{"repo":"lszeremeta/SDFEater","free":true,"listed":false,"github":"https://github.com/lszeremeta/SDFEater","clone":"git clone https://github.com/lszeremeta/SDFEater.git","description":"Always hungry SDF chemical file format parser with many output formats","language":"Java","stars":10,"topics":["sdf","parser","chemical-data","cheminformatics","cypher","neo4j","cvme","chebi","drugbank","data-structures"],"license":"MIT","category":"deployment-docker-iac","readme_excerpt":"SDF parser written in Java is run from the command-line interface (CLI). You don't need to have new Java installed! Java 8 and above are supported. Do you love️ Docker? You can use a lightweight SDFEater container! SDFEater not only eats parses your SDF files, but also can add additional data to the output. The choice of output formats is really wide. Quick start Use SDFEater in 3 easy steps. In this example, we will use the ChEBI dataset and ready to use JAR file. You need Java 8+ installed. 1. Download the ready-to-use JAR SDFEater-VERSION-jar-with-dependencies.jar file from project release asset. SDFEater is also available as a Docker image. In most scenarios, JAR file or the Docker image should be sufficient and convenient to run SDFEater, but you may want to build everything yourself. 2. Download ChEBI complete 3-star dataset file and unpack downloaded gz archive. ChEBI datasets are shared via FTP, so if your browser or operating system does not support FTP, you may need an additional program such as FileZilla. 3. Assuming the ChEBI complete 3star.sdf file is in the current directory and the output format you're interested in is RDFa, the command will be as follows: That's all. Now you have the RDFa file ready in the current directory. You can try other output formats and options as described below. You can also use SDFEater to convert DrugBank SDF files or prepare your own SDF input file with supported keys. Docker image If you have Docker installed, you can use a tiny ","default_branch":null,"files":null,"tree":[],"storefront":"/r/lszeremeta","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/lszeremeta/SDFEater/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}