2. InChI and SMILES identifiers for chemical structures¶

Recipe Overview

Reading Time

15 minutes

Executable Code

Yes

Difficulty

InChI and SMILES identifiers for chemical structures

Recipe Type

Hands-on

Audience

Chemoinformatician, Data Curator, Data Manager, Data Scientist

Maturity Level & Indicator

[F+MM-1.1C] [F+MM-1.2C]

Cite me with FCB007

2.1. Main Objectives¶

The main purpose of this recipe is:

To take an SDF file, validate the content for chemical inconsistencies, and generate InChIs, InChIKeys, and SMILES for each entry in the SDF file.

FAIRification Objectives, Inputs and Outputs

Actions.Objectives.Tasks	Input	Output
validation	Structure Data File (SDF)	report
calculation	Structure Data File (SDF)	InChI
calculation	Structure Data File (SDF)	SMILES

Requirements

Skill dependency:
- Bash experience
Technical requirements:
- Groovy

2.2. Creating InChI and SMILES identifiers for chemical structures¶

To run the below scripts, you need a Groovy installation. The Groovy scripts use version 2.7.1 of the Chemistry Development Kit (see 2). This library and its use in Groovy is further explain in the book Groovy Cheminformatics with the Chemistry Development Kit. Check this git repository for more detailed use instructions and where to find the tools: https://github.com/FAIRplus/fairplus-sdf

2.2.1. Record validation¶

When generating InChIs, the InChI library (see 1) may return several success states reflecting issues with the compound record in the SDF file, including: WARNING and ERROR. This first script reports such issues:

groovy badRecords.groovy -f foo.sdf

The output may look like this:

Sulfinpyrazone  Omitted undefined stereo        WARNING
Isosorbide mononitrate  Charges were rearranged WARNING
Compound52      Proton(s) added/removed WARNING

2.2.2. Calculate InChls¶

Similarly, InChIKeys can be generated:

groovy inchikeys.groovy -f foo.sdf

When the success state is ERROR, nothing is outputted.

2.2.3. Calculate SMILES strings¶

The last script calculates a SMILES for each entry in the SDF file:

groovy smiles.groovy -f foo.sdf

2.3. Conclusion¶

This recipe explained who to validate the chemical structures in an SDF file, and convert them to SMILES, InChI, and InChIKey. The latter can then be used with BridgeDb and its metabolite ID mapping databases to get additional identifiers.