From: D. T. <dtc...@ni...> - 2005-07-25 21:56:26
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At 04:23 PM 7/25/2005, Peter Murray-Rust wrote: >On Sun, 2005-07-24 at 21:25 -0400, Dmitrii Tchekhovskoi wrote: > > Peter, > > > > InChI does the following in the following order: > > >Thanks, this looks useful. > > > 1. preprocesses the whole structure: > > 1a. creates disconnected preprocessed structure > > 1b. creates reconnected preprocessed structure > > 2. Extracts a component from 1a > > 3a. Normalizes a component as the one that has mobile H > > 4a. Normalizes a component as the one that has fixed mobile H > > 5. Canonicalizes 3a+4a results (constitutional) > > 6. Canonicalizes 5+3a+4a results (stereo) > > 7. Repeats 2-6 for the rest of components from 1a > > 8. Executes 2-6 for all components from 1b instead of 1a > > 9. Sorts the all the canonicalized components > > 10. Serializes all the results > > >Although steps 2-6 are concatenated, could the normalization be done >independently of the canonicalization? -DT: Yes, one can do this at the expense of increasing memory allocation. In the CreateOneStructureINChI() [runichi.c:3285] the Main Cycle [runichi.c:3603] for ( i = 0, nRet = 0; !sd->bUserQuitComponent && i < cur_prep_inp_data->num_components; i ++ ) {...} should be split in two, and a container for holding all structures that are sequentially extracted by GetOneComponent() into inp_cur_data should be created, etc. Regards Dmitrii >P. > > > Regards > > > > Dmitrii > > > > > > At 03:30 PM 7/24/2005, you wrote: > > >It was great to see the InChI team at the Frederick meeting last week. > > >>From many presentations - and from conversations elsewhere - it is clear > > >that the InChI concept is now widely accepted as an important tool. > > >Congratulations and thanks to all. > > > > > >One idea that came up was capturing the intermediate data within the > > >InChI flow. At coarse granularity [...] are processing steps and <...> > > >are data this is something like: > > > > > ><input file (MDL or CML)> > > >[flagprocessing - wedges, hydrogens, etc.] > > ><data 1> > > >[normalization] > > ><data 2> > > >[canonicalization] > > ><data 3> > > >[serialization] > > ><output InChI> > > > > > >Does the program architecture break down like this? > > >If data1,2,3 can be dumped (preferably as XML) then it is possible to > > >write algorithms that explore part of the process. For example and InChI > > >parser could roundtrip with <data 3>. It would also make it possible to > > >isolate various parts of the process for testing. > > > > > >How feasible is this? > > > > > >P. > > > > > > > > > > > >-- > > >Peter Murray-Rust > > >Unilever Centre for Molecular Informatics, > > >Department of Chemistry, University of Cambridge > > >Cambridge, CB2 1EW, UK > > >Tel: +44-1223-760369 > > > > > > > > > > > >------------------------------------------------------- > > >SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > > >from IBM. Find simple to follow Roadmaps, straightforward articles, > > >informative Webcasts and more! Get everything you need to get up to > > >speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > > >_______________________________________________ > > >InChI-discuss mailing list > > >InC...@li... > > >https://lists.sourceforge.net/lists/listinfo/inchi-discuss > > > > > > > > ------------------------------------------------------- > > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > > from IBM. Find simple to follow Roadmaps, straightforward articles, > > informative Webcasts and more! Get everything you need to get up to > > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > > _______________________________________________ > > InChI-discuss mailing list > > InC...@li... > > https://lists.sourceforge.net/lists/listinfo/inchi-discuss >-- >Peter Murray-Rust >Unilever Centre for Molecular Informatics, >Department of Chemistry, University of Cambridge >Cambridge, CB2 1EW, UK >Tel: +44-1223-760369 > > > >------------------------------------------------------- >SF.Net email is sponsored by: Discover Easy Linux Migration Strategies >from IBM. Find simple to follow Roadmaps, straightforward articles, >informative Webcasts and more! Get everything you need to get up to >speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click >_______________________________________________ >InChI-discuss mailing list >InC...@li... >https://lists.sourceforge.net/lists/listinfo/inchi-discuss |