AB3 Developer Notes - Revision history

Sstrizhov at 23:57, 13 January 2025

2025-01-13T23:57:33Z

← Older revision		Revision as of 23:57, 13 January 2025
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	== Restarting ==		== Restarting ==
	AB3 runs on the Epyc node. If AB3 is down first start by ssh-ing into Epyc. Use sudo docker logs --since 30m ab3 to see logs of AB3 and check to see if there was a reason for the crash. Then you can use the following commands "sudo docker restart redis" and "sudo docker restart AB3" to get AB3 back up and running. If that doesn't work replace "restart" with "start" and run those commands again.		AB3 runs on the Epyc node. If AB3 is down first start by ssh-ing into Epyc. Use sudo docker logs --since 30m ab3 to see logs of AB3 and check to see if there was a reason for the crash. Then you can use the following commands "sudo docker restart redis" and "sudo docker restart AB3" to get AB3 back up and running. If that doesn't work replace "restart" with "start" and run those commands again.

			[[Category: AB3]]

Mtsukanov at 19:48, 5 December 2023

2023-12-05T19:48:57Z

← Older revision		Revision as of 19:48, 5 December 2023
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	== Backend ==		== Backend ==
	The backend runs on Flask and has two main scripts running that do all the main calculations, which are BespokeAnaloging.py and arthorquery.py. The Bespoke Analoging script gets called in the routes section with the call_ABBB function. There we use a JSON file with all our reaction information as the first input and a smiles string as the second input which we get from the front-end. This script takes those inputs and runs the smiles against all those reactions and spits out building blocks if any of the reactions worked on the smiles. Those building blocks as well as a Tanimoto coefficient can then be used in the following script: arthorquery.py. The script takes all the building blocks that were derived from the first script and uses Arthor to find analogs of the building blocks using similarity against the Tanimoto coefficient and inclusion and exclusion rules as a basis.		The backend runs on Flask and has two main scripts running that do all the main calculations, which are BespokeAnaloging.py and arthorquery.py. The Bespoke Analoging script gets called in the routes section with the call_ABBB function. There we use a JSON file with all our reaction information as the first input and a smiles string as the second input which we get from the front-end. This script takes those inputs and runs the smiles against all those reactions and spits out building blocks if any of the reactions worked on the smiles. Those building blocks as well as a Tanimoto coefficient can then be used in the following script: arthorquery.py. The script takes all the building blocks that were derived from the first script and uses Arthor to find analogs of the building blocks using similarity against the Tanimoto coefficient and inclusion and exclusion rules as a basis.

			== Restarting ==
			AB3 runs on the Epyc node. If AB3 is down first start by ssh-ing into Epyc. Use sudo docker logs --since 30m ab3 to see logs of AB3 and check to see if there was a reason for the crash. Then you can use the following commands "sudo docker restart redis" and "sudo docker restart AB3" to get AB3 back up and running. If that doesn't work replace "restart" with "start" and run those commands again.

Mtsukanov at 18:55, 21 March 2023

2023-03-21T18:55:17Z

← Older revision		Revision as of 18:55, 21 March 2023
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	'''UNDER DEVELOPMENT'''		'''UNDER DEVELOPMENT'''

	The back-end and the front-end of this tool can be accessed at ABBB and AB3FrontEnd repositories at https://gitlab.docking.org, respectively. The backend runs on Flask and has two main scripts running that do all the main calculations, which are BespokeAnaloging.py and arthorquery.py. The Bespoke Analoging script gets called in the routes section with the call_ABBB function. There we use a JSON file with all our reaction information as the first input and a smiles string as the second input which we get from the front-end. This script takes those inputs and runs the smiles against all those reactions and spits out building blocks if any of the reactions worked on the smiles. Those building blocks as well as a Tanimoto coefficient can then be used in the following script: arthorquery.py. The script takes all the building blocks that were derived from the first script and uses Arthor to find analogs of the building blocks using similarity against the Tanimoto coefficient and inclusion and exclusion rules as a basis.		The back-end and the front-end of this tool can be accessed at ABBB and AB3FrontEnd repositories at https://gitlab.docking.org, respectively.

			== Backend ==
			The backend runs on Flask and has two main scripts running that do all the main calculations, which are BespokeAnaloging.py and arthorquery.py. The Bespoke Analoging script gets called in the routes section with the call_ABBB function. There we use a JSON file with all our reaction information as the first input and a smiles string as the second input which we get from the front-end. This script takes those inputs and runs the smiles against all those reactions and spits out building blocks if any of the reactions worked on the smiles. Those building blocks as well as a Tanimoto coefficient can then be used in the following script: arthorquery.py. The script takes all the building blocks that were derived from the first script and uses Arthor to find analogs of the building blocks using similarity against the Tanimoto coefficient and inclusion and exclusion rules as a basis.

Mtsukanov at 18:52, 21 March 2023

2023-03-21T18:52:59Z

← Older revision		Revision as of 18:52, 21 March 2023
Line 1:		Line 1:
	'''UNDER DEVELOPMENT'''		'''UNDER DEVELOPMENT'''

	The back-end and the front-end of this tool can be accessed at ABBB and AB3FrontEnd repositories at https://gitlab.docking.org, respectively. The backend runs on ~~flask~~ and has two main scripts running that do all the main calculations, which are BespokeAnaloging.py and arthorquery.py. The Bespoke Analoging script gets called in the routes section with the call_ABBB function. There we use a ~~json~~ file with all our reaction information as the first input and a smiles string as the second input which we get from the ~~frontend~~. This script takes those inputs and runs the smiles against all those reactions and spits out building blocks if any of the reactions worked on the smiles. Those building blocks as well as a ~~tanimoto coefficent~~ can then be used in the following ~~sctipt~~: arthorquery.py. The script takes all the building blocks that were ~~dereived~~ from the first script and uses ~~arthor~~ to find ~~similar~~ building blocks using the ~~tanimoto~~ coefficient and ~~using~~ inclusion and exclusion rules as a basis ~~for the new analogs~~.		The back-end and the front-end of this tool can be accessed at ABBB and AB3FrontEnd repositories at https://gitlab.docking.org, respectively. The backend runs on Flask and has two main scripts running that do all the main calculations, which are BespokeAnaloging.py and arthorquery.py. The Bespoke Analoging script gets called in the routes section with the call_ABBB function. There we use a JSON file with all our reaction information as the first input and a smiles string as the second input which we get from the front-end. This script takes those inputs and runs the smiles against all those reactions and spits out building blocks if any of the reactions worked on the smiles. Those building blocks as well as a Tanimoto coefficient can then be used in the following script: arthorquery.py. The script takes all the building blocks that were derived from the first script and uses Arthor to find analogs of the building blocks using similarity against the Tanimoto coefficient and inclusion and exclusion rules as a basis.

Mtsukanov: Created page with "'''UNDER DEVELOPMENT''' The back-end and the front-end of this tool can be accessed at ABBB and AB3FrontEnd repositories at https://gitlab.docking.org, respectively. The backend runs on flask and has two main scripts running that do all the main calculations, which are BespokeAnaloging.py and arthorquery.py. The Bespoke Analoging script gets called in the routes section with the call_ABBB function. There we use a json file with all our reaction information as the first..."

2023-03-21T18:50:15Z

Created page with "'''UNDER DEVELOPMENT''' The back-end and the front-end of this tool can be accessed at ABBB and AB3FrontEnd repositories at https://gitlab.docking.org, respectively. The backend runs on flask and has two main scripts running that do all the main calculations, which are BespokeAnaloging.py and arthorquery.py. The Bespoke Analoging script gets called in the routes section with the call_ABBB function. There we use a json file with all our reaction information as the first..."

New page

'''UNDER DEVELOPMENT'''

The back-end and the front-end of this tool can be accessed at ABBB and AB3FrontEnd repositories at https://gitlab.docking.org, respectively. The backend runs on flask and has two main scripts running that do all the main calculations, which are BespokeAnaloging.py and arthorquery.py. The Bespoke Analoging script gets called in the routes section with the call_ABBB function. There we use a json file with all our reaction information as the first input and a smiles string as the second input which we get from the frontend. This script takes those inputs and runs the smiles against all those reactions and spits out building blocks if any of the reactions worked on the smiles. Those building blocks as well as a tanimoto coefficent can then be used in the following sctipt: arthorquery.py. The script takes all the building blocks that were dereived from the first script and uses arthor to find similar building blocks using the tanimoto coefficient and using inclusion and exclusion rules as a basis for the new analogs.