I have seen in previous posts that Generatemd doesn't yet offer calculating multiple descriptors at once. though there are promises that this will be avaialbe soon.
I have some experience in Java programming. My question is how can i use the API's to generate multiple descriptors?
Also is there a comprehensive list of descriptors available?
Any help is highly appreciated.
In case if you have experience in java coding then it should be fairly straightforward to generate multiple descriptors for each input molecules.
You can either use an MDSet (ie. molecular descriptor set object) or several MolecularDescriptor objects at the same time. If you would like to get the decimal values and print them in a text output file then I'd recommend the latter approach, as MDSets can be useful if you do the similarity scoring on-the-fly as descriptors are generated.
The workflow is quite simple, the simple example in the class documentation of GenerateMD, it should be helpful.
If not, then please get back to this forum for further assistance.
Where can I find the test files 'scaffoldhopp.xml', 'veryselective.xml'. I failed to locate them in JChem package.
I tried to create using XML gui but failed.
Where did you find references to these XML configuration files? As far as I know we have never provided such examples files but we could use these names to illustrate some use-cases.
I am referring to the following commands. I have tried to generate xml files using XML GUI but failed.
generatemd a my_mols pharma_for_H1 "Asymmetric Euclidean with very high Enrichment" veryselective.xml
generatemd a my_mols pharma_for_H1 "Weighted Euclidean for scaffold hopping" scaffoldhopp.xml
Could you please help me with these files & how to generate them.
Ok. I see. These serve just illustration those aren't available I'm afraid.
However, perhaps I can help you find ways to generate some kind of virtual screening configuration that one would call "very selective etc.". The Screen product suite provide a commandline application program called optimizemetrics. You may wish to look at the user's documentation and get back to this forum if the documentation does not help. Though before you consult with that material please note, that optimizemetrics requires a set of compounds with known activity in the therapeutic area you research.
I fail to understand the documentation properly. Could you please let me know brief execution steps to be followed to create the XML config files.
I am enclosing a subset of test molecules presently I am working.
Could you please help me with XML config files & how to generate them.
sure, no problem.
Try to read the related documentation first, perhaps the best starting point this: examples/screen/index.html#opti_batch. You find this in your JChem installation directory.
Does this help?