Re: [Cdk-user] Stereochemistry is disregarded when creating SMILES from MOL-File
Legacy reasons i guess …. No actual reason not to upgrade, though. From: John Mayfield Sent: Wednesday, July 17, 2019 10:51 AM To: Wehner, Sebastian Cc: cdk-user@lists.sourceforge.net Subject: Re: [Cdk-user] Stereochemistry is disregarded when creating SMILES from MOL-File Why were you using that version? On Wed, 17 Jul 2019 at 06:37, Wehner, Sebastian mailto:sebastian.weh...@bruker.com>> wrote: Hi John, That is what I suspected. I had some hope that there was still a way to properly convert stereochemistry in this version… Anyways, thanks for your quick answer and explanations. Sebastian From: John Mayfield mailto:john.wilkinson...@gmail.com>> Sent: Tuesday, July 16, 2019 6:05 PM To: Wehner, Sebastian mailto:sebastian.weh...@bruker.com>> Cc: cdk-user@lists.sourceforge.net<mailto:cdk-user@lists.sourceforge.net> Subject: Re: [Cdk-user] Stereochemistry is disregarded when creating SMILES from MOL-File Hi Sebastian, > I am using CDK version 1.4.17 That is a very old version and does not convert stereochemistry correctly. Essentially there wasn't data structures to represent it so it was store different for 0D (e.g. SMILES) vs 2D vs 3D. This will all fixed about 7 years ago :-). Latest release is 2.2 BTW - https://github.com/cdk/cdk/releases John On Tue, 16 Jul 2019 at 15:04, Wehner, Sebastian via Cdk-user mailto:cdk-user@lists.sourceforge.net>> wrote: Hi, I could use your help! I am using CDK version 1.4.17 and want to build a SMILES string from a mol-file (SDF from lipid maps). The molecule has two isomers, but this information should be included in the mol-file, should it not? Anyways, I pass the mol-file as ByteArrayInputStream into MDLV2000Reader and then create a new AtomContainer from this. Iterating over each atom of the AtomContainer, using a CDKAtomTypeMatcher to get the IAtomType of the atom which I then use to configure this atom with via AtomTypeManipulator.configure(). Finally adding implicit hydrogens to the AtomContainer, creating a SmilesGenerator and returning the smiles of the AtomContainer with smilesGenerator.createSMILES(AtomContainer). However this produces a SMILES of the molecule which disregards the stereochemistry. The documentation states, that stereochemistry is taken into account (http://cdk.github.io/cdk/1.4/docs/api/org/openscience/cdk/smiles/SmilesGenerator.html). Am I missing something? Would be great I someone could help! Added the link to lipid maps for the example: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMGL02010378. Best regards, Sebastian Wehner ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net<mailto:Cdk-user@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/cdk-user ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
Re: [Cdk-user] Stereochemistry is disregarded when creating SMILES from MOL-File
Why were you using that version? On Wed, 17 Jul 2019 at 06:37, Wehner, Sebastian wrote: > Hi John, > > > > That is what I suspected. I had some hope that there was still a way to > properly convert stereochemistry in this version… > > Anyways, thanks for your quick answer and explanations. > > > > Sebastian > > > > *From:* John Mayfield > *Sent:* Tuesday, July 16, 2019 6:05 PM > *To:* Wehner, Sebastian > *Cc:* cdk-user@lists.sourceforge.net > *Subject:* Re: [Cdk-user] Stereochemistry is disregarded when creating > SMILES from MOL-File > > > > Hi Sebastian, > > > > > I am using CDK version 1.4.17 > > > > That is a very old version and does not convert stereochemistry > correctly. Essentially there wasn't data structures to represent it so it > was store different for 0D (e.g. SMILES) vs 2D vs 3D. This will all fixed > about 7 years ago :-). Latest release is 2.2 BTW - > https://github.com/cdk/cdk/releases > > > > John > > > > On Tue, 16 Jul 2019 at 15:04, Wehner, Sebastian via Cdk-user < > cdk-user@lists.sourceforge.net> wrote: > > Hi, > > > > I could use your help! I am using CDK version 1.4.17 and want to build a > SMILES string from a mol-file (SDF from lipid maps). The molecule has two > isomers, but this information should be included in the mol-file, should it > not? > > > > Anyways, I pass the mol-file as ByteArrayInputStream into MDLV2000Reader and > then create a new AtomContainer from this. Iterating over each atom of > the AtomContainer, using a CDKAtomTypeMatcher to get the IAtomType of the > atom which I then use to configure this atom with via AtomTypeManipulator > .configure(). > > > > Finally adding implicit hydrogens to the AtomContainer, creating a > SmilesGenerator and returning the smiles of the AtomContainer with > smilesGenerator.createSMILES(AtomContainer). > > > > However this produces a SMILES of the molecule which disregards the > stereochemistry. The documentation states, that stereochemistry is taken > into account ( > http://cdk.github.io/cdk/1.4/docs/api/org/openscience/cdk/smiles/SmilesGenerator.html). > Am I missing something? > > > > Would be great I someone could help! Added the link to lipid maps for the > example: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMGL02010378. > > > > > > Best regards, > > Sebastian Wehner > > > > ___ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user > > ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
Re: [Cdk-user] Stereochemistry is disregarded when creating SMILES from MOL-File
Hi John, That is what I suspected. I had some hope that there was still a way to properly convert stereochemistry in this version… Anyways, thanks for your quick answer and explanations. Sebastian From: John Mayfield Sent: Tuesday, July 16, 2019 6:05 PM To: Wehner, Sebastian Cc: cdk-user@lists.sourceforge.net Subject: Re: [Cdk-user] Stereochemistry is disregarded when creating SMILES from MOL-File Hi Sebastian, > I am using CDK version 1.4.17 That is a very old version and does not convert stereochemistry correctly. Essentially there wasn't data structures to represent it so it was store different for 0D (e.g. SMILES) vs 2D vs 3D. This will all fixed about 7 years ago :-). Latest release is 2.2 BTW - https://github.com/cdk/cdk/releases John On Tue, 16 Jul 2019 at 15:04, Wehner, Sebastian via Cdk-user mailto:cdk-user@lists.sourceforge.net>> wrote: Hi, I could use your help! I am using CDK version 1.4.17 and want to build a SMILES string from a mol-file (SDF from lipid maps). The molecule has two isomers, but this information should be included in the mol-file, should it not? Anyways, I pass the mol-file as ByteArrayInputStream into MDLV2000Reader and then create a new AtomContainer from this. Iterating over each atom of the AtomContainer, using a CDKAtomTypeMatcher to get the IAtomType of the atom which I then use to configure this atom with via AtomTypeManipulator.configure(). Finally adding implicit hydrogens to the AtomContainer, creating a SmilesGenerator and returning the smiles of the AtomContainer with smilesGenerator.createSMILES(AtomContainer). However this produces a SMILES of the molecule which disregards the stereochemistry. The documentation states, that stereochemistry is taken into account (http://cdk.github.io/cdk/1.4/docs/api/org/openscience/cdk/smiles/SmilesGenerator.html). Am I missing something? Would be great I someone could help! Added the link to lipid maps for the example: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMGL02010378. Best regards, Sebastian Wehner ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net<mailto:Cdk-user@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/cdk-user ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
Re: [Cdk-user] Stereochemistry is disregarded when creating SMILES from MOL-File
Hi Sebastian, > I am using CDK version 1.4.17 That is a very old version and does not convert stereochemistry correctly. Essentially there wasn't data structures to represent it so it was store different for 0D (e.g. SMILES) vs 2D vs 3D. This will all fixed about 7 years ago :-). Latest release is 2.2 BTW - https://github.com/cdk/cdk/releases John On Tue, 16 Jul 2019 at 15:04, Wehner, Sebastian via Cdk-user < cdk-user@lists.sourceforge.net> wrote: > Hi, > > > > I could use your help! I am using CDK version 1.4.17 and want to build a > SMILES string from a mol-file (SDF from lipid maps). The molecule has two > isomers, but this information should be included in the mol-file, should it > not? > > > > Anyways, I pass the mol-file as ByteArrayInputStream into MDLV2000Reader and > then create a new AtomContainer from this. Iterating over each atom of > the AtomContainer, using a CDKAtomTypeMatcher to get the IAtomType of the > atom which I then use to configure this atom with via AtomTypeManipulator > .configure(). > > > > Finally adding implicit hydrogens to the AtomContainer, creating a > SmilesGenerator and returning the smiles of the AtomContainer with > smilesGenerator.createSMILES(AtomContainer). > > > > However this produces a SMILES of the molecule which disregards the > stereochemistry. The documentation states, that stereochemistry is taken > into account ( > http://cdk.github.io/cdk/1.4/docs/api/org/openscience/cdk/smiles/SmilesGenerator.html). > Am I missing something? > > > > Would be great I someone could help! Added the link to lipid maps for the > example: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMGL02010378. > > > > > > Best regards, > > Sebastian Wehner > > > ___ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user > ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
[Cdk-user] Stereochemistry is disregarded when creating SMILES from MOL-File
Hi, I could use your help! I am using CDK version 1.4.17 and want to build a SMILES string from a mol-file (SDF from lipid maps). The molecule has two isomers, but this information should be included in the mol-file, should it not? Anyways, I pass the mol-file as ByteArrayInputStream into MDLV2000Reader and then create a new AtomContainer from this. Iterating over each atom of the AtomContainer, using a CDKAtomTypeMatcher to get the IAtomType of the atom which I then use to configure this atom with via AtomTypeManipulator.configure(). Finally adding implicit hydrogens to the AtomContainer, creating a SmilesGenerator and returning the smiles of the AtomContainer with smilesGenerator.createSMILES(AtomContainer). However this produces a SMILES of the molecule which disregards the stereochemistry. The documentation states, that stereochemistry is taken into account (http://cdk.github.io/cdk/1.4/docs/api/org/openscience/cdk/smiles/SmilesGenerator.html). Am I missing something? Would be great I someone could help! Added the link to lipid maps for the example: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMGL02010378. Best regards, Sebastian Wehner ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
