How to calculate descriptors in Instant Jchem
Can you tell me How to calculate descriptors like LogP and all which are avilable in marvinview in Instant Jchem?
A wide range of descriptors can be calculated in Instant JChem.
To do this add a new Chemical Terms field to your table and specify the chemical terms expression for the descriptor you require. Favourites (shortcuts) for many of the common descriptors such as logP, donor/acceptor count, Lipinski... are present, but there are a much wider range also available.
Adding the chemical terms field has been added its values will be created for every structure in the table, and will be updated if you add additional structres or edit exisitng structures.
Note: you will need licenses for many of the chemical terms expressions. Enter these inot the standard marvin license file.
for a more detailed guide.
for an overview of chemical terms.
While filtering molecules using lipinski I got error message as indicated in image.
Please do suggest me what to do?
This looks like you have entered an incorrect chemical terms expression.
Looking at the expression you have it seems that you might have added a favourite for 2 different expressions (Lipinski and bioavailability) and ended up with an expression that is a mixture of the two and is invalid.
Just run the search again and re-enter the expression. If you find you chose the wrong favourite and need to use a different one then delete the current expression before adding the second one.
looking at your error, it seems you are missing a && before (mass() <= 500)...
My first question is about computing a set of molecular descriptors in IJC (let’s say all available topological descriptors) resulting in new columns for each descriptor. For the moment, this can be done separately and imported to IJC or by using chemical terms one by one in IJC. Is there anyway to compute all of them in IJC in one time and generate instantly corresponding columns?
My second question concerns import/merge. After constructing a table in IJC. I wanted to import the computed descriptors, but when importing the csv file, there was no way to map the two fields that contain the common ID. When I try with a tabulated text file, I have the message “Unsupported file format”. What could be the reason?
Thanks in advance,
About the descriptors:
Currently you need to add the chem terms fields individually. For IJC2.0 we are investigating some approaches for improving this, but its going to take some time to do this.
For now one thing tha can help is to add the chem terms fields to an empty JChem table and then import the structures into this table, rather than into a new one. If you do this you don't have to wait for the values to be calculated before you add the next field, so the process is much faster. Of course, the import will be slower as all the descriptors are being calculated as you import.
Can you let us know which version of IJC (import is quite different betweeen 1.0 and 2.0), and if possible give us a sample file that we can use to reproduce your problem (just a few lines should be sufficient).
I am using IJC 2.0.0. I have attached a text file with different descriptors computed for 10 molecules with their corresponding SD file. The SDF contains an additional structure (ID_MOL: 70) for which deliberately no descriptor has been calculated.
Thank you in advance,
Thanks for that information.
We have now fixed the problem.
We are hoping to do an update tomorrow (Tuesday 17th) via the update center that will include this fix.
The fix to the text file parsing problem in IJC 2.0 is now ready. You can get it from the update center (Tools menu).
Please note that there are some bugs remaining:
1. The data that is currently being displayed may not appear to be updated after the import is complete. You may need to restart IJC to get it refreshed.
2. The is potential a problem when you do the merge with a view (e.g. grdview) open you may a occasionally see a conflict. There is a workaround in place that seems to fix this, but if you do see it then do the import with all views closed.
Both these problems will be fixed shortly.