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MSP - Molecular Structure Predictor
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README.md

README.md

MSP

MSP stands for Molecular Structure Predictor and it is a novel approach to predict molecular structures next-step while these are drawn.

How to Build Rest API

  1. get RDKit repo: gradle cloneRDKit

  2. you are required to generate the RDkit wrappers: buildRDKit.sh (you might need some dependices) (takes sometime)

     * alterantive - If you do not require to run the clean up function button (which you will more likely not need to):
     	replace file StructurePredictionService.java with StructurePredictionService.java.replace
     	files found in folder: /rest-api/src/main/java/com/index
    
  3. Move into the /rest-api from root and run: gradle build

Run database

Run it locally

1.You now need to download and run hsqldb. (The database script can be found in /rest-api/database.script) download link: https://sourceforge.net/projects/hsqldb/files/

  1. Take database.script file from /rest-api folder.

  2. run with command from hsqldb folder: sudo java -cp hsqldb.jar org.hsqldb.Server -database.0 file:database.script -dbname.0 jacr_structure_prediction

  3. change file /rest-api/application.properties to the properties with (comment out others): spring.datasource.url=jdbc:mysql://jacr.host.cs.st-andrews.ac.uk/spring.datasource.url=jdbc:hsqldb:hsql://localhost:9001/jacr_structure_prediction

Run it in School of Computer Science

  1. change file /rest-api/application.properties to the properties with (comment out other): spring.datasource.url=jdbc:mysql://jacr.host.cs.st-andrews.ac.uk/jacr_structure_prediction

Run Rest API

To run the rest-api from command line run bash file /rest-api/run.sh

How to run web page

open file /front-end/structure-preidtion.js and set the server address at the top of the javascript file to:

http://localhost:17938/structure-prediction

To open the front end componenet run: google-chrome --allow-file-access-from-files

And open struct-predicion.html in that window.


Study

The data of the study is at this link: https://quicksilver.hg.cs.st-andrews.ac.uk/msp_sensitive_data/

Access to the study data is private. Contact Simone or Prof. Dobson for more info.

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