The project aims to develop methods to employ deep learning to recognize and interpret chemical structure from images in the printed and online literature with the aim of re-discovering scientific facts about natural products and their meta-data. The method, of course, will be generically applicable to most organic chemistry publications.
The project is co-supervised by Prof. Christoph Steinbeck, Jena, and Prof. Achim Zielesny, Westphalian University of Applied Sciences, Recklinghausen.
- This repository contains scripts written in Java using CDK Libraries at the back end.
- Here we have scripts that we used to explore various ways in depicting images.
- We have scripts used to generate SMILES, Inchis from SDF files, and vice versa.
- We also have scripts written to curate big chemical databases, to get relevant data for our own use case
- You can also find tools to check the validation of our machine learning algorithm written in Python. Which is hosted in DECIMER-I2S and DECIMER-Python Repositories.
├── DECIMER/src/org/openscience/
└─decimer/
├ ─ ConformerGeneration.java
├ ─ DescriptorCalculator.java
├ ─ HIsotopeFinder.java
├ ─ Image2Array.java
├ ─ Image2ArrayRandom.java
├ ─ ImageResizer.java
├ ─ IndividualAtomCount.java
├ ─ LabelCreator.java
├ ─ MolWeightCalculator.java
├ ─ MoleculeFilters.java
├ ─ MoleculeSelector.java
├ ─ RejectChargedMols.java
├ ─ SmilesDepictor.java
├ ─ StrcutureDepitor8bit.java
├ ─ StructureDepictor.java
├ ─ StructureDepictorGrayscale.java
└ ─ TanimotoCalculator.java
-
The java codes can be used by cloning the repository and compiling them using CDK as referenced library.
- you have to change the input and output directory in every code before you use them.
- for example : - Generating Images - We can use SmilesDepictor.java
e.g: javac -cp cdk-2.3.jar:. SmilesDepictor.java # Compiling the script on your local directory. java -cp cdk-2.3.jar:. SmilesDepictor # Run the compiled script.
- This project is licensed under the MIT License - see the LICENSE file for details
