jasn1-pubchem-compounds-decoder

Java decoder for pubchem ASN compound files

This is a parser for the binary encoded ASN.1 files of PubChem, specifically the 2DCompound files from PubChem's ftp Server: ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/ASN/

This project is based on the jASN1 parser : https://www.openmuc.org/asn1/, which was used to generate the pojos, using the asn definition file from PubChem. However, the classes were heavily refactored due to following problems:

• PubChem uses indefinite length encoding, which is not fully supported by jASN1.
• PubChem uses a different encoding for REAL values than defined in the asn standard.
• jASN1 expects, due to a minor bug whichn will be fixed, that InputSreams act greedy, which isn't always the case.
• PubChem uses integers to encode state of certain objects (e.g. 1=SingleBond, 2=DoubleBond). Functionality was added to decode those integers to the corresponding textual representation.
• A filter system was added, which allows drop uninteresting information during parse.

Usage

Just run de.uni_leipzig.dbs.jasn1.pubchem.example.ExampleParse to see the parser in action.

##Maven Artifact

Add this as a Repository:

<repositories>
    <repository>
        <id>jasn1-pubchem-compounds-decoder-mvn-repo</id>
        <url>https://raw.github.com/USERNAME/jasn1-pubchem-compounds-decoder/mvn-repo/</url>
        <snapshots>
            <enabled>true</enabled>
            <updatePolicy>always</updatePolicy>
        </snapshots>
    </repository>
</repositories>

And this is the dependency:

	<dependency>
	    <groupId>de.uni_leipzig.dbs</groupId>
	    <artifactId>jasn1-pubchem-compounds-decoder</artifactId>
	    <version>0.0.1</version>
	</dependency>