Hello, Egon Willighagen <[EMAIL PROTECTED]> wrote:
> On Sunday 28 January 2007 21:58, Rajarshi Guha wrote: > > Invariably I will know the names of my SD tags, so I can always create a > > temporary HashMap and extract the relevant properties via getProperty() > > and populate the HashMap and then send it setSdFields(). > > Well, I guess my hesitation comes from the fact that I have to know about SD > internals when wanting to read or store simple molecular properties... I > understand the step is not large, the math rather simple, but still... CDK > has set/getProperty() to store properties... why add another layer? > I aggree with Egon, adding another layer doesn't seem an elegant approach. Few more thoughts: 1)User calculates some descriptors and saves them as SDF file properties. Then at some moment this SDF file is read and properties loaded - how they should be loaded - as special_SDF_properties or as regular properties? 2)Imagine another file format appears that is able to store properties - should we introduce another my_file_special_Properties? That's not hypothetical - I already have implemented classes extending DefaultChemObjectWriter able to store / read compounds (as SMILES) along with properties in comma delimited , tab delimited and MSExcel XLS files. That was done by user request - is CDK team interested in these classes? 3)My problem with SDF fields are that they come with many different names - for example CAS number can be "CAS RN", "CAS", "CAS#" , "CAS Registry Number", etc. The same with chemical names, smiles, descriptor names. Once properties are loaded, there is no easy way to recognise which field means what, without asking the user. When working with multiple SDF files coming from different sources, and trying to combine information, it becomes a nightmare. Some solutions to be discussed: - introduce something like "translator facility" to perform translation property_name_in_file -> property_name_to_use_in_this_software - separate properties into different Hashmaps - like identifiers (cas, names), descriptors, measured properties, etc. Does something like this already exist in CDK? Best regards, Nina > > Egon ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
