Peter, > At 09:59 13/12/2005, Nina Jeliazkova wrote: > >Greetings, > > > >I would like to ask if there is a way to store in CML a nonspecific structure > >(i.e. - any structure which contains a repeating group where repeat count is > >not fixed). > > By "structure" do you mean chemical structure or generic data > structure? If you mean the former (such as -(CH2CHCl)n- then there
Yes, I mean chemical structure. However, it could be that only a part of the structure has a repeating group, the rest being a "normal" structure. > isn't at present. We are working on polymer informatics here but we > haven't formulated definite rules yet. The difficulty is that the > representation has to be supportable in software - it is relatively > easy to *design* structures that support this but not so easy to > create the complete software - among the questions are: > - should the structures be explicitly enumerated? > - what ids should the atoms have? > - how are the bonds between the units represented > - how are branched polymers represented? > - is the resulting structured deterministically generatable > Aggree, this is a complex thing. I got this question myself from a colleague who is interested in working with surfactants. > When there is an InChI for polymers we shall definitely look carefully at > that. > > I can't promise rapid progress here but it could be useful to know > what you were interested in doing. Apparently a first objective is to be able to store such structures, and then perhaps do a substructure search and/or some kind of structural similarity. It seems MDL SDF format http://www.mdl.com/downloads/public/ctfile/ctfile.pdf has some support under the notion of SGroup (please correct me if I am wrong). I've just found that Marvin applet is exporting such structures in XML format <?xml version="1.0" encoding="Cp1251" ?> <MDocument> <MChemicalStruct> <molecule molID="m1"> <atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18" elementType="S * O O O C C C C C C C C C C C O Na" formalCharge="0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 1" sgroupRef="sg1 sg1 sg1 sg1 sg1 sg1 sg1 sg1 sg1 sg1 sg1 sg1 sg1 sg1 sg1 sg1 sg1 0" mrvQueryProps="0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0" x2="0.8478766177436599 -1.3872990002097494 0.8478766177436599 0.8478766177436599 2.1517290615498155 -2.9031205984518196 -2.9031205984518196 -4.2391968240834705 -1.580082897258231 -4.23267756186444 -1.5735636350392002 -5.562234525277059 -0.2505259338456113 -5.56875378749609 -0.23767367404237916 5.1576677384274925 6.686341596472794 10.29596395483272" y2="0.025704519606464207 0.025704519606464207 1.284667186418722 -1.2332581472057935 0.025704519606464207 0.7707630589242673 -0.7707630589242673 1.5286738580453025 1.5415261178485347 -1.547859115432736 -1.535006855629504 0.7642437967052365 0.7836153187274995 -0.7770960565084687 -0.7642437967052365 -0.051409039212928415 -0.051409039212928415 -0.07059429660036184" /> <bondArray> <bond atomRefs2="a1 a4" order="2" /> <bond atomRefs2="a6 a7" order="1" /> <bond atomRefs2="a6 a8" order="2" /> <bond atomRefs2="a6 a9" order="1" /> <bond atomRefs2="a7 a10" order="2" /> <bond atomRefs2="a7 a11" order="1" /> <bond atomRefs2="a8 a12" order="1" /> <bond atomRefs2="a9 a13" order="2" /> <bond atomRefs2="a10 a14" order="1" /> <bond atomRefs2="a11 a15" order="2" /> <bond atomRefs2="a12 a14" order="2" /> <bond atomRefs2="a13 a15" order="1" /> <bond atomRefs2="a1 a5" order="1" /> <bond atomRefs2="a1 a2" order="1" /> <bond atomRefs2="a16 a17" order="2" /> <bond atomRefs2="a1 a3" order="2" /> </bondArray> <molecule id="sg1" role="Sgroup" title="n" molID="m2" /> </molecule> </MChemicalStruct> </MDocument> I would be interested to hear what do you think of these two examples? Best regards, Nina > > P. > > However > >If it is not possible in CML, is there CDK support (beside Polymer class)? > > > >Regards, > >Nina > > > > > >-- > >------------------------------------------------------------------ > > Assoc. Prof. Dr. Nina Nikolova-Jeliazkova > > * * Institute for Parallel Processing > > * * Bulgarian Academy of Sciences > > * IST Foundation * Acad. G. Bonchev St 25-A > > * The Bulgarian NREN * 1113 Sofia, Bulgaria > > * * Tel: +359 886 802011 > > * * ICQ: 10705013 > > http://www.ist.bg www: http://ambit.acad.bg/nina > >------------------------------------------------------------------ > > PGP Public Key > >http://cert.acad.bg/pgp-keys/keys/nina-nikolova-0xEEABA669.asc > > 8E99 8BAD D804 1A43 27B7 7F87 CF04 C7D1 EEAB A669 > >------------------------------------------------------------------ > > > > > > > > > >------------------------------------------------------- > >This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > >for problems? Stop! Download the new AJAX search engine that makes > >searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > >http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > >_______________________________________________ > >cml-discuss mailing list > >[EMAIL PROTECTED] > >https://lists.sourceforge.net/lists/listinfo/cml-discuss > > Peter Murray-Rust > Unilever Centre for Molecular Sciences Informatics > University of Cambridge, > Lensfield Road, Cambridge CB2 1EW, UK > +44-1223-763069 > -- ------------------------------------------------------------------ Assoc. Prof. Dr. Nina Nikolova-Jeliazkova * * Institute for Parallel Processing * * Bulgarian Academy of Sciences * IST Foundation * Acad. G. 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