Integrating InChI and RInChI Native Libraries into Java Applications
- 1. Integrating InChI and RInChI Native Libraries into Java Applications István Őri
- 2. We are your scientific partner to build a sustainable future through innovating best-in-class software solutions for chemistry and biology. About ChemAxon
- 3. About me Name: István Őri Job title: Technical Lead Company: ChemAxon Team: Representation & IO
- 4. WHY DID WE INTEGRATE?
- 5. Why? Basically, because InChI and InChIKey are working. They are useful identifiers which can represent chemical structures in a canonical form, in a compact, machine-friendly way.
- 6. HOW DID WE DO IT?
- 7. Access InChI software from Java ● Option A: Expect the user to install and configure the InChI library and use it in a process from Java ● Option B: Wrap the native libraries within the Java application and access it via JNI or JNA as an API
- 8. Option A Pros: ● No extra trick required, can be used as a command line tool. Cons: ● It is inconvenient for the user ● Handling of different versions of the InChI software is required ● The API offers more than the command line interface.
- 9. Option B Pros: ● The API offers more than the command line interface. ● It is more convenient for the user ● Full control over the version of the library Cons: ● It is inconvenient for the developer ● It is quite easy to work with C libraries in Java, but in case of C++ libraries it can be difficult to manage complex data structures
- 10. Option B - Inconveniences ● Memory management in C/C++ and Java is very different ● It is relatively easy to manage structs and primitive variables, but the management of class instances is on a whole other level Option B - Weapon of choice ● JNI or JNA?
- 11. Option B - Solutions ● Memory management in C/C++ and Java is very different Get used to it! ● It is relatively easy to manage structs and primitive variables, but the management of class instances is on a whole other level Use the subset of the API where structs and primitive variables are enough.
- 12. DTOs for Java API JNA Structs for C API InChI v1.05 Toolkits and services Data transformations in Option B (InChI)
- 13. Data transformations in Option B (RInChI) DTOs for Java API JNA String from C++ API RInChI v1.00 Toolkits and services RXN Export JNA String for C++ API Fallback to InChI workflow
- 14. The result
- 15. Issues ● No Mac support ● No agents for RInChI export
- 16. FUTURE PLANS
- 17. Plans ● We would like to integrate InChI v1.06 instead of v1.05 ● Make our Java library opensource