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Maven Central Javadoc MIT license Build Status

JNA-InChI

Wrapper to access InChI and RInchI from Java. This wraps the latest version of InChI (1.06) and RInChI (1.00) using JNA. A simple native Java interface can then be used to call InChI. Java 8 or higher is required. Detailed information about the capabilities and limitations when converting from and to RInChI can be found in the io.github.dan2097.jnarinchi package documentation.

Examples

Mol file to StdInChI

InchiOutput output = JnaInchi.molToInchi(molText);
if (output.getStatus() == InchiStatus.SUCCESS || output.getStatus() == InchiStatus.WARNING) {
  String inchi = output.getInchi();
}

SMILES to StdInChI

InchiOutput output = SmilesToInchi.toInchi(smiles);
if (output.getStatus() == InchiStatus.SUCCESS || output.getStatus() == InchiStatus.WARNING) {
  String inchi = output.getInchi();
}

InChI to InChIKey

InchiKeyOutput output = JnaInchi.inchiToInchiKey(inchi);
if (output.getStatus() == InchiKeyStatus.OK) {
  String inchiKey = output.getInchiKey();
}

Custom molecule to StdInChI

InchiInput inchiInput = new InchiInput();
inchiInput.addAtom(atom);
inchiInput.addBond(bond);
inchiInput.addStereo(stereo);
InchiOutput output = JnaInchi.toInchi(inchiInput);

Reaction file to RInChI

RinchiOutput rinchiOutput = JnaRinchi.fileTextToRinchi(reactionFileText);
if (rinchiOutput.getStatus() == Status.SUCCESS || rinchiOutput.getStatus() == Status.WARNING) {
  String rinchi = rinchiOutput.getRinchi();
}

RInChI to RInChIKey-Long

RinchiKeyOutput rinchiKeyOutput = JnaRinchi.fileTextToRinchiKey(reactionFileText, RinchiKeyType.LONG);
if (rinchiKeyOutput.getStatus() == Status.SUCCESS) {
  String longRinchiKey = rinchiKeyOutput.getRinchiKey();
}

Decompose RInChI into its constituent InChIs (and associated AuxInfo if any)

RinchiDecompositionOutput rinchiDecompositionOutput = JnaRinchi.decomposeRinchi(rinchi, rauxInfo);
if (rinchiDecompositionOutput.getStatus() == Status.SUCCESS) {
  String[] inchis = rinchiDecompositionOutput.getInchis();
  String[] auxInfos = rinchiDecompositionOutput.getAuxInfos();
}

Supported platforms

InChI and RInChI are C libraries and hence require platform-specific binaries. The following table lists the availability of the binaries for specific platforms. Pull requests for other platforms are welcome.

Platform InChI RInChI
Linux x86 Yes Yes
Linux x86-64 Yes Yes
Linux ARM Yes Yes
Linux ARM64 Yes No
Mac x86-64 Yes No
Mac ARM64 Yes No
Windows x86 Yes Yes
Windows x86-64 Yes Yes

Maven artifacts

The simplest way to use the library is with:

<dependency>
  <groupId>io.github.dan2097</groupId>
  <artifactId>jna-inchi-all</artifactId>
  <version>1.2.1</version>
</dependency>

which includes binaries for most common platforms, support for converting SMILES to InChI/InChIKey and MDL RDfile and RXN to RInChI/RInChIKey.

If you don't need SMILES to InChI support, RInChI support, or do not require support for all platforms, the dependency size can be reduced by only including the required modules.

Artifact Description
jna-inchi-all Includes all artifacts
jna-inchi-smiles JNA-InChI API with SMILES to InChI support
jna-inchi-core JNA-InChI API with binaries for all platforms
jna-inchi-api JNA-InChI API
jna-inchi-darwin-aarch64 InChI 64-bit ARM Mac support
jna-inchi-darwin-x86-64 InChI 64-bit Intel Mac support
jna-inchi-linux-aarch64 InChI 64-bit ARM Linux support e.g. Apple M1
jna-inchi-linux-arm InChI 32-bit ARM Linux support e.g. Raspberry Pi
jna-inchi-linux-x86 InChI 32-bit Linux support
jna-inchi-linux-x86-64 InChI 64-bit Linux support
jna-inchi-win32-x86 InChI 32-bit Windows support
jna-inchi-win32-x86-64 InChI 64-bit Windows support
jna-rinchi-core JNA-RInChI API with binaries for Windows and Linux
jna-rinchi-linux-arm RInChI 32-bit ARM Linux support e.g. Raspberry Pi
jna-rinchi-linux-x86 RInChI 32-bit Linux support
jna-rinchi-linux-x86-64 RInChI 64-bit Linux support
jna-rinchi-win32-x86 RInChI 32-bit Windows support
jna-rinchi-win32-x86-64 RInChI 64-bit Windows support

For example, jna-inchi-core omits SMILES support. If you only need 64-bit linux support, depending on if SMILES support was desired, you would choose jna-inchi-smiles + jna-inchi-linux-x86-64, or jna-inchi-api + jna-inchi-linux-x86-64

License

This project is licensed under the GNU Lesser General Public License v2.1 or later

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