Looks doable. Everything is easier in Python but you can achieve the same goal either way.
- Noel On 11 May 2015 at 16:20, amprimiriam <dalrin.amaladha...@mail.mcgill.ca> wrote: > Hi Noel, > > Thank you for your response. I can see that Python makes it possible to > match the SMARTS rule with the desired element in the molecule. I am > currently using Openbabel in Visual Studio C++. And I want to use a separate > file that contains all of my SMARTS rules for functional groups along with a > name for each SMARTS such as: > [#6]!@[$(C=!@O)]!@[#6] ketone > [#6]!@[$([O;H1])] hydroxyl > [#6]-!@[#6] singlebond-alkyl > > And say I initially consider two input molecules in SMILES format for > simplicity sake, > 1) 2-methyl 2-butanol : CCC(C)(C)O > 2) Diethyl ketone : CCC(=O)CC > > Now the desired output for the above molecules is: (The molecules are > separated by a period which denotes the separation between each functional > group where the bonds are cleaved) > 1) 2-methyl 2-butanol : C.C.C.(C).(C).O > 2) Diethyl ketone : C.CC(=O).C.C > > The total number of functional groups that need to be identified as starters > by the SMARTS rules for the input target molecules are: > CHn (Alkyl) - 8 // Suffix `n` stands for 0, or 1, or 2, or 3 > Hydrogen > atoms > OH (Hydroxyl) – 1 > CHnCO (Ketone) – 1. > > When this has been done, now comes the crucial yet the most significant of > tasks that I need to design. I wish to break down the identified functional > groups into sub-categories based on UNIFAC model. This involves the > identification of Alkyl groups that are mainly classified into four types: > CHn - Plain Alkyl > CHn - Alkyl in alcohols > CHn - Alkyl in hydrophobic tails of Alcohols > CHn – Alkyl with OH group > > So for the given input molecules the Alkyl groups need to be classified as > follows://Please <http://forums.openbabel.org/file/n4658536/openbabel.png> > see the images that I have attached > 1. 2-methyl 2-butanol > i. CHn (Alkyl with OH group) – 1 > ii. CHn (Alkyl in alcohols) – 2 // the two > branching alkyl groups > connected to the alkyl with OH group without any tails > iii. CHn (Alkyl in hydrophobic tails of Alcohols) – 2 // the two alkyl > groups connected to the alkyl with OH group with a tail > 2. Diethyl ether > i. CHn (Plain Alkyl) – 3 // without OH groups > > Can you tell me if it is possible to use Openbabel API for accomplishing > this task and if you think using Python would be better than C++? I would be > very grateful if you can share any ideas that you might have with me. Any > advice on the functionalities available in OpenBabel that can help me design > the algorithm to identify the alkyl groups in the input molecules will be > appreciated. > > > > > -- > View this message in context: > http://forums.openbabel.org/Identifying-functional-groups-in-a-molecule-using-OpenBabel-tp4658507p4658536.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > One dashboard for servers and applications across Physical-Virtual-Cloud > Widest out-of-the-box monitoring support with 50+ applications > Performance metrics, stats and reports that give you Actionable Insights > Deep dive visibility with transaction tracing using APM Insight. > http://ad.doubleclick.net/ddm/clk/290420510;117567292;y > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
