Difference between revisions of "Btz"

From DISI
Jump to: navigation, search
(Search in bulk)
Line 29: Line 29:
 
</pre>
 
</pre>
  
As of March 30, 2020:  
+
As of April 13, 2020:  
  
There are 3,785,736,058 codes in m_enamine. There will eventually be about 11 billion.
+
There are 10,107,024,050 codes in m_enamine. There will eventually be about 11 billion.
  
 
There are 1,542,514,329 codes in s_enamine. There will eventually be about 11 billion
 
There are 1,542,514,329 codes in s_enamine. There will eventually be about 11 billion
  
 
We are working on how to load it faster.
 
We are working on how to load it faster.

Revision as of 11:17, 14 April 2020

I wrote a tool for looking up molecules on the BTZ (Bigger than ZINC) db. The idea is the have an api that can tell you which database in SmallWorld (i.e s enamine, m enamine, wuxi) the molecule belongs to. At the moment, it only support molecule id search. Smiles search is on the work. Please note that I'm still loading the molecules into BTZ, so many molecules might not be up there yet. Please let me know your feedbacks and issues.

Example (it works with Z, PV, s_ codes from enamines): curl http://gimel.compbio.ucsf.edu:5022/api/_search_btz?molecule_id=s_270004__7454808__7549222

Output

{

  "db_name": "S-Enamine-20Q1-797M", 
  "mol_id": "s_270004__7454808__7549222", 
  "query_type": "mol_id", 
  "smiles": "Cc1cc2cc(CN3CCN(C)CC3c3ccccc3)oc2cc1C", 
  "table_name": "s_enamine"
}

Search in bulk

To do search from a list of molecule in text file and output in json and text format

## Search molecules with txt output
curl -X POST -F "input_file=@/nfs/exa/work/khtang/btz_api/mol_id.txt" http://gimel.compbio.ucsf.edu:5022/api/_bulk_search_btz?output='txt'

## Search molecules with json output
curl -X POST -F "input_file=@/nfs/exa/work/khtang/btz_api/mol_id.txt" http://gimel.compbio.ucsf.edu:5022/api/_bulk_search_btz?output='json'

As of April 13, 2020:

There are 10,107,024,050 codes in m_enamine. There will eventually be about 11 billion.

There are 1,542,514,329 codes in s_enamine. There will eventually be about 11 billion

We are working on how to load it faster.