMS" + w.toString()); > > boolean aromatic_3 = false; > for (IBond bond : mol_with_hydrogen.bonds()) if > (bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_3 = true; break;} > System.out.println("IS AROMATIC AFTER HYDRO?? " + > aromatic_3); > } > > > System.out.println(mol_with_hydrogen); > SmilesGenerator sg = new SmilesGenerator(); > System.out.println(sg.create(mol_with_hydrogen)); > > > String name = (String) molecule.getProperty(CDKConstants.TITLE); > IAtomContainerSet metabolites = > generateAllMetabolitesFromAtomContainer(mol_with_hydrogen, reaction, > smrkMan); > System.out.println("METABOLITES" + metabolites); > } > |
|
From: Yannick .D. <y.d...@gm...> - 2015-04-21 18:07:56
|
Hello guys,
I am dealing with an issue here. I would like to apply a transformation on
the attached molecules. Below is a function that I wrote to apply a
transformation with single copy for each position (with
smrkMan.applyTransformationWithSingleCopyForEachPos). Because CDK has
issues dealing with bond type 4, I tried to transform the same molecule
(aniline) using different bond types.
In test1.sdf, the bond types in the benzene ring have type 1 and 2,
alternatively. This, however produces 5 metabolites. In test2.sdf, the
aromatic bonds of the molecule are of type 4. The transformation does not
produce any product, which is wrong.
Procedure:
----------
(1) I tested whether CDK viewed the input molecule as aromatic or not, by
checking the bond types. For my own preference, I also added explicit
hydrogen atoms in order to use my smirks pattern more efficiently. For
test1, aniline is not first viewed as aromatic. Thus, I aromatized it using
CDK's SMSDNormalizer.aromatizeMolecule. In test2, aniline is viewed as
aromatic. Because the bonds in the benzene ring are of type 4, I decided to
kekulize it, so that CDK with better deal with the molecule. Somehow, the
resulting molecule still has bond type 4. The resulting molecules after
these edits are stored in test1_after_aromatizing_and_adding_hydrogen.sdf
and test2_after_kekulizing_and_adding_hydrogen.sdf. Somehow, the molecule
in the later files does not have explicit hydrogen atoms attached to the
benzene ring.
(2) Following the first step, I ran
smrkMan.applyTransformationWithSingleCopyForEachPos on the container
obtained after the first step, where smrkMan is an instance of the SMRIKS
Manager. As mentioned earlier, aniline in the first form (ring bonds with
types 1 and 2) was transformed. the five products are in the file
test1_metabolites.sdf. In the second file (ring bonds with type 4) is not
transformed.
I used the smirks: [c;H1:1]>>[c:1][OX2H1] and [c:1]>>[c:1][OX2H1] foe each
molecule, which returned the same output.
This procedure was implemented in the function transform_from_sdf below.
Could you please help me here? How can I get the same results whether I
submit my molecule in the kekule or the aromatic form? I have tried
different things, but without success. by the way, I am using the AMBIT
2.6.0 and CDK version 1.5.6 versions. I really need help here.
Thank you for your consideration.
Best regards,
Yannick
public LinkedHashMap<String, IAtomContainerSet> transform_from_sdf(File
sdf_input, SMIRKSReaction reaction) throws Exception{
LinkedHashMap<String, IAtomContainerSet> sdf_metabolites = new
LinkedHashMap<String, IAtomContainerSet>();
IteratingSDFReader reader = new IteratingSDFReader(new
FileInputStream(sdf_input), DefaultChemObjectBuilder.getInstance());
SMIRKSManager smrkMan = new
SMIRKSManager(SilentChemObjectBuilder.getInstance());
StringWriter writer=new StringWriter(); //
http://www.programcreek.com/java-api-examples/index.php?api=org.openscience.cdk.AtomContainerSet
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
DeduceBondSystemTool dbst = new DeduceBondSystemTool();
FixBondOrdersTool kekulizer = new FixBondOrdersTool();
int i = 0;
while (reader.hasNext()) {
i = i+1;
IAtomContainer molecule = (IAtomContainer)reader.next();
System.out.println("Query molecule: " + molecule);
boolean aromatic_0 = false;
for (IBond bond : molecule.bonds()) if
(bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_0 = true; break;}
System.out.println("IS THE ORIGINAL MOLECULE AROMATIC?: " +
aromatic_0);
StringWriter w = new StringWriter();
MDLWriter mw = new MDLWriter(w);
mw.write(molecule);
System.out.println("ORIGINAL MOLECULE" + w.toString());
AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);
sdg.setMolecule(molecule);
sdg.generateCoordinates();
IAtomContainer mol_with_hydrogen = sdg.getMolecule();
if(!aromatic_0){
SMSDNormalizer.aromatizeMolecule(mol_with_hydrogen);
boolean aromatic = false;
for (IBond bond : mol_with_hydrogen.bonds()) if
(bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic = true; break;}
System.out.println("HAS THE MOLECULE BEEN AROMATIZED?: " +
aromatic);
mw.write(mol_with_hydrogen);
System.out.println("AROMATIZED MOLECULE WITH HYDROGEN EXPLICIT
ATOMS" + w.toString());
}
else{
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol_with_hydrogen);
mol_with_hydrogen =
kekulizer.kekuliseAromaticRings(mol_with_hydrogen);
mw.write(mol_with_hydrogen);
System.out.println(mol_with_hydrogen);
System.out.println("AROMATIZED MOLECULE WITH HYDROGEN EXPLICIT
ATOMS" + w.toString());
boolean aromatic_3 = false;
for (IBond bond : mol_with_hydrogen.bonds()) if
(bond.getFlag(CDKConstants.ISAROMATIC)) {aromatic_3 = true; break;}
System.out.println("IS AROMATIC AFTER HYDRO?? " +
aromatic_3);
}
System.out.println(mol_with_hydrogen);
SmilesGenerator sg = new SmilesGenerator();
System.out.println(sg.create(mol_with_hydrogen));
String name = (String) molecule.getProperty(CDKConstants.TITLE);
IAtomContainerSet metabolites =
generateAllMetabolitesFromAtomContainer(mol_with_hydrogen, reaction,
smrkMan);
System.out.println("METABOLITES" + metabolites);
}
|
|
From: Nina J. <jel...@gm...> - 2015-01-20 06:09:37
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Dear Yannick, On 20 January 2015 at 00:16, Yannick .Djoumbou <y.d...@gm...> wrote: > > Thanks for letting me know, > > I guess I will have to find a way to use different versions of cdk. > You may try the ambit branch 2.6.0-SNAPSHOT I have mentioned (CDK 1.5.6 dependency). Mixing the different CDK versions is not a good idea, unless you have control on class loaders via OSGi or similar. The artifacts are available at http://ambit.uni-plovdiv.bg:8083/nexus/#nexus-search;gav~ambit~~2.6.0-SNAPSHOT~~ Please have in mind the current 2.7.2 release, while depending on CDK 1.4.11, has a number of improvements in the SMIRKS package. Nick may answer your specific question on stereochemistry later. Best regards, Nina > I also noticed something: SmartsHelper.moleculeToSMILES seems not to > reproduce the stereochemistry from the input molecule to the output. e.g.: > the molecule COC1=CC=C(C=C1)[C@@H](C1=CC(C)=C(O)C(O)=C1)C(Cl)(Cl)Cl, when > converted to from the original mol format to the smiles returns a smiles > string without stereo info: > COC1=CC=C(C=C1)C(C1=CC(C)=C(O)C(O)=C1)C(Cl)(Cl)Cl. > > Is there a method which allows to reproduce the stereochemistry? This is > very important for my task. > > Thank you. > > Regards, > > Yannick > > On Mon, Jan 19, 2015 at 2:03 PM, Nina Jeliazkova < > jel...@gm...> wrote: > >> Hello Yannick, >> >> On 19 January 2015 at 22:51, Yannick .Djoumbou <y.d...@gm...> >> wrote: >> >>> Hello, >>> >>> First off, I would like to wish everyone a happy new year. >>> >>> I would like to know if there is a version of Ambit which is compatible >>> to CDK 1.5.8. >>> >> >> The short answer is no. >> >> >>> I have been using the smarts helper to generate molecules from smiles, >>> as in: >>> >>> IAtomContainer molecule = SmartsHelper.getMoleculeFromSmiles(smiles); >>> >>> However, in the recent versions of CDK (1.5.x), IMolecule seems to have >>> disappeared. The error message I get is "The method >>> getMoleculeFromSmiles(String) from the type SmartsHelper refers to the >>> missing type IMolecule". >>> And the following link shows that IMolecule is now missing: >>> http://cdk.github.io/cdk/1.5/docs/api/ >>> >> >> Yes, we are aware of this CDK refactoring. >> >> >>> >>> Could you pleae help me to deal with it? We are working with the recent >>> versions of CDK because there are some functions and tools that we need. >>> >>> >> Upgrade is planned, but not currently available, due to time >> constraints. There is a two years old branch of ambit, supporting CDK >> 1.5.6 , but it is probably also outdated for your purposes. >> >> Best regards, >> Nina >> >> >> >>> Regards, >>> >>> Yannick >>> >> >> > |
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From: Yannick .D. <y.d...@gm...> - 2015-01-19 22:16:32
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Thanks for letting me know, I guess I will have to find a way to use different versions of cdk. I also noticed something: SmartsHelper.moleculeToSMILES seems not to reproduce the stereochemistry from the input molecule to the output. e.g.: the molecule COC1=CC=C(C=C1)[C@@H](C1=CC(C)=C(O)C(O)=C1)C(Cl)(Cl)Cl, when converted to from the original mol format to the smiles returns a smiles string without stereo info: COC1=CC=C(C=C1)C(C1=CC(C)=C(O)C(O)=C1)C(Cl)(Cl)Cl. Is there a method which allows to reproduce the stereochemistry? This is very important for my task. Thank you. Regards, Yannick On Mon, Jan 19, 2015 at 2:03 PM, Nina Jeliazkova <jel...@gm...> wrote: > Hello Yannick, > > On 19 January 2015 at 22:51, Yannick .Djoumbou <y.d...@gm...> > wrote: > >> Hello, >> >> First off, I would like to wish everyone a happy new year. >> >> I would like to know if there is a version of Ambit which is compatible >> to CDK 1.5.8. >> > > The short answer is no. > > >> I have been using the smarts helper to generate molecules from smiles, as >> in: >> >> IAtomContainer molecule = SmartsHelper.getMoleculeFromSmiles(smiles); >> >> However, in the recent versions of CDK (1.5.x), IMolecule seems to have >> disappeared. The error message I get is "The method >> getMoleculeFromSmiles(String) from the type SmartsHelper refers to the >> missing type IMolecule". >> And the following link shows that IMolecule is now missing: >> http://cdk.github.io/cdk/1.5/docs/api/ >> > > Yes, we are aware of this CDK refactoring. > > >> >> Could you pleae help me to deal with it? We are working with the recent >> versions of CDK because there are some functions and tools that we need. >> >> > Upgrade is planned, but not currently available, due to time constraints. > There is a two years old branch of ambit, supporting CDK 1.5.6 , but it is > probably also outdated for your purposes. > > Best regards, > Nina > > > >> Regards, >> >> Yannick >> > > |
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From: Nina J. <jel...@gm...> - 2015-01-19 21:03:38
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Hello Yannick, On 19 January 2015 at 22:51, Yannick .Djoumbou <y.d...@gm...> wrote: > Hello, > > First off, I would like to wish everyone a happy new year. > > I would like to know if there is a version of Ambit which is compatible to > CDK 1.5.8. > The short answer is no. > I have been using the smarts helper to generate molecules from smiles, as > in: > > IAtomContainer molecule = SmartsHelper.getMoleculeFromSmiles(smiles); > > However, in the recent versions of CDK (1.5.x), IMolecule seems to have > disappeared. The error message I get is "The method > getMoleculeFromSmiles(String) from the type SmartsHelper refers to the > missing type IMolecule". > And the following link shows that IMolecule is now missing: > http://cdk.github.io/cdk/1.5/docs/api/ > Yes, we are aware of this CDK refactoring. > > Could you pleae help me to deal with it? We are working with the recent > versions of CDK because there are some functions and tools that we need. > > Upgrade is planned, but not currently available, due to time constraints. There is a two years old branch of ambit, supporting CDK 1.5.6 , but it is probably also outdated for your purposes. Best regards, Nina > Regards, > > Yannick > |
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From: Yannick .D. <y.d...@gm...> - 2015-01-19 20:51:18
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Hello, First off, I would like to wish everyone a happy new year. I would like to know if there is a version of Ambit which is compatible to CDK 1.5.8. I have been using the smarts helper to generate molecules from smiles, as in: IAtomContainer molecule = SmartsHelper.getMoleculeFromSmiles(smiles); However, in the recent versions of CDK (1.5.x), IMolecule seems to have disappeared. The error message I get is "The method getMoleculeFromSmiles(String) from the type SmartsHelper refers to the missing type IMolecule". And the following link shows that IMolecule is now missing: http://cdk.github.io/cdk/1.5/docs/api/ Could you pleae help me to deal with it? We are working with the recent versions of CDK because there are some functions and tools that we need. Regards, Yannick |
