https://github.com/cheminfo/autolearning
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.6%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: cheminfo
- Language: JavaScript
- Default Branch: master
- Size: 165 MB
Statistics
- Stars: 7
- Watchers: 8
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
autolearning
Try Ask Ern in our visualizer (It could take a while the first time.)
Installation
Pre-requisites
- Install mysql on your host.
- java 1.7 or latter.
Steps
Change to the project folder
cd autolearningDownload the maybridge dataset and cheminfo443 dataset
curl http://script.epfl.ch/script/HD/Load/1ZGgqjWVbr?filename=test%40patiny.com%2FResearch%2FNMR%2FAutoAssign%2Fdata%2Fmaybridge%2Fjcamp.bz2 > src/data/maybridge/jcamp.bz2; bzip2 -d src/data/maybridge/jcamp.bz2 ;./src/data/maybridge/split.sh ./src/data/maybridge/jcamp
curl http://script.epfl.ch/script/HD/Load/WA8LUhjzYi?filename=test%40patiny.com%2FResearch%2FNMR%2FAutoAssign%2Fdata%2Fcheminfo443.zip > src/data/cheminfo443.zip ; src/data/cheminfo443.zip -d src/data/
The .bz2 of the maybridge dataset contains a tab separated file, which includes the maybridge catalogID, the molfile and the jcamp-dx of the corresponding spectrum for each molecule in the dataset.
The .zip of the cheminfo443 dataset contains the molfiles and jcamp-dx for each of the molecules in the dataset as separate files.
- Modify src/schemas/nmrshiftdb.sql if you want to change the database name or password:
``` CREATE USER 'nmrshiftdb'@'localhost' IDENTIFIED BY 'my_secret'; CREATE DATABASE mynmrshiftdb1;
GRANT ALL PRIVILEGES ON mynmrshiftdb1.* TO 'nmrshiftdb'@'localhost'; FLUSH PRIVILEGES;
USE mynmrshiftdb1; ```
Create the database to store your chemical shifts assignments
mysql -u root < src/schemas/nmrshiftdb.sqlChange to src folfer
cd srcModify the database.js information to fit your database connection(Not needed if you did not change anything in step 2)
Start the train process
./train.shCongratulations! You have a database that can be used to make new 1H-chemical shifts predictions.
You may be intersted in creating a condensed table from the database to simplify and speedup the prediction by running
createPredictionTable.sh. An example of how to use this table for predictions of 1H-NMR chemical shifts can be found in src/test
define(["../core/fastNmrShiftDBPred1H"],function (nmrShiftDBPred1H) {
var molecule = File.load("/test/mol_0.mol");
var db = File.loadJSON("/h1_database.json");//Our condensed table for off-line predictions
var h1pred = nmrShiftDBPred1H(molecule, {
"db": db,
"debug":false,
"ignoreLabile":false,
"getCouplings":true,
"hoseLevels":[5,4,3,2]//HOSE sizes to consider in the query
});
console.log("Each group of magnetically equivalent atoms share the same atomID");
console.log(h1pred);
});
Owner
- Name: Cheminfo
- Login: cheminfo
- Kind: organization
- Website: https://www.cheminfo.org/
- Repositories: 242
- Profile: https://github.com/cheminfo
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0